diff --git a/.gitignore b/.gitignore
index 7a9b4a3aef7f3d25398e7d82a09bb94d8dc11d76..3c68f93a6aabe9b6c0526bcd160ae3357d710ae2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -474,5 +474,5 @@ pip-selfcheck.json
# TODO: remove line below if we want to keep eclipse metadata
.settings/
-
+.vscode
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3f65fec62ed3ae46affde42750e0f7077e0f4f61..577c5b4807222ad334b11352ef76a2502ad080e4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -15,14 +15,18 @@ stages:
build:
stage: build
script:
- - docker login -u gitlab-ci-token -p "$CI_BUILD_TOKEN" registry-gitlab.pasteur.fr
- - docker build --pull -t "$CI_REGISTRY_IMAGE:$CI_BUILD_REF_NAME" .
- - docker push "$CI_REGISTRY_IMAGE:$CI_BUILD_REF_NAME"
+ - docker login -u gitlab-ci-token -p "$CI_JOB_TOKEN" registry-gitlab.pasteur.fr
+ - docker build --pull -t "$CI_REGISTRY_IMAGE:latest" .
+ - docker push "$CI_REGISTRY_IMAGE:latest"
only:
- - master
+ changes:
+ - .gitlab-ci.yml
+ - Dockerfile
+ - package.json
+ - setup.py
pytest:
- image: registry-gitlab.pasteur.fr/bis-aria/ariaec:$CI_BUILD_REF_NAME
+ image: $CI_REGISTRY_IMAGE:latest
stage: test
script:
- cd ${CI_PROJECT_DIR}
@@ -31,16 +35,22 @@ pytest:
coverage:
stage: coverage
- image: registry-gitlab.pasteur.fr/bis-aria/ariaec:$CI_BUILD_REF_NAME
+ image: $CI_REGISTRY_IMAGE:latest
script:
- pytest --cov=aria --cov-report html --cov-report term
coverage: '/TOTAL.+ ([0-9]{1,3}%)/'
artifacts:
paths:
- htmlcov/
-
+ only:
+ refs:
+ - production
+ - master
+ changes:
+ - src/**/*
+
pages:
- image: registry-gitlab.pasteur.fr/bis-aria/ariaec:$CI_BUILD_REF_NAME
+ image: $CI_REGISTRY_IMAGE:latest
stage: deploy
dependencies:
- coverage
@@ -54,14 +64,31 @@ pages:
paths:
- public
only:
- - master
+ refs:
+ - master
+ - production
+ changes:
+ - docs/**/*
cleanup_pypirc:
stage: cleanup
when: always # this is important; run even if preceding stages failed.
script:
- rm -vf ~/.pypirc # we don't want to leave these around, but GitLab may clean up anyway.
-
+
+deliver:
+ image:
+ name: registry.gitlab.com/hyper-expanse/open-source/semantic-delivery-gitlab:9.0.0
+ entrypoint: [""]
+ script:
+ - semantic-delivery-gitlab --token $SEMANTIC_TOKEN
+ stage: deploy
+ environment:
+ name: production
+ only:
+ - production
+
+
# deploy_pypi:
# stage: deploy
# script: # Configure the PyPI credentials, then push the package, and cleanup the creds.
diff --git a/CHANGELOG b/CHANGELOG
deleted file mode 100644
index 672bf7f1bf3d42cd199a5327746be3ca1e99e0c8..0000000000000000000000000000000000000000
--- a/CHANGELOG
+++ /dev/null
@@ -1,500 +0,0 @@
-<a name="0.0.18"></a>
-## <small>0.0.18 (2018-04-26)</small>
-
-* docs: Added bpt1 setup in examples ([a76abff](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a76abff))
-* docs: Added link to example archive in docs ([9ec966b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9ec966b))
-* docs: Added MALE_ECOLI example data ([4877131](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4877131))
-* docs: updated changelog ([ceececc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ceececc))
-* docs: updated changelog ([95d3f62](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/95d3f62))
-* docs: Updated changelog (removed old tags) ([a59416d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a59416d))
-* docs: updated examples ([794f14e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/794f14e))
-* docs: updated usage section ([d171f05](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d171f05))
-* *: Fix bug during pdf generation in analysis command; Added analysis example for bpt1 ([e159414](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e159414))
-* Added casp rr support when there is no header (pfrmatrr) ([d9d7349](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d9d7349))
-* Added coverage report in generated ci files ([476478c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/476478c))
-* Added future to setup ([6540e57](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6540e57))
-* added logo files ([9a4d273](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9a4d273))
-* Added new prefix option for analysis command ([d00926a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d00926a))
-* Added rst contributing file ([0b807b0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0b807b0))
-* Added static files ([93c6e41](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/93c6e41))
-* Added template files ([91485ec](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/91485ec))
-* Automatic version tag in PKG_INFO ([ecf63ec](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ecf63ec))
-* Bug revision within get_version ([c9df814](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c9df814))
-* Changed aria header docstrings in rest format ([feb5e17](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/feb5e17))
-* Changed README ([69d770f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/69d770f))
-* commitlint support for git message formatting ([4d73e55](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4d73e55))
-* Corrected AriaPeak format ([f352612](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f352612))
-* Corrected coverage report parameters ([c775351](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c775351))
-* Dependencies section in installation doc ([c7a543a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c7a543a))
-* Finished installation doc ([e3af353](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e3af353))
-* Fix issue #21 ([5b93f73](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5b93f73)), closes [#21](https://gitlab.pasteur.fr/bis-aria/Ariaec/issues/21)
-* Installation doc revision, a command was missing in pip installation instructions ([26193c4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/26193c4))
-* Moved get_version again due to import errors with pip installation ([018524c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/018524c))
-* Moved get_version function ([4705325](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4705325))
-* Path revision in scientific/PDB docstring ([b7ed251](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b7ed251))
-* Previous bug revision was wrong ... ([ec2560e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ec2560e))
-* Removed old readme files ([156ee0a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/156ee0a))
-* removed reference to bootstrap theme within sphinx documentation ([e78370a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e78370a))
-* Revert "Update Dockerfile" ([b4598c3](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b4598c3))
-* Revised documentation ([705ef9e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/705ef9e))
-* Solved issue within analysis command. If the native and ensemble segids didn't correspond, the viola ([5071ec0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5071ec0))
-* Update .gitlab-ci.yml ([ef27cca](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ef27cca))
-* Update .gitlab-ci.yml ([33f9575](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/33f9575))
-* Update .gitlab-ci.yml ([0fd6683](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0fd6683))
-* Update .gitlab-ci.yml ([9ddd3ba](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9ddd3ba))
-* Update .gitlab-ci.yml ([6a84129](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6a84129))
-* Update .gitlab-ci.yml ([ca8c15e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ca8c15e))
-* Update .gitlab-ci.yml ([8e679df](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8e679df))
-* Update .gitlab-ci.yml ([7d37392](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/7d37392))
-* Update CONTRIBUTING.md ([3c6b9a2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3c6b9a2))
-* Update CONTRIBUTING.md ([64f0a8a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/64f0a8a))
-* Update CONTRIBUTING.rst ([e000d1e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e000d1e))
-* Update Dockerfile ([c650124](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c650124))
-* Update Dockerfile ([da41768](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/da41768))
-* Update Dockerfile ([ae12b86](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ae12b86))
-* Update README.md ([6ee017a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6ee017a))
-* Updated API doc ([6c1b229](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6c1b229))
-* Updated changelog ([6c72ac0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6c72ac0))
-* updated changeolog ([237c8bd](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/237c8bd))
-* Updated configuration ([c374466](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c374466))
-* updated contributing ([7f9ccda](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/7f9ccda))
-* Updated doc ([8d44d75](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8d44d75))
-* Updated docs tree & moved examples folder ([ad95b08](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ad95b08))
-* Updated documentation content ([a249ee6](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a249ee6))
-* Updated general documentation (git guidelines) ([9ee7b2f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9ee7b2f))
-* Updated gitignore file ([476be05](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/476be05))
-* Updated installation doc ([3a18457](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3a18457))
-* Updated installation doc ([2f0f443](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/2f0f443))
-* updated logo file ([774713a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/774713a))
-* Updated README.rst and installation doc ([aa67392](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/aa67392))
-* Updated toctree & ariaec setup command within sphinx documentation ([3ee3140](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3ee3140))
-* feat: Automatic changelog ([23e095b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/23e095b))
-* fix: wrong installation order in dockerfile for husky npm module ([c83c314](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c83c314))
-
-
-
-<a name="0.0.17"></a>
-## <small>0.0.17 (2018-03-23)</small>
-
-* Add .gitlab-ci.yml ([ad3cfd2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ad3cfd2))
-* Add changelog ([20104b7](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/20104b7))
-* Add CONTRIBUTING file ([1b30e83](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1b30e83))
-* Add license ([7eda697](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/7eda697))
-* Add new file ([926cbc3](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/926cbc3))
-* Added ariaproject support to extract supplementary data ([49c72d3](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/49c72d3))
-* Added configuration file converter ([0db97d4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0db97d4))
-* Added empty test files ([ee28ce7](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ee28ce7))
-* Added PKG-INFO file ([95c99ce](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/95c99ce))
-* Added possibility to chose distance restraint file in analysis command ([3c803b3](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3c803b3))
-* added short reminder ([e9599c1](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e9599c1))
-* Added support of ss2 psipred format ([4edb53c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4edb53c))
-* Adding example files ([21b3f0b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/21b3f0b))
-* Also update sequence section from ARIA project file ([bccbaeb](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bccbaeb))
-* aria integration update ([5dade88](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5dade88))
-* Bug revision during loading of external settings ([3441970](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3441970))
-* Bug revision in iniconv ([5087010](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5087010))
-* Bug revision in maplot (removed old args) ([9f09f55](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9f09f55))
-* Bug revision when giving wrong file type ([c730770](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c730770))
-* Bug revision when updating sequence field ([a009eaf](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a009eaf))
-* Bug revision with no filter option ([0ced19b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0ced19b))
-* Bug revision, wrong import in conversion ([9f391ee](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9f391ee))
-* Bug revision: handle missing files in previous template versions ([52ef164](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/52ef164))
-* Bug revision: Since there is nan values instead of null when reading a scoremap, maplot no longer wo ([f551fc0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f551fc0))
-* Bug revision: wrong call when reading seq file instead of fasta ([4cb7b31](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4cb7b31))
-* Bug revision: wrong index in filtering step......... ([bde5974](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bde5974))
-* Bug revision: wrong loop in analysis ([82cf56e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/82cf56e))
-* Can data from an existing aria project file ([11daeaf](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/11daeaf))
-* Changed default segid ([040fe74](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/040fe74))
-* changed entry points location ([14d82a9](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/14d82a9))
-* Changed secondary structure args in setup as optional args ([fcff1b2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/fcff1b2))
-* Changed setup.py ([8d42961](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8d42961))
-* Conkit reader now supported in conbox.reader. Close #4 ([74b5ef6](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/74b5ef6)), closes [#4](https://gitlab.pasteur.fr/bis-aria/Ariaec/issues/4)
-* Contacts can now be selected using a percentage ([f3835df](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f3835df))
-* ec file are now optional ([fcde165](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/fcde165))
-* First attempt to change aria nested tree for setuptools installation ([912fc3b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/912fc3b))
-* gui behaviour seems ok ([956ca75](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/956ca75))
-* Ignore example files for dev ([2852dc1](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/2852dc1))
-* Implementation of a new filtering step checking for unassigned contacts if amino acid information is ([2459181](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/2459181))
-* import revision in aria part ([43469d7](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/43469d7))
-* merging not fully functionnal ([6c3162f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6c3162f))
-* Missing dependency for ariaec in singularity recipe ([c6ef2b4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c6ef2b4))
-* No filter option in maplot ([5e1e9b4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5e1e9b4))
-* path revision in aria2 script ([4c930f8](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4c930f8))
-* pkg_resources revision for cns ([78090bc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/78090bc))
-* Preparing for aria integration ([470859b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/470859b))
-* Put old readme file since sphinx documentation is not finished ([a8c1e63](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a8c1e63))
-* Refactored part of ariaecsettings ([48ea9d1](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/48ea9d1))
-* Refactored some parts in conbox + beginning of seqrange option ([74bee78](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/74bee78))
-* removed a print .... ([58314ae](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/58314ae))
-* Removed annoying warnings with metadata attributes in protmap.py ([71905c3](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/71905c3))
-* Secondary structure restraints are now optional ([e0b18b9](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e0b18b9))
-* Singularity file added ([ea99f88](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ea99f88))
-* small syntax revision ([40e7a07](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/40e7a07))
-* small syntax revision ([62d1c7c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/62d1c7c))
-* Solved bug due to % syntax in n_factors ([7fde3a0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/7fde3a0))
-* syntax revision for prefix option in maplot ([36fda83](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/36fda83))
-* Update .gitlab-ci.yml ([438e268](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/438e268))
-* Update .gitlab-ci.yml ([6d775d4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6d775d4))
-* Update .gitlab-ci.yml ([6e62d0f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6e62d0f))
-* Update .gitlab-ci.yml ([80cd86c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/80cd86c))
-* Update .gitlab-ci.yml ([904194f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/904194f))
-* Update .gitlab-ci.yml ([fc10d09](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/fc10d09))
-* Update .gitlab-ci.yml ([d46d7e8](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d46d7e8))
-* Update .gitlab-ci.yml ([1a11d55](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1a11d55))
-* Update .gitlab-ci.yml ([1e378a3](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1e378a3))
-* Update .gitlab-ci.yml ([b4fd0d4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b4fd0d4))
-* Update .gitlab-ci.yml ([b865530](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b865530))
-* Update .gitlab-ci.yml ([d462e14](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d462e14))
-* Update .gitlab-ci.yml ([77e2689](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/77e2689))
-* Update .gitlab-ci.yml ([12b17ae](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/12b17ae))
-* Update .gitlab-ci.yml ([071c954](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/071c954))
-* Update .gitlab-ci.yml ([600d96c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/600d96c))
-* Update .gitlab-ci.yml ([3e9e043](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3e9e043))
-* Update .gitlab-ci.yml ([fb7dd46](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/fb7dd46))
-* Update .gitlab-ci.yml ([00667cc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/00667cc))
-* Update .gitlab-ci.yml ([0c84592](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0c84592))
-* Update .gitlab-ci.yml ([3a9e6ca](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3a9e6ca))
-* Update .gitlab-ci.yml ([fedaf61](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/fedaf61))
-* Update .gitlab-ci.yml ([a8336c4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a8336c4))
-* Update .gitlab-ci.yml ([68c3209](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/68c3209))
-* Update .gitlab-ci.yml ([00ad7f2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/00ad7f2))
-* Update .gitlab-ci.yml ([3b4b205](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3b4b205))
-* Update .gitlab-ci.yml ([3bbaf04](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3bbaf04))
-* Update .gitlab-ci.yml ([715ab24](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/715ab24))
-* Update .gitlab-ci.yml ([90be395](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/90be395))
-* Update .gitlab-ci.yml ([cc99435](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/cc99435))
-* Update .gitlab-ci.yml ([c956430](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c956430))
-* Update .gitlab-ci.yml ([9a39227](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9a39227))
-* Update .gitlab-ci.yml ([d416946](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d416946))
-* Update .gitlab-ci.yml ([b226b94](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b226b94))
-* Update .gitlab-ci.yml ([f3636ed](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f3636ed))
-* Update .gitlab-ci.yml ([8d867ef](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8d867ef))
-* Update .gitlab-ci.yml ([001eb5b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/001eb5b))
-* Update .gitlab-ci.yml ([ec9941c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ec9941c))
-* Update .gitlab-ci.yml ([f17efc6](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f17efc6))
-* Update .gitlab-ci.yml ([a41dbe4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a41dbe4))
-* Update .gitlab-ci.yml ([829160a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/829160a))
-* Update .gitlab-ci.yml ([9019d4c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9019d4c))
-* Update .gitlab-ci.yml ([d78ff48](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d78ff48))
-* Update CONTRIBUTING.md ([594d24b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/594d24b))
-* Update CONTRIBUTING.md ([f1fb306](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f1fb306))
-* Update Dockerfile ([4498f35](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4498f35))
-* Update Dockerfile ([ef2abb0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ef2abb0))
-* Update Dockerfile ([19e082f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/19e082f))
-* Update Dockerfile ([5f8e2ba](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5f8e2ba))
-* Update Dockerfile ([5263bca](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5263bca))
-* Update Dockerfile ([6857a24](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6857a24))
-* Update Dockerfile ([0a24f4c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0a24f4c))
-* Update Dockerfile ([dde69c7](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/dde69c7))
-* Update Dockerfile ([bea2af9](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bea2af9))
-* Update Dockerfile ([7620522](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/7620522))
-* Update Dockerfile ([1585092](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1585092))
-* Update Dockerfile ([7722337](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/7722337))
-* Update Dockerfile ([01f2d7a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/01f2d7a))
-* Update Dockerfile ([4dfa22f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4dfa22f))
-* Update Dockerfile ([084f23a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/084f23a))
-* Update Dockerfile ([fbdee64](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/fbdee64))
-* Update Dockerfile ([bdb46d3](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bdb46d3))
-* Update README.md ([f5a30f6](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f5a30f6))
-* Update README.md ([c67c406](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c67c406))
-* Update README.md ([2394807](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/2394807))
-* Update README.md ([491a281](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/491a281))
-* Update README.md ([de2b1c4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/de2b1c4))
-* Update README.md ([a620daf](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a620daf))
-* Update README.md ([3c4b415](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3c4b415))
-* Update README.md ([5e81779](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5e81779))
-* Update README.md ([ef36131](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ef36131))
-* Update README.md ([f87b087](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f87b087))
-* Update README.md ([bd49362](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bd49362))
-* Update README.md ([e2b95e0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e2b95e0))
-* Update setup.py ([1e94cad](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1e94cad))
-* Update setup.py ([a4ff2ae](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a4ff2ae))
-* Updated doc ([3e4142d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3e4142d))
-* Updated DTD file ([5244de6](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5244de6))
-* Updated generated files in analysis step ([c52565a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c52565a))
-* Updated help inside singularity recipe ([e41ddb5](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e41ddb5))
-* Updated installation process ([7704234](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/7704234))
-* updated sphinx doc (make html call) ([24585f0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/24585f0))
-* Updated sspred parser in order to support ss3 file format ([91ebaf0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/91ebaf0))
-* Updated tempate files ([76fa394](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/76fa394))
-* Updated violation file in analysis step (avoid putting None values in the csv file) ([475afb9](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/475afb9))
-* wrong condition in maplot when there is only reference map ([f988490](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f988490))
-
-
-
-<a name="0.0.16"></a>
-## <small>0.0.16 (2017-06-01)</small>
-
-* Changed deprecated functions with panda in pdbstat part ([ceb1d13](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ceb1d13))
-* Updated violation analysis if clusters ([6c7a379](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6c7a379))
-
-
-
-<a name="0.0.15"></a>
-## <small>0.0.15 (2017-05-31)</small>
-
-* Cleaner version of setuptools installation ([ec11aa3](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ec11aa3))
-
-
-
-<a name="0.0.14"></a>
-## <small>0.0.14 (2017-05-30)</small>
-
-* Bug revision: removed hard coded lines... ([57f42c7](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/57f42c7))
-
-
-
-<a name="0.0.13"></a>
-## <small>0.0.13 (2017-05-30)</small>
-
-* Add README file ([b987c0f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b987c0f))
-* Added --no-filter option in setup command ([5a60a1e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5a60a1e))
-* Added cullpdb files in package_data attribute (setup.py) ([49b450f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/49b450f))
-* Added data folder ([bca5553](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bca5553))
-* Added docstrings in default config file ([0949374](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0949374))
-* Added ec2aria command line for backward compatibility ([89c0873](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/89c0873))
-* Added neighbor search ([38db34d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/38db34d))
-* Added new flags for restraint building. Pair_product filters atom pair list for each restraint to th ([68bd460](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/68bd460))
-* Added pdbdist cmd ([284f897](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/284f897))
-* Added plmc and plm as contact map types ([330e140](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/330e140))
-* Added project template 2.3.6 (new clustering field) ([d928bdf](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d928bdf))
-* Added scoring tag support ([c2e2196](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c2e2196))
-* Added seed for random contact selection (e.g.: with native contact) ([c685576](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c685576))
-* Added some comments for future implementations ([ce3a45d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ce3a45d))
-* Added sphinx documentation files generated with sphinx-apidoc ([3696334](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3696334))
-* Added svnignore file ([b02decd](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b02decd))
-* Added verbosity option ([ae29b7b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ae29b7b))
-* Avoid disordered atoms for the moment in pdbdist (not compatible with seen matrix index actually) ([83753ba](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/83753ba))
-* Bug revision in ResAtmMap when calling reduce method ([8c85936](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8c85936))
-* Bug revision pdbviol argparse command ([977eefd](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/977eefd))
-* Bug revision: avoid raising of matplotlib event error for contactmap tool ([814fbdc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/814fbdc))
-* Bug revision: avoid sampling when using all contacts ([a9b93ba](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a9b93ba))
-* Bug revision: conservation score ignored if missing field ([b2b22a4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b2b22a4))
-* Bug revision: filter.out merged when there is more than one contact file... ([a36c0e2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a36c0e2))
-* Bug revision: regex for plm contacts revised ([22c7124](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/22c7124))
-* Bug revision: reset contribution id at each new restraint ([5db6b92](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5db6b92))
-* catch potential errors with retrieve_pdb function ([aaa1441](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/aaa1441))
-* Changed defaults options in config file ([923cf82](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/923cf82))
-* Changed delimiter in pdbdist output file ([8526fe4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8526fe4))
-* Changed filter steps in pdbdists ([1960099](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1960099))
-* Changed infra dir for setup (removed others folder) ([f9a80da](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f9a80da))
-* Contributions are now always in the same order when generating xml distance file ([e4f1d0d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e4f1d0d))
-* Create subfolders related to molecule and datas in tmp root ([0c139e8](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0c139e8))
-* Faster subdist computation in pdbdist ([161d26e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/161d26e))
-* Finalized first version of pdbviol command ([3e10b6c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3e10b6c))
-* First step to modular restraint generation ([a4d1efa](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a4d1efa))
-* First step to pdbdist based distance restraints ([bff274b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bff274b))
-* First steps for pdbstat parallelization ([c72944d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c72944d))
-* force file format to pdb when downloading files in pdbdist section ([76b6712](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/76b6712))
-* Implemented copy method for all protein maps ([3fb57a2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3fb57a2))
-* mapreport format revision ([a1c17f2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a1c17f2))
-* Maptype checker updated -> show error msg only after 2nd line ([b0a339d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b0a339d))
-* mmCIF support in downloading process (pdbdist command) ([79b21dd](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/79b21dd))
-* Moved data folder for testing ([12ff9a2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/12ff9a2))
-* n_factor in configuration file accept 'all' as a valid parameter now ([5cef0cd](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5cef0cd))
-* New template for avg_exponent ([0207045](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0207045))
-* Parallelization process done on pdbstat (could be improved) ([8de0dde](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8de0dde))
-* PCA projection done in ensemble analysis part ([e11080d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e11080d))
-* PCA projection of clusters done ([52be20e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/52be20e))
-* Pdbdist command functionnal ([997944e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/997944e))
-* pdblist moved to pdbdist init ([632ec39](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/632ec39))
-* Pdbqual command added ([994315a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/994315a))
-* PDBStat command with GMM ([f4ccfd4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f4ccfd4))
-* Pdbstat distance type functionnal ([c6e1807](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c6e1807))
-* pdbviol analyze with ensemble of previous iteration in the same way as aria ([2d3528a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/2d3528a))
-* pep revision ([6352972](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6352972))
-* PEP8tized base, commands and econverter ([d5c35c5](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d5c35c5))
-* Redefined several commands in order to be more explicit ([a63afa9](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a63afa9))
-* Removed bin folder and moved ec2aria command into entry point ([5f394e6](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5f394e6))
-* Removed pyc files... ([6ecb9c5](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6ecb9c5))
-* Removed update of host command ([53035e9](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/53035e9))
-* Second step for parallelization of pdbstat (using pathos and tqdm) ([d2531c8](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d2531c8))
-* Second step to modular restraints ([998a96f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/998a96f))
-* Smarter RegexFile class (check if the file exists or not in package data) ([d33cbb7](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d33cbb7))
-* SsAaAtmMap implementation ([5f5715a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5f5715a))
-* Start writing pdbviol cmd ([8fcdfd6](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8fcdfd6))
-* Starting tbl2xml cmd dev ([661f02a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/661f02a))
-* tbl2xml command functionnal ([19fef77](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/19fef77))
-* Toggle on capture of warnings with dssp inside logger ([f855d81](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f855d81))
-* Update contactmap settings ([e62d90e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e62d90e))
-* Update ensemble pickling in ensemble analysis ([84f96cf](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/84f96cf))
-* Update host command for slurm log file ([f00f9e1](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f00f9e1))
-* Update host command for slurm log file (logger revision) ([c51fa8e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c51fa8e))
-* Update host command for slurm log file (logger revision) ([664e666](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/664e666))
-* Update README.md ([641978d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/641978d))
-* Updated aa conversion in pdbdist ([9f30a32](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9f30a32))
-* Updated config options in pdbstat ([567944c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/567944c))
-* Updated docstrings in converter ([12e36a2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/12e36a2))
-* Updated doctstring in contactmap section and changed naming convention for output files ([cbf6c79](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/cbf6c79))
-* Updated documentation inside aria_ec.ini file ([87d4d52](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/87d4d52))
-* Updated formatting function for setting parser (try to get absolute path if file field) ([d5b7502](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d5b7502))
-* Updated host_command modification for scheduler output ([0becc74](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0becc74))
-* Updated host_command modification for scheduler output. Only print a warning now (will lead to an er ([7765d37](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/7765d37))
-* Updated logger in pdbdist ([ced6775](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ced6775))
-* Updated logger in setup step ([1dc5e8e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1dc5e8e))
-* Updated output error file for job manager in host_command ([64eb7c5](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/64eb7c5))
-* Updated pdbdists data files and intra ss distance analysis ([65aaebe](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/65aaebe))
-* Updated protein blocks index in pdbdists command ([f2195c8](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f2195c8))
-* Updated README file ([2d3a27a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/2d3a27a))
-* Updated secondary structure index function ([4bb7202](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4bb7202))
-* Updated settings ([3531d1f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3531d1f))
-* Updated setup for pdbstat with ss information ([76d84b0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/76d84b0))
-* Updated setup for targetdistmap part 1 ([247ce2f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/247ce2f))
-* Updated setup.py file (same structure as in aria setup file) ([2d17bbd](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/2d17bbd))
-* Updated several doctypes & config file ([41e1ac0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/41e1ac0))
-* Updated some fields in violation file ([ff1880f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ff1880f))
-* Updated sphinx documentation ([68c15ad](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/68c15ad))
-* Updated sphinx documentation v2 ([5577a98](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5577a98))
-* Updated sphninx documentation ([c6f5a11](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c6f5a11))
-* Updated string formatting in mapreport ([baed6c5](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/baed6c5))
-* Using manager to share pdbdistances ([4b85864](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4b85864))
-
-
-
-<a name="0.0.12"></a>
-## <small>0.0.12 (2016-08-02)</small>
-
-* Add new section in ariaec.ini setup ([72674c8](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/72674c8))
-* Added exponent parameter ([0fe842e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0fe842e))
-* Added host_executable option in config file ([6897527](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6897527))
-* Added native_reliable option in config file ([b1e477c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b1e477c))
-* Added sequence information inside contactmap report ([c942dd3](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c942dd3))
-* Addign sigma mode parameter in aria project templates ([cab261f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/cab261f))
-* Bug fixe: generated ssdist restraints were empty ([a290852](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a290852))
-* Bug Fixe: N_factor convert to int during mapfilter step. Float values wasn't taken into account befo ([171a1ae](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/171a1ae))
-* Bug fixe: wrong conditionnal test when creating output directory ([02494b4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/02494b4))
-* Bug revision: dealing with empty contactlist file in maplot ([603f202](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/603f202))
-* Changed again default cutoff in contact definition section. Lower treshold fit better when using oth ([4239f50](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4239f50))
-* changed default cutoff to 8 in contactdef. We want to give the highest precision values as in CASD.. ([bdb256a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bdb256a))
-* Def_upper_bound set to 5 A ([082a369](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/082a369))
-* Error printing revision in ariaec/setup.py ([9c17de1](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9c17de1))
-* Removed working directory path in .ini file. ariaproject now generated using outdir command line arg ([f2ec107](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f2ec107))
-* Simplified temp_root path since too many contact map types give too long path (> 80 char) ([232150e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/232150e))
-* Since cns do not like long path, project_name correspond only to molecule name now ([f9e6ef8](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f9e6ef8))
-* Since cns do not like long path, project_name correspond only to molecule name now v2 ([2bedc48](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/2bedc48))
-* syntax modifications (report file name) ([92f7149](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/92f7149))
-* Syntax update according to pylint res ([e38c758](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e38c758))
-* Trouble with capturing and unicode syntax with python 3 compatibility... ([1452fe8](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1452fe8))
-* Trouble with capturing and unicode syntax with python 3 compatibility... ([287cc73](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/287cc73))
-* Update hbdb potential tag ([4108c51](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4108c51))
-* Updated to python 3.5 syntax ([6767d22](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6767d22))
-* Using mako library to generate dynamically iteration tag in the project template ([ea0d92d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ea0d92d))
-
-
-
-<a name="0.0.11"></a>
-## <small>0.0.11 (2016-03-02)</small>
-
-* Bug fixe: wrong atom list when pair_list set to all (add terminal atoms) ([1cf6e97](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1cf6e97))
-
-
-
-<a name="0.0.10"></a>
-## <small>0.0.10 (2016-03-01)</small>
-
-* Add max_contribution in setup config ([69784cf](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/69784cf))
-* Bug fixe: only heavy atoms when atom list set to all + upp_bound not fixed when ambig_restraint turn ([8d07798](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8d07798))
-* Reorganized/renamed output files in setup section ([5978a31](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5978a31))
-* Syntax revision in generated filter.out ([fa3f608](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/fa3f608))
-
-
-
-<a name="0.0.9"></a>
-## <small>0.0.9 (2016-02-15)</small>
-
-* Bug Fixe: error when writing boolean values aria project file (yes/no only accepted) ([9d6b572](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9d6b572))
-* Changed aria_ec.ini default contact_def (only default treshold) ([8dc289a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8dc289a))
-* Config filename changed in bbconv section ([3e7e1ca](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3e7e1ca))
-* Flush before each maplot ([57556cc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/57556cc))
-* Moving nb_c selection criteria in mapfilter object ([29f9581](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/29f9581))
-* onlyreport option ([7708a0c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/7708a0c))
-* Setting position filter mandatory in contactmap section (have to do the same in setup section) ([3108a9c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3108a9c))
-
-
-
-<a name="0.0.8"></a>
-## <small>0.0.8 (2016-02-03)</small>
-
-* Bug fixe: error pdb contact list ([db56bc6](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/db56bc6))
-* Bug fixe: error pdb contact list ([f57d7d4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f57d7d4))
-* Bug Fixe: error pdb contact list ([dec91ec](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/dec91ec))
-* Bug Fixe: error reading pdb contactlist file during check_maptype step ([dbcbbe4](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/dbcbbe4))
-* Bug Fixe: error using pdb contact file generated from ariaec ([3c421af](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3c421af))
-* Bug fixe: error when scoremap doesn't exist for report file (contactmap section) ([8e4a6f6](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8e4a6f6))
-* Bug Fixe: remove duplicates in generated contact files ([1d26bd0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1d26bd0))
-* pep8tized ([6dba452](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6dba452))
-* pep8tized v2 ([dc8fc3f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/dc8fc3f))
-* pep8tized v3 ([402cdec](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/402cdec))
-* removed ariaec/econtacts.py ([c783cfa](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c783cfa))
-* removed ariaec/econtacts.py ([c07a495](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c07a495))
-* Reordering metrics in report file ([f57fc58](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f57fc58))
-* syntax revision for contactmap logger ([fb04f44](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/fb04f44))
-* syntax revision precall plot ([64042ac](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/64042ac))
-
-
-
-<a name="0.0.7"></a>
-## <small>0.0.7 (2016-01-27)</small>
-
-* Add new formats (metapsicov_stg1/2,pconsc1/2) ([cbd0b94](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/cbd0b94))
-* Bug fixe: Missing parameter desc in pdb maps after reduce call. Report file implementation ([d57cf95](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d57cf95))
-* Changed infra call;New infra functions (ariaecsettings);infra for contactmap section ([8f85025](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8f85025))
-
-
-
-<a name="0.0.6"></a>
-## <small>0.0.6 (2016-01-21)</small>
-
-* Bug fixe: issue when launching contactmaplot on erc cluster (Tk error) ([159556f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/159556f))
-
-
-
-<a name="0.0.5"></a>
-## <small>0.0.5 (2016-01-21)</small>
-
-* Bug fixe: save_fig flag doesn't work with refmaplot ([f31ff4b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f31ff4b))
-* Change matplotlib to pdf output (should solve issue when x-server is disconnected) ([cff3bc2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/cff3bc2))
-* Change matplotlib to pdf output (should solve issue when x-server is disconnected) ([c5ddfa1](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c5ddfa1))
-* Issue with using contactmap on the cluster (plt.subplot fail) ([f2ac0b3](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/f2ac0b3))
-* Update logger infos in contactmap section ([87fbb59](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/87fbb59))
-
-
-
-<a name="0.0.4"></a>
-## <small>0.0.4 (2016-01-20)</small>
-
-* Bug fixe: wrong arguments for contactmaplot... ([381475a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/381475a))
-* Prefix argument (contactmap) ([22e21af](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/22e21af))
-* Version number following git tag system ([bf6fec2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bf6fec2))
-* Version number following git tag system ([850c70a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/850c70a))
-
-
-
-<a name="0.0.3"></a>
-## <small>0.0.3 (2016-01-19)</small>
-
-* Bug fix: sc_sc contactdef ignored ([50b2839](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/50b2839))
-
-
-
-<a name="0.0.2"></a>
-## <small>0.0.2 (2016-01-18)</small>
-
-* Bug fixe: error when using only one contactfilter ([ac09277](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ac09277))
-
-
-
-<a name="0.0.1"></a>
-## <small>0.0.1 (2016-01-18)</small>
-
-* bug fixes when template or contactfilter fields are empty in ini file ([34b074a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/34b074a))
-
-
-
-<a name="0.0.0"></a>
-## 0.0.0 (2016-01-18)
-
-* Initial commit ([35d8304](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/35d8304))
-
-
-
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000000000000000000000000000000000000..99a64c3e5f6b0660539d7010f936d9277a4fbba7
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,58 @@
+## [0.0.21](https://gitlab.pasteur.fr/bis-aria/Ariaec/compare/0.1.0...0.0.21) (2019-07-08)
+
+
+### Bug Fixes
+
+* add debug log message in ssclash ([8e50b10](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8e50b10))
+* add debug log message in ssclash ([beb4935](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/beb4935))
+* avoid key errors if all parameters don't exist with pdbqual command ([ea0e556](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ea0e556))
+* change api key for semantic delivery ([8eba464](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8eba464))
+* change dependencies in setup.py ([eb5c0be](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/eb5c0be))
+* change depreacted CI var in gitlab ci conf file ([74463c0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/74463c0))
+* change depreacted CI var in gitlab ci conf file ([4464019](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4464019))
+* escape percent character within csh script for format function ([a785ce9](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a785ce9))
+* force python 2.7 dependency ([99041c7](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/99041c7))
+* force python 2.7 dependency ([5f3380d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5f3380d))
+* future dependency in dockerfile ([0d1d39e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0d1d39e))
+* implement setting.get method used within pdbqual tool ([a8d66dc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a8d66dc))
+* implement setting.get method used within pdbqual tool ([1832c26](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1832c26))
+* remove logger during serialization for distance restraint class ([0465e1b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0465e1b))
+* remove sge_job_id var in csh script refine for sbatch options ([a036e7f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a036e7f))
+* removed unicode strings during convert part ([39d1d47](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/39d1d47))
+* revision of output slurm file for cns refine.csh ([8d14ebd](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8d14ebd))
+* solve conflict issue between pdbqual and setup config parameters ([48a05e2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/48a05e2))
+* solve import issue with pdbqual command ([737dd53](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/737dd53))
+* solve issue [#24](https://gitlab.pasteur.fr/bis-aria/Ariaec/issues/24) ([aeda4d1](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/aeda4d1))
+* solve issue with missing alignment for evcoupling contacts ([c6f3afc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c6f3afc))
+* solve issue with warnings in the logger ([990419e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/990419e))
+* solve numpy dependency issue with hdbscan ([bf3c81c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bf3c81c))
+* solve several format issues in the new logging system ([eff5776](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/eff5776))
+* sphinx crash with 1.8 due to python 3 dependencies ([fd0efa1](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/fd0efa1))
+* syntax error for clashlist flag in aria project templates ([9b270f0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9b270f0))
+* Update ariabase.py getstate ([6c209af](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6c209af))
+* update doc confs with the new project tree ([46dff44](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/46dff44))
+* update dockerfile ([541d72c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/541d72c))
+* update dockerfile ([40b59e9](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/40b59e9))
+* update dockerfile ([00d6865](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/00d6865))
+* wget dependency in dockerfile ([bdf572c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bdf572c))
+* wrong installation order in dockerfile for husky npm module ([934a449](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/934a449))
+* wrong installation order in dockerfile for husky npm module ([c83c314](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c83c314))
+* **aria.core.TypeChecking:** overwrite previous python3 patch ([dbca55a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/dbca55a))
+* **aria.core.TypeChecking:** solve byte string type checker issue when running the package with python3 ([07fb1c6](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/07fb1c6))
+
+
+### Features
+
+* add options to activate or deactivate pdq quality tools (pdbqual command) ([4a54d05](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4a54d05))
+* add structure_analysis_enabled option within conbox commands ([e88a654](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e88a654))
+* add v2.3.7 aria project template ([1b9fa48](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1b9fa48))
+* Automatic changelog ([8fda476](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8fda476))
+* Automatic changelog ([23e095b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/23e095b))
+* molecule settings hack in order to support multiple chains ([164f187](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/164f187))
+* new logging system for aria core ([223c58d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/223c58d))
+* new logging system for aria core ([1fd579c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1fd579c))
+* safe xml tag checker for python3 ([d8b091e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d8b091e))
+* semantic delivery gitlab ([b11664f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b11664f))
+
+
+
diff --git a/COPYRIGHT b/COPYRIGHT.md
similarity index 85%
rename from COPYRIGHT
rename to COPYRIGHT.md
index 2a9a10ebd9dbc087d60391013cc9095dbb219674..f9894eebc05583e03fd37a4d622c76a020b07bf5 100644
--- a/COPYRIGHT
+++ b/COPYRIGHT.md
@@ -1,4 +1,6 @@
- ARIA -- Ambiguous Restraints for Iterative Assignment
+ ARIA
+
+ Ambiguous Restraints for Iterative Assignment
A software for automated NOE assignment
diff --git a/Dockerfile b/Dockerfile
index e90241f11af2b043299a10b4068ba435bfe685f2..4f8c73d40c843e737231fc91f602e3ed35a51303 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,18 +2,20 @@ FROM centos:centos7
MAINTAINER Fabrice Allain <fabrice.allain@pasteur.fr>
RUN yum install -y epel-release
-RUN yum install -y python2-pip python-devel gcc make git
+RUN yum install -y python2-pip python-devel gcc gcc-c++ make git wget which
RUN curl --silent --location https://rpm.nodesource.com/setup_8.x | bash -; yum -y install nodejs
RUN npm install -g --save-dev @commitlint/{cli,config-conventional}; npm install -g conventional-changelog-cli
RUN echo "module.exports = {extends: ['@commitlint/config-conventional']};" > commitlint.config.js
-RUN pip install --upgrade pip ; pip install --upgrade setuptools; pip install sphinx; pip install numpy; pip install matplotlib; pip install coverage; pip install pytest; pip install pytest-cov
+RUN pip install --upgrade pip setuptools; pip install coverage; pip install pytest; pip install pytest-cov
RUN wget http://www2.ccpn.ac.uk/download/ccpnmr/analysis2.4.2.tar.gz; tar xvzf analysis2.4.2.tar.gz; export CCPNMR_TOP_DIR=$(pwd)/ccpnmr; export PYTHONPATH=${PYTHONPATH}:$CCPNMR_TOP_DIR/ccpnmr2.4/python
-RUN mkdir build-aria
-ADD aria /build-aria/aria
+RUN mkdir build-aria && mkdir build-aria/src
+ADD src/aria /build-aria/src/aria
ADD *.py PKG-INFO /build-aria/
-RUN cd build-aria && pip install .; npm install --save-dev husky
+RUN ls build-aria/src/aria
+RUN which pip; which python
+RUN cd build-aria; pip install .; npm install --save-dev husky
RUN npx yarn add husky --dev
diff --git a/MANIFEST.in b/MANIFEST.in
index 729a637787d5eb18f151a3f5efed633e0ba39684..ba60c5c9c6f6e4db48f37b474cd1b0e88da50b9b 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,4 +1,4 @@
-graft aria
+graft src
graft docs
include *.md
include COPYRIGHT
diff --git a/PKG-INFO b/PKG-INFO
index 6f6eb7a27be74a8350c7c32c2c12ee7df9621e8e..7241f738e36aa612401a649ab6dc8383116d16b7 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1 +1 @@
-Version: 0.0.20
\ No newline at end of file
+Version: 0.1.01
\ No newline at end of file
diff --git a/README.md b/README.md
index 4005e5658849337fce83a099c167190ed76faf3d..9485def8fd4b1b3f00d323f22118c3fae8d86323 100644
--- a/README.md
+++ b/README.md
@@ -21,18 +21,21 @@ list of PDB files.
Be sure to check if the following packages are correctly installed with
your python installation or virtual environment.
-- **pip** (>= 9.0)
-- **setuptools** (>= 18.0)
+- **pip** (>= 18.0)
+- **git** (>= 2.0)
- **cns-solve** (1.21)
+- **ccpnmr analysis** (optional)
+- **ccpn data model** (optional)
Then the easiest solution is to call the **pip** command below :
- `pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec`
+ `pip install --user git+http://gitlab.pasteur.fr/bis-aria/ariaec.git`
For more information about installation and usage, please refer to the
[ARIAEC documentation](http://bis-aria.pages.pasteur.fr/ariaec)
-**ARIA contains patches for CNS-solve which needs to be compiled after the installation. Please follow [post installation instructions](http://bis-aria.pages.pasteur.fr/ariaec/installation.html#post-installation-instructions).**
+**ARIA contains patches for CNS-solve which needs to be compiled after the
+installation. Please follow [post installation instructions](http://bis-aria.pages.pasteur.fr/ariaec/installation.html#post-installation-instructions).**
## Contributing
diff --git a/aria/core/test/test_AriaXML.py b/aria/core/test/test_AriaXML.py
deleted file mode 100644
index 800ba983ceaeacebfe215c866d3f9380e0987d32..0000000000000000000000000000000000000000
--- a/aria/core/test/test_AriaXML.py
+++ /dev/null
@@ -1,36 +0,0 @@
-import os
-import pytest
-from aria.core.Settings import Path
-from aria.core.AriaXML import AriaXMLPickler
-from aria.core.ariabase import PROJECT_TEMPLATE, AriaBaseClass
-
-
-@pytest.fixture
-def pickler():
- return AriaXMLPickler()
-
-
-@pytest.fixture
-def projectemplate():
- return os.path.join(AriaBaseClass.data_path, PROJECT_TEMPLATE)
-
-
-@pytest.fixture
-def project(pickler, projectemplate):
- Path.global_mandatory = 0
- return pickler.load_relaxed(projectemplate)
-
-
-def test_pickler_create_document(project, pickler):
- pickler.create_document(project)
-
-
-def test_pickler_dumps(project, pickler):
- pickler.dumps(project)
-
-
-if __name__ == '__main__':
- print("Test load aria xml template")
- test_pickler_create_document(project(pickler(), projectemplate()), pickler())
- test_pickler_dumps(project(pickler(), projectemplate()), pickler())
-
diff --git a/conda.recipe/build.sh b/conda.recipe/build.sh
new file mode 100644
index 0000000000000000000000000000000000000000..79c35d3d6c5ef6a32ddd4c90ea7d1e8fb1fe6268
--- /dev/null
+++ b/conda.recipe/build.sh
@@ -0,0 +1,2 @@
+#!/usr/bin/env bash
+$PYTHON -m pip install --no-deps .
diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..3ed4f4ea019cfb0121740e29eafb4e63c9e5b74f
--- /dev/null
+++ b/conda.recipe/meta.yaml
@@ -0,0 +1,48 @@
+{% set data = load_setup_py_data() %}
+
+package:
+ name: ariaec
+ version: {{ data['version'] }}
+
+source:
+ path: ..
+
+build:
+ # If the installation is complex, or different between Unix and Windows, use
+ # separate bld.bat and build.sh files instead of this key. Add the line
+ # "skip: True # [py<35]" (for example) to limit to Python 3.5 and newer, or
+ # "skip: True # [not win]" to limit to Windows.
+# script: python setup.py install --single-version-externally-managed --record=record.txt
+# number: {{ environ.get('CI_PIPELINE_ID', 0) }}
+
+requirements:
+ build:
+ - python
+ - setuptools
+
+ run:
+ - python
+ - # dependencies are defined in setup.py
+ {% for dep in data['install_requires'] %}
+ - {{ dep.lower() }}
+ {% endfor %}
+
+test:
+ requires:
+ - bandit
+ - pylint
+ - pytest
+ - pytest-cov
+
+ imports:
+ - ariaec
+
+about:
+ summary: "de Novo Ambiguous Restraints for Iterative Assignment"
+ home: https://gitlab.pasteur.fr/bis-aria/ariaec
+# license: Proprietary
+ extra:
+ sphinx:
+ language: en
+ intersphinx:
+ # project: Parent URL of the "objects.inv" file
diff --git a/docs/api/aria.aria2.rst b/docs/api/aria.aria2.rst
new file mode 100644
index 0000000000000000000000000000000000000000..6fd6fc9c6596729ee3e60767470b80f5c8464b35
--- /dev/null
+++ b/docs/api/aria.aria2.rst
@@ -0,0 +1,7 @@
+aria.aria2 module
+=================
+
+.. automodule:: aria.aria2
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/api/aria.ariacns.rst b/docs/api/aria.ariacns.rst
index fd627d212df851d0f6dc2b91d87cb6f7e5525948..aa2509269c97b652091e5452e34b0f1b2278a8df 100644
--- a/docs/api/aria.ariacns.rst
+++ b/docs/api/aria.ariacns.rst
@@ -1,37 +1,7 @@
-
-:autogenerated:
-
aria.ariacns module
===================
-.. currentmodule:: aria.ariacns
-
.. automodule:: aria.ariacns
- :members: CNSPatchCommand, main
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
-
-Summary
--------
-
-Classes:
-
-.. autosummary::
- :nosignatures:
-
- CNSPatchCommand
-
-Functions:
-
-.. autosummary::
- :nosignatures:
-
- main
-
-
-
-
-
-Reference
----------
\ No newline at end of file
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/api/aria.check.rst b/docs/api/aria.check.rst
new file mode 100644
index 0000000000000000000000000000000000000000..0a7e30b5155f5e6c9e4439fe66d9bdf73fa97088
--- /dev/null
+++ b/docs/api/aria.check.rst
@@ -0,0 +1,7 @@
+aria.check module
+=================
+
+.. automodule:: aria.check
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/api/aria.conbox.analysis.rst b/docs/api/aria.conbox.analysis.rst
index ced5db791a4d850e63174e5419ff9cec2dc22324..675f9d18ed591e6c28f7aeebd85cbba11c6152bd 100644
--- a/docs/api/aria.conbox.analysis.rst
+++ b/docs/api/aria.conbox.analysis.rst
@@ -7,7 +7,7 @@ aria.conbox.analysis module
.. currentmodule:: aria.conbox.analysis
.. automodule:: aria.conbox.analysis
- :members: EnsembleAnalysis, colscatter
+ :members: DATA_SEQUENCE, EnsembleAnalysis, colscatter
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -29,6 +29,13 @@ Functions:
colscatter
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ DATA_SEQUENCE
+
diff --git a/docs/api/aria.conbox.commands.rst b/docs/api/aria.conbox.commands.rst
index 536614776f9e00b0b6c9c26a276d7a55b52f847b..1a07b899774950ef70955078417a9365bbc4fbee 100644
--- a/docs/api/aria.conbox.commands.rst
+++ b/docs/api/aria.conbox.commands.rst
@@ -7,7 +7,7 @@ aria.conbox.commands module
.. currentmodule:: aria.conbox.commands
.. automodule:: aria.conbox.commands
- :members: AriaEcCommands, CLI, ReadableDir, ReadableFile, check_file, main, seqrange_type
+ :members: AriaEcCommands, CLI, CONTACT_FILE_PARSERS, ReadableDir, ReadableFile, check_file, conboxdoc, main, seqrange_type
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -34,6 +34,14 @@ Functions:
main
seqrange_type
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ CONTACT_FILE_PARSERS
+ conboxdoc
+
diff --git a/docs/api/aria.conbox.common.rst b/docs/api/aria.conbox.common.rst
index 183df3cf84bf74a2671afadd6a65d86b23f58c2e..06a3200cf902d2c0aad12abc26731700cbee4256 100644
--- a/docs/api/aria.conbox.common.rst
+++ b/docs/api/aria.conbox.common.rst
@@ -7,7 +7,7 @@ aria.conbox.common module
.. currentmodule:: aria.conbox.common
.. automodule:: aria.conbox.common
- :members: Capturing, CommandProtocol, CustomLogging, NotDisordered, RedirectStdStreams, TqdmToLogger, addtup, cart_dist, format_dict, format_str, get_filename, parmap, ppdict, reg_load, sort_2dict, tickmin, tickrot, titleprint, worker
+ :members: AbcLogFilter, Capturing, CommandProtocol, CustomLogging, NotDisordered, RedirectStdStreams, TqdmToLogger, addtup, cart_dist, format_dict, format_str, get_filename, parmap, ppdict, reg_load, sort_2dict, tickmin, tickrot, titleprint, worker
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -20,6 +20,7 @@ Classes:
.. autosummary::
:nosignatures:
+ AbcLogFilter
Capturing
CommandProtocol
CustomLogging
diff --git a/docs/api/aria.conbox.converter.rst b/docs/api/aria.conbox.converter.rst
index f2bcd85ab4288f60a888f451c59ff72b105aa3f7..cb90336294f0479bff4f9fe138cec6016d791b1a 100644
--- a/docs/api/aria.conbox.converter.rst
+++ b/docs/api/aria.conbox.converter.rst
@@ -7,7 +7,7 @@ aria.conbox.converter module
.. currentmodule:: aria.conbox.converter
.. automodule:: aria.conbox.converter
- :members: AriaEcBbConverter, AriaEcConfigConverter, AriaEcXMLConverter, AriaXMLConverter
+ :members: AriaEcBbConverter, AriaEcConfigConverter, AriaEcXMLConverter, AriaXMLConverter, DATA_ANNEALING_RDC, DATA_RDCS, DATA_SEQUENCE, DATA_TYPES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -25,6 +25,16 @@ Classes:
AriaEcXMLConverter
AriaXMLConverter
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ DATA_ANNEALING_RDC
+ DATA_RDCS
+ DATA_SEQUENCE
+ DATA_TYPES
+
diff --git a/docs/api/aria.conbox.pdbqual.rst b/docs/api/aria.conbox.pdbqual.rst
index 2c6c297e4310907a3f85cb4b61d8e7012ef66837..b4dda99c26f1db332907639f170199fb6a65bdb5 100644
--- a/docs/api/aria.conbox.pdbqual.rst
+++ b/docs/api/aria.conbox.pdbqual.rst
@@ -7,7 +7,7 @@ aria.conbox.pdbqual module
.. currentmodule:: aria.conbox.pdbqual
.. automodule:: aria.conbox.pdbqual
- :members: AriaEcPdbqual
+ :members: AriaEcPdbqual, FILENAME_REPORT
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -22,6 +22,13 @@ Classes:
AriaEcPdbqual
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ FILENAME_REPORT
+
diff --git a/docs/api/aria.core.Analyser.rst b/docs/api/aria.core.Analyser.rst
index 1592a58b6e285be5581f6cb9462d5b486f9a2c1f..db6776f9ee72351108c461fa315757a322a3a6b4 100644
--- a/docs/api/aria.core.Analyser.rst
+++ b/docs/api/aria.core.Analyser.rst
@@ -7,7 +7,7 @@ aria.core.Analyser module
.. currentmodule:: aria.core.Analyser
.. automodule:: aria.core.Analyser
- :members: Analyser, AnalyserXMLPickler, AnalysisParameters
+ :members: ALWAYS, ARIA_ENV, ARRAY, Analyser, AnalyserXMLPickler, AnalysisParameters, BOOL, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -24,6 +24,38 @@ Classes:
AnalyserXMLPickler
AnalysisParameters
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.AriaPeak.rst b/docs/api/aria.core.AriaPeak.rst
index 9dd2f0be56a5a4fa5cb2aa05679eb47445b253e2..d4591010b24d953b50f25541cfdffa03b642cb3c 100644
--- a/docs/api/aria.core.AriaPeak.rst
+++ b/docs/api/aria.core.AriaPeak.rst
@@ -7,7 +7,7 @@ aria.core.AriaPeak module
.. currentmodule:: aria.core.AriaPeak
.. automodule:: aria.core.AriaPeak
- :members: AbstractPeak, AriaPeak, AriaPeakAnalysis, AriaPeakAnalysisXMLPickler, AriaPeakListTextPickler, AriaPeakListTextPicklerSettings, AriaPeakTextPickler, AriaPeakXMLPickler, ContributionTextPickler, DistanceRestraint, DistanceRestraintXMLPickler, TextPickler
+ :members: ABBREVIATIONS_CONTRIBUTIONS, ALWAYS, ARIA_ENV, ARRAY, ASSIGNMENT_TYPE_DICT, AbstractPeak, AriaPeak, AriaPeakAnalysis, AriaPeakAnalysisXMLPickler, AriaPeakListTextPickler, AriaPeakListTextPicklerSettings, AriaPeakTextPickler, AriaPeakXMLPickler, BOOL, CCPN_EXTENSION, CONTRIBUTIONS_HEADER, CONTRIBUTION_SINGLE, CONTRIBUTION_SPINPAIR, ContributionTextPickler, DICT, DistanceRestraint, DistanceRestraintXMLPickler, FLOAT, FLOAT64, GZIP, HEADER_ABBREVIATIONS, HEADER_AMBIG, HEADER_ASSIGNMENT_TYPE, HEADER_DICT, HEADER_PROJECT, HEADER_RESTRAINT_ACTIVE, HEADER_RESTRAINT_BOUNDS, HEADER_RESTRAINT_DEFINITION, HEADER_SEQUENCE_SEPARATION, HEADER_UNAMBIG, HEADER_VIOLATIONS, INT, LIST, MODULE_NAME, NA, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, TextPickler, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -33,6 +33,55 @@ Classes:
DistanceRestraintXMLPickler
TextPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ABBREVIATIONS_CONTRIBUTIONS
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ ASSIGNMENT_TYPE_DICT
+ BOOL
+ CCPN_EXTENSION
+ CONTRIBUTIONS_HEADER
+ CONTRIBUTION_SINGLE
+ CONTRIBUTION_SPINPAIR
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ HEADER_ABBREVIATIONS
+ HEADER_AMBIG
+ HEADER_ASSIGNMENT_TYPE
+ HEADER_DICT
+ HEADER_PROJECT
+ HEADER_RESTRAINT_ACTIVE
+ HEADER_RESTRAINT_BOUNDS
+ HEADER_RESTRAINT_DEFINITION
+ HEADER_SEQUENCE_SEPARATION
+ HEADER_UNAMBIG
+ HEADER_VIOLATIONS
+ INT
+ LIST
+ MODULE_NAME
+ NA
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.AriaXML.rst b/docs/api/aria.core.AriaXML.rst
index 5163197859d011b7d9ea02324464145cbee48a3d..b20384e004896fcaffc116881f35fa2dce1d03b7 100644
--- a/docs/api/aria.core.AriaXML.rst
+++ b/docs/api/aria.core.AriaXML.rst
@@ -7,7 +7,7 @@ aria.core.AriaXML module
.. currentmodule:: aria.core.AriaXML
.. automodule:: aria.core.AriaXML
- :members: AriaXMLContentHandler, AriaXMLPickler, DOCManager
+ :members: ALWAYS, ARIA_ENV, ARRAY, AriaXMLContentHandler, AriaXMLPickler, BOOL, CCPN_EXTENSION, DICT, DOCManager, DOCTYPE_DIST_RESTRAINTS, DOCTYPE_NOE_RESTRAINTS, DTD_CHEMICAL_SHIFT_LIST, DTD_DIST_RESTRAINT, DTD_MOLECULE, DTD_NOESY_SPECTRUM, DTD_NOE_RESTRAINT, DTD_PROJECT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -24,6 +24,46 @@ Classes:
AriaXMLPickler
DOCManager
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ DOCTYPE_DIST_RESTRAINTS
+ DOCTYPE_NOE_RESTRAINTS
+ DTD_CHEMICAL_SHIFT_LIST
+ DTD_DIST_RESTRAINT
+ DTD_MOLECULE
+ DTD_NOESY_SPECTRUM
+ DTD_NOE_RESTRAINT
+ DTD_PROJECT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.Assignment.rst b/docs/api/aria.core.Assignment.rst
index bdbae3f1ee8e7a09415829fa1762ed20b432a0a0..60eada4f843a66292bde2e0dbbf65d378b59f7e0 100644
--- a/docs/api/aria.core.Assignment.rst
+++ b/docs/api/aria.core.Assignment.rst
@@ -7,7 +7,7 @@ aria.core.Assignment module
.. currentmodule:: aria.core.Assignment
.. automodule:: aria.core.Assignment
- :members: Assignment, AssignmentXMLPickler
+ :members: ASSIGNMENT_TYPES, ASSIGNMENT_TYPE_AUTOMATIC, ASSIGNMENT_TYPE_MANUAL, Assignment, AssignmentXMLPickler
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -23,6 +23,15 @@ Classes:
Assignment
AssignmentXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ASSIGNMENT_TYPES
+ ASSIGNMENT_TYPE_AUTOMATIC
+ ASSIGNMENT_TYPE_MANUAL
+
diff --git a/docs/api/aria.core.AssignmentFilter.rst b/docs/api/aria.core.AssignmentFilter.rst
index c7b6865d45d2c96bd21a9ed7e1b5495bda80ceeb..65f27b83bab071f1956a4104d0d3d9964bc258d2 100644
--- a/docs/api/aria.core.AssignmentFilter.rst
+++ b/docs/api/aria.core.AssignmentFilter.rst
@@ -7,7 +7,7 @@ aria.core.AssignmentFilter module
.. currentmodule:: aria.core.AssignmentFilter
.. automodule:: aria.core.AssignmentFilter
- :members: AssignmentFilter
+ :members: ALWAYS, ARIA_ENV, ARRAY, AssignmentFilter, BOOL, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -22,6 +22,38 @@ Classes:
AssignmentFilter
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.Atom.rst b/docs/api/aria.core.Atom.rst
index 027d3c704514a59885e7038cd588eab5f8f918f7..851f90431c4596676495c67158735734787017bf 100644
--- a/docs/api/aria.core.Atom.rst
+++ b/docs/api/aria.core.Atom.rst
@@ -7,7 +7,7 @@ aria.core.Atom module
.. currentmodule:: aria.core.Atom
.. automodule:: aria.core.Atom
- :members: Atom, AtomSettings, AtomXMLPickler
+ :members: ARRAY, Atom, AtomSettings, AtomXMLPickler, BOOL, DICT, FLOAT, FLOAT64, INT, LIST, NONE, NOT_INIT, ORDEREDICT, STRING, TUPLE, TYPES, UNICODE
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -24,6 +24,26 @@ Classes:
AtomSettings
AtomXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ARRAY
+ BOOL
+ DICT
+ FLOAT
+ FLOAT64
+ INT
+ LIST
+ NONE
+ NOT_INIT
+ ORDEREDICT
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+
diff --git a/docs/api/aria.core.Chain.rst b/docs/api/aria.core.Chain.rst
index 5ede965ac1c4683441bcff9f2bec625d87cfde77..8b472e34227722914cc8e92c9bd71afba15d73d2 100644
--- a/docs/api/aria.core.Chain.rst
+++ b/docs/api/aria.core.Chain.rst
@@ -7,7 +7,7 @@ aria.core.Chain module
.. currentmodule:: aria.core.Chain
.. automodule:: aria.core.Chain
- :members: AtomNomenclatureEntity, Chain, ChainSettings, ChainXMLPickler
+ :members: ALWAYS, ARIA_ENV, ARRAY, AtomNomenclatureEntity, BOOL, CCPN_EXTENSION, Chain, ChainSettings, ChainXMLPickler, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, TYPE_DNA, TYPE_NONPOLYMER, TYPE_PROTEIN, TYPE_RNA, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -25,6 +25,42 @@ Classes:
ChainSettings
ChainXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ TYPE_DNA
+ TYPE_NONPOLYMER
+ TYPE_PROTEIN
+ TYPE_RNA
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.ChemicalShiftFilter.rst b/docs/api/aria.core.ChemicalShiftFilter.rst
index c45096ca8848d527fdb0175c8428f692371bd09c..dec5702c23a1e39a7d8094926dcc69323ccadba4 100644
--- a/docs/api/aria.core.ChemicalShiftFilter.rst
+++ b/docs/api/aria.core.ChemicalShiftFilter.rst
@@ -7,7 +7,7 @@ aria.core.ChemicalShiftFilter module
.. currentmodule:: aria.core.ChemicalShiftFilter
.. automodule:: aria.core.ChemicalShiftFilter
- :members: ChemicalShiftFilter, ChemicalShiftFilterSettings
+ :members: ChemicalShiftFilter, ChemicalShiftFilterSettings, INVALID_SHIFT_VALUE, NEGATIVE_SHIFT_ERROR
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -23,6 +23,14 @@ Classes:
ChemicalShiftFilter
ChemicalShiftFilterSettings
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ INVALID_SHIFT_VALUE
+ NEGATIVE_SHIFT_ERROR
+
diff --git a/docs/api/aria.core.Cluster.rst b/docs/api/aria.core.Cluster.rst
index b0fe4493ea0ffba404d2a971c5545341e9f56342..ca96ba14c30ad2984734206a1267d1b42dfff73a 100644
--- a/docs/api/aria.core.Cluster.rst
+++ b/docs/api/aria.core.Cluster.rst
@@ -7,7 +7,7 @@ aria.core.Cluster module
.. currentmodule:: aria.core.Cluster
.. automodule:: aria.core.Cluster
- :members: Clustering, ClusteringSettings, ClusteringXMLPickler
+ :members: Clustering, ClusteringSettings, ClusteringXMLPickler, NO
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -24,6 +24,13 @@ Classes:
ClusteringSettings
ClusteringXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ NO
+
diff --git a/docs/api/aria.core.Contribution.rst b/docs/api/aria.core.Contribution.rst
index e12df9523c6090ddb2a35981ae1ed9bfd9cd0452..6fca3ceb7ff63895d479ee78fe72b1318aef13a2 100644
--- a/docs/api/aria.core.Contribution.rst
+++ b/docs/api/aria.core.Contribution.rst
@@ -7,7 +7,7 @@ aria.core.Contribution module
.. currentmodule:: aria.core.Contribution
.. automodule:: aria.core.Contribution
- :members: Contribution, Contribution2XMLPickler, ContributionEvaluator, ContributionXMLPickler
+ :members: CONTRIBUTION_TYPE_FAST_EXCHANGE, CONTRIBUTION_TYPE_FLOATING_ASSIGNMENT, CONTRIBUTION_TYPE_NORMAL, CONTRIBUTION_TYPE_TEST, Contribution, Contribution2XMLPickler, ContributionEvaluator, ContributionXMLPickler
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -25,6 +25,16 @@ Classes:
ContributionEvaluator
ContributionXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ CONTRIBUTION_TYPE_FAST_EXCHANGE
+ CONTRIBUTION_TYPE_FLOATING_ASSIGNMENT
+ CONTRIBUTION_TYPE_NORMAL
+ CONTRIBUTION_TYPE_TEST
+
diff --git a/docs/api/aria.core.ConversionTable.rst b/docs/api/aria.core.ConversionTable.rst
index f2b63253de83143c79472d1e1e51fabb4cab2682..49c9723e7eef2710cc8867efde1ba460fe334403 100644
--- a/docs/api/aria.core.ConversionTable.rst
+++ b/docs/api/aria.core.ConversionTable.rst
@@ -7,7 +7,7 @@ aria.core.ConversionTable module
.. currentmodule:: aria.core.ConversionTable
.. automodule:: aria.core.ConversionTable
- :members: AtomnameConversionError, ConversionTable
+ :members: AtomnameConversionError, CNS_CONVENTION, CONVERSION_DATA, ConversionTable, DYANA_CONVENTION, IUPAC_CONVENTION, NAMING_CONVENTIONS
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -29,6 +29,17 @@ Classes:
ConversionTable
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ CNS_CONVENTION
+ CONVERSION_DATA
+ DYANA_CONVENTION
+ IUPAC_CONVENTION
+ NAMING_CONVENTIONS
+
diff --git a/docs/api/aria.core.CovalentDistances.rst b/docs/api/aria.core.CovalentDistances.rst
index 2062ce5d4fa9655aeb8e910c84e1f3b1fb03d0f3..c94b9ad2b89c57edc8bc459a4908fa056fae09e2 100644
--- a/docs/api/aria.core.CovalentDistances.rst
+++ b/docs/api/aria.core.CovalentDistances.rst
@@ -7,7 +7,7 @@ aria.core.CovalentDistances module
.. currentmodule:: aria.core.CovalentDistances
.. automodule:: aria.core.CovalentDistances
- :members: CovalentDistances
+ :members: COVALENT_DATA, CovalentDistances
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -22,6 +22,13 @@ Classes:
CovalentDistances
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ COVALENT_DATA
+
diff --git a/docs/api/aria.core.CrossPeak.rst b/docs/api/aria.core.CrossPeak.rst
index 5c553c6a482de29e4674b48e69668c06a0fd3213..eba27a3bbbbc7946927d0825bf9eb4f2e06f88d5 100644
--- a/docs/api/aria.core.CrossPeak.rst
+++ b/docs/api/aria.core.CrossPeak.rst
@@ -7,7 +7,7 @@ aria.core.CrossPeak module
.. currentmodule:: aria.core.CrossPeak
.. automodule:: aria.core.CrossPeak
- :members: CrossPeak, CrossPeakXMLPickler
+ :members: CROSSPEAK_ASSIGNMENT_TYPE_AUTOMATIC, CROSSPEAK_ASSIGNMENT_TYPE_MANUAL, CROSSPEAK_ASSIGNMENT_TYPE_SEMIAUTOMATIC, CrossPeak, CrossPeakXMLPickler
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -23,6 +23,15 @@ Classes:
CrossPeak
CrossPeakXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ CROSSPEAK_ASSIGNMENT_TYPE_AUTOMATIC
+ CROSSPEAK_ASSIGNMENT_TYPE_MANUAL
+ CROSSPEAK_ASSIGNMENT_TYPE_SEMIAUTOMATIC
+
diff --git a/docs/api/aria.core.CrossPeakFilter.rst b/docs/api/aria.core.CrossPeakFilter.rst
index 3dc46dc22a1485a3974698c85fc95654cc2e74c6..823dfa99bba9ca2cd6c525b499fafd62cfa0b232 100644
--- a/docs/api/aria.core.CrossPeakFilter.rst
+++ b/docs/api/aria.core.CrossPeakFilter.rst
@@ -7,7 +7,7 @@ aria.core.CrossPeakFilter module
.. currentmodule:: aria.core.CrossPeakFilter
.. automodule:: aria.core.CrossPeakFilter
- :members: CrossPeakFilter, CrossPeakFilterSettings
+ :members: CrossPeakFilter, CrossPeakFilterSettings, DIAGONAL_PEAK, NEGATIVE_PEAK, NO_PEAK_SIZE, UNASSIGNED_PEAK
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -23,6 +23,16 @@ Classes:
CrossPeakFilter
CrossPeakFilterSettings
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ DIAGONAL_PEAK
+ NEGATIVE_PEAK
+ NO_PEAK_SIZE
+ UNASSIGNED_PEAK
+
diff --git a/docs/api/aria.core.DataContainer.rst b/docs/api/aria.core.DataContainer.rst
index 16e001a4c31cd56ea433a7dc15d3d8f5a7982f86..99fc5c45060efe9be64df1f81b1b2921c211deb8 100644
--- a/docs/api/aria.core.DataContainer.rst
+++ b/docs/api/aria.core.DataContainer.rst
@@ -7,7 +7,7 @@ aria.core.DataContainer module
.. currentmodule:: aria.core.DataContainer
.. automodule:: aria.core.DataContainer
- :members: AmbiguousDistanceData, AmbiguousDistanceDataXMLPickler, AmbiguousParameters, AmbiguousParametersXMLPickler, AnnealingParameters, AnnealingParametersXMLPickler, BASE, BoundCorrection, BoundCorrectionXMLPickler, CCPNData, CCPNDataXMLPickler, CisProPatch, CisProPatchXMLPickler, CysPatch, CysPatchXMLPickler, DRParametersXMLPickler, DataContainer, DataContainerXMLPickler, DihedralData, DihedralDataXMLPickler, DihedralParameters, DihedralParametersXMLPickler, DistanceDataXMLPickler, ExperimentData, ExperimentDataXMLPickler, FBHWParameters, FBHWParametersXMLPickler, FFP, FileFormatXMLPickler, HBDBParameters, HBDBParametersXMLPickler, HBondData, HBondDataXMLPickler, HBondParameters, HBondParametersXMLPickler, HisPatch, HisPatchXMLPickler, InitialStructureData, InitialStructureDataXMLPickler, IsoPeptidePatch, IsoPeptidePatchXMLPickler, KarplusData, KarplusDataXMLPickler, KarplusParameters, KarplusParametersXMLPickler, LogHarmonicParameters, LogHarmonicParametersXMLPickler, LowerBoundCorrection, MDParameters, MDParametersXMLPickler, OtherData, OtherDataXMLPickler, PeakData, PeakDataXMLPickler, RDCData, RDCDataXMLPickler, RDCParameters, RDCParametersXMLPickler, RamaParameters, RamaParametersXMLPickler, SSBondData, SSBondDataXMLPickler, SSBridge, SSBridgeXMLPickler, ScoringParameters, ScoringParametersXMLPickler, SequenceData, SequenceDataXMLPickler, ShiftData, ShiftDataXMLPickler, SimpleDCXMLPickler, SimpleDataContainer, SpectrumData, SpectrumDataXMLPickler, Symmetry, SymmetryParameters, SymmetryParametersXMLPickler, SymmetryXMLPickler, TemplateData, TemplateDataXMLPickler, UnambiguousDistanceData, UnambiguousDistanceDataXMLPickler, UnambiguousParameters, UnambiguousParametersXMLPickler, UpperBoundCorrection, WaterRefinementParameters, WaterRefinementXMLPickler, ZnPatch, ZnPatchXMLPickler
+ :members: ALWAYS, ARIA_ENV, ARRAY, AmbiguousDistanceData, AmbiguousDistanceDataXMLPickler, AmbiguousParameters, AmbiguousParametersXMLPickler, AnnealingParameters, AnnealingParametersXMLPickler, BASE, BOOL, BoundCorrection, BoundCorrectionXMLPickler, CCPNData, CCPNDataXMLPickler, CCPN_EXTENSION, CisProPatch, CisProPatchXMLPickler, CysPatch, CysPatchXMLPickler, DATA_AMBIGUOUS, DATA_ANNEALING, DATA_ANNEALING_AMBIG, DATA_ANNEALING_DIHEDRAL, DATA_ANNEALING_FBHW, DATA_ANNEALING_HBDB, DATA_ANNEALING_HBOND, DATA_ANNEALING_KARPLUS, DATA_ANNEALING_LOGHARMONIC, DATA_ANNEALING_RAMA, DATA_ANNEALING_RDC, DATA_ANNEALING_SCORING, DATA_ANNEALING_SYM, DATA_ANNEALING_UNAMBIG, DATA_CCPN, DATA_CISPROPATCH, DATA_CYSPATCH, DATA_DEFAULT, DATA_DIHEDRALS, DATA_DYNAMICS, DATA_EXPERIMENT, DATA_HBONDS, DATA_HISPATCH, DATA_INITIAL_STRUCTURE, DATA_ISOPATCH, DATA_ITERATION, DATA_KARPLUS, DATA_OTHER, DATA_PEAKS, DATA_RDCS, DATA_SEQUENCE, DATA_SHIFTS, DATA_SPECTRUM, DATA_SSBONDS, DATA_SSBRIDGE, DATA_SYMMETRY, DATA_TEMPLATE_STRUCTURE, DATA_TYPES, DATA_UNAMBIGUOUS, DATA_ZNPATCH, DICT, DRParametersXMLPickler, DataContainer, DataContainerXMLPickler, DihedralData, DihedralDataXMLPickler, DihedralParameters, DihedralParametersXMLPickler, DistanceDataXMLPickler, ExperimentData, ExperimentDataXMLPickler, FBHWParameters, FBHWParametersXMLPickler, FFP, FLOAT, FLOAT64, FileFormatXMLPickler, GZIP, HBDBParameters, HBDBParametersXMLPickler, HBondData, HBondDataXMLPickler, HBondParameters, HBondParametersXMLPickler, HisPatch, HisPatchXMLPickler, INT, InitialStructureData, InitialStructureDataXMLPickler, IsoPeptidePatch, IsoPeptidePatchXMLPickler, KarplusData, KarplusDataXMLPickler, KarplusParameters, KarplusParametersXMLPickler, LIST, LogHarmonicParameters, LogHarmonicParametersXMLPickler, LowerBoundCorrection, MDParameters, MDParametersXMLPickler, MODULE_NAME, NO, NONE, ORDEREDICT, OtherData, OtherDataXMLPickler, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, PeakData, PeakDataXMLPickler, RDCData, RDCDataXMLPickler, RDCParameters, RDCParametersXMLPickler, RamaParameters, RamaParametersXMLPickler, SSBondData, SSBondDataXMLPickler, SSBridge, SSBridgeXMLPickler, STRING, ScoringParameters, ScoringParametersXMLPickler, SequenceData, SequenceDataXMLPickler, ShiftData, ShiftDataXMLPickler, SimpleDCXMLPickler, SimpleDataContainer, SpectrumData, SpectrumDataXMLPickler, Symmetry, SymmetryParameters, SymmetryParametersXMLPickler, SymmetryXMLPickler, TUPLE, TYPES, TemplateData, TemplateDataXMLPickler, UNICODE, UnambiguousDistanceData, UnambiguousDistanceDataXMLPickler, UnambiguousParameters, UnambiguousParametersXMLPickler, UpperBoundCorrection, VL_LOW, VL_SETTINGS, VL_STANDARD, WaterRefinementParameters, WaterRefinementXMLPickler, YES, ZnPatch, ZnPatchXMLPickler
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -110,6 +110,78 @@ Classes:
ZnPatch
ZnPatchXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DATA_AMBIGUOUS
+ DATA_ANNEALING
+ DATA_ANNEALING_AMBIG
+ DATA_ANNEALING_DIHEDRAL
+ DATA_ANNEALING_FBHW
+ DATA_ANNEALING_HBDB
+ DATA_ANNEALING_HBOND
+ DATA_ANNEALING_KARPLUS
+ DATA_ANNEALING_LOGHARMONIC
+ DATA_ANNEALING_RAMA
+ DATA_ANNEALING_RDC
+ DATA_ANNEALING_SCORING
+ DATA_ANNEALING_SYM
+ DATA_ANNEALING_UNAMBIG
+ DATA_CCPN
+ DATA_CISPROPATCH
+ DATA_CYSPATCH
+ DATA_DEFAULT
+ DATA_DIHEDRALS
+ DATA_DYNAMICS
+ DATA_EXPERIMENT
+ DATA_HBONDS
+ DATA_HISPATCH
+ DATA_INITIAL_STRUCTURE
+ DATA_ISOPATCH
+ DATA_ITERATION
+ DATA_KARPLUS
+ DATA_OTHER
+ DATA_PEAKS
+ DATA_RDCS
+ DATA_SEQUENCE
+ DATA_SHIFTS
+ DATA_SPECTRUM
+ DATA_SSBONDS
+ DATA_SSBRIDGE
+ DATA_SYMMETRY
+ DATA_TEMPLATE_STRUCTURE
+ DATA_TYPES
+ DATA_UNAMBIGUOUS
+ DATA_ZNPATCH
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.Datum.rst b/docs/api/aria.core.Datum.rst
index b10e3974d0d9ec21ed0c735bd661509335b3f869..0b6c8ad77db427e44adf3a5162e0aba2913f00b3 100644
--- a/docs/api/aria.core.Datum.rst
+++ b/docs/api/aria.core.Datum.rst
@@ -7,7 +7,7 @@ aria.core.Datum module
.. currentmodule:: aria.core.Datum
.. automodule:: aria.core.Datum
- :members: ChemicalShift, ChemicalShiftXMLPickler, Datum, DatumXMLPickler
+ :members: ALWAYS, ARIA_ENV, ARRAY, BOOL, CCPN_EXTENSION, ChemicalShift, ChemicalShiftXMLPickler, DICT, Datum, DatumXMLPickler, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -25,6 +25,38 @@ Classes:
Datum
DatumXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.Experiment.rst b/docs/api/aria.core.Experiment.rst
index 5d31fd58d9ef92741f76516b21065a40d6424659..30d0bf6e96503b68aa3d13d7bfdf5291eb9a0483 100644
--- a/docs/api/aria.core.Experiment.rst
+++ b/docs/api/aria.core.Experiment.rst
@@ -7,7 +7,7 @@ aria.core.Experiment module
.. currentmodule:: aria.core.Experiment
.. automodule:: aria.core.Experiment
- :members: Experiment
+ :members: ALWAYS, ARIA_ENV, ARRAY, BOOL, CCPN_EXTENSION, DICT, Experiment, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -22,6 +22,38 @@ Classes:
Experiment
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.Factory.rst b/docs/api/aria.core.Factory.rst
index eecf70e1408b127c899bfe2c1b8d0aa631a136b6..32d587bda6335bbf7960919e0377a302a18b2f15 100644
--- a/docs/api/aria.core.Factory.rst
+++ b/docs/api/aria.core.Factory.rst
@@ -7,7 +7,7 @@ aria.core.Factory module
.. currentmodule:: aria.core.Factory
.. automodule:: aria.core.Factory
- :members: AtomFactory, SpinPairFactory, SpinPairListFactory
+ :members: ARRAY, AtomFactory, BOOL, DICT, FLOAT, FLOAT64, INT, LIST, NONE, ORDEREDICT, STRING, SpinPairFactory, SpinPairListFactory, TUPLE, TYPES, UNICODE
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -24,6 +24,25 @@ Classes:
SpinPairFactory
SpinPairListFactory
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ARRAY
+ BOOL
+ DICT
+ FLOAT
+ FLOAT64
+ INT
+ LIST
+ NONE
+ ORDEREDICT
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+
diff --git a/docs/api/aria.core.Infrastructure.rst b/docs/api/aria.core.Infrastructure.rst
index 06b5b1e62304feb8fd908dedbfd9f0a3fd3396f4..f1289c9d1f94a9dd9f9df2e82c6c7651b6cdfa25 100644
--- a/docs/api/aria.core.Infrastructure.rst
+++ b/docs/api/aria.core.Infrastructure.rst
@@ -7,7 +7,7 @@ aria.core.Infrastructure module
.. currentmodule:: aria.core.Infrastructure
.. automodule:: aria.core.Infrastructure
- :members: AriaDirectoryCreationError, Infrastructure
+ :members: ALWAYS, ARIA_ENV, ARRAY, AriaDirectoryCreationError, BOOL, CACHE_FILENAME, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, INT, Infrastructure, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -29,6 +29,39 @@ Classes:
Infrastructure
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CACHE_FILENAME
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.Iteration.rst b/docs/api/aria.core.Iteration.rst
index 006d07b089d0af59890e3efcb35e3e9be78e516c..66a546027ac3448040ae7888b39b4446b74f331e 100644
--- a/docs/api/aria.core.Iteration.rst
+++ b/docs/api/aria.core.Iteration.rst
@@ -7,7 +7,7 @@ aria.core.Iteration module
.. currentmodule:: aria.core.Iteration
.. automodule:: aria.core.Iteration
- :members: Iteration, IterationTextPickler
+ :members: ALLOW_THREADS, ALWAYS, AMBIG_REPORT, ARIA_ENV, ARRAY, BOOL, BUFSIZE, CCPN_EXTENSION, CLIP, CONSTRAINT_LIST_REPORT, DICT, ERR_CALL, ERR_DEFAULT, ERR_IGNORE, ERR_LOG, ERR_PRINT, ERR_RAISE, ERR_WARN, FLOAT, FLOAT64, FLOATING_POINT_SUPPORT, FPE_DIVIDEBYZERO, FPE_INVALID, FPE_OVERFLOW, FPE_UNDERFLOW, False_, GZIP, INT, Inf, Infinity, Iteration, IterationTextPickler, LIST, MAXDIMS, MAY_SHARE_BOUNDS, MAY_SHARE_EXACT, MODULE_NAME, NA, NAN, NINF, NO, NONE, NZERO, NaN, ORDEREDICT, PATH_MODULES, PINF, PRINT_LOCK, PROJECT_TEMPLATE, PZERO, RAISE, REPORT, SHIFT_DIVIDEBYZERO, SHIFT_INVALID, SHIFT_OVERFLOW, SHIFT_UNDERFLOW, SPECTRUM_REPORT, STRING, ScalarType, TUPLE, TYPES, True_, UFUNC_BUFSIZE_DEFAULT, UFUNC_PYVALS_NAME, UNAMBIG_REPORT, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, WRAP, YES, absolute, add, arccos, arccosh, arcsin, arcsinh, arctan, arctan2, arctanh, bitwise_and, bitwise_not, bitwise_or, bitwise_xor, cbrt, ceil, conj, conjugate, copysign, cos, cosh, deg2rad, degrees, divide, divmod, e, equal, euler_gamma, exp, exp2, expm1, fabs, float_power, floor, floor_divide, fmax, fmin, fmod, frexp, gcd, greater, greater_equal, heaviside, hypot, inf, infty, invert, isfinite, isinf, isnan, isnat, lcm, ldexp, left_shift, less, less_equal, little_endian, log, log10, log1p, log2, logaddexp, logaddexp2, logical_and, logical_not, logical_or, logical_xor, matmul, maximum, minimum, mod, modf, multiply, nan, negative, newaxis, nextafter, not_equal, pi, positive, power, rad2deg, radians, reciprocal, remainder, right_shift, rint, sctypeDict, sctypes, sign, signbit, sin, sinh, spacing, sqrt, square, subtract, tan, tanh, tracemalloc_domain, true_divide, trunc, typeDict, typecodes
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -23,6 +23,184 @@ Classes:
Iteration
IterationTextPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALLOW_THREADS
+ ALWAYS
+ AMBIG_REPORT
+ ARIA_ENV
+ ARRAY
+ BOOL
+ BUFSIZE
+ CCPN_EXTENSION
+ CLIP
+ CONSTRAINT_LIST_REPORT
+ DICT
+ ERR_CALL
+ ERR_DEFAULT
+ ERR_IGNORE
+ ERR_LOG
+ ERR_PRINT
+ ERR_RAISE
+ ERR_WARN
+ FLOAT
+ FLOAT64
+ FLOATING_POINT_SUPPORT
+ FPE_DIVIDEBYZERO
+ FPE_INVALID
+ FPE_OVERFLOW
+ FPE_UNDERFLOW
+ False_
+ GZIP
+ INT
+ Inf
+ Infinity
+ LIST
+ MAXDIMS
+ MAY_SHARE_BOUNDS
+ MAY_SHARE_EXACT
+ MODULE_NAME
+ NA
+ NAN
+ NINF
+ NO
+ NONE
+ NZERO
+ NaN
+ ORDEREDICT
+ PATH_MODULES
+ PINF
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ PZERO
+ RAISE
+ REPORT
+ SHIFT_DIVIDEBYZERO
+ SHIFT_INVALID
+ SHIFT_OVERFLOW
+ SHIFT_UNDERFLOW
+ SPECTRUM_REPORT
+ STRING
+ ScalarType
+ TUPLE
+ TYPES
+ True_
+ UFUNC_BUFSIZE_DEFAULT
+ UFUNC_PYVALS_NAME
+ UNAMBIG_REPORT
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ WRAP
+ YES
+ absolute
+ add
+ arccos
+ arccosh
+ arcsin
+ arcsinh
+ arctan
+ arctan2
+ arctanh
+ bitwise_and
+ bitwise_not
+ bitwise_or
+ bitwise_xor
+ cbrt
+ ceil
+ conj
+ conjugate
+ copysign
+ cos
+ cosh
+ deg2rad
+ degrees
+ divide
+ divmod
+ e
+ equal
+ euler_gamma
+ exp
+ exp2
+ expm1
+ fabs
+ float_power
+ floor
+ floor_divide
+ fmax
+ fmin
+ fmod
+ frexp
+ gcd
+ greater
+ greater_equal
+ heaviside
+ hypot
+ inf
+ infty
+ invert
+ isfinite
+ isinf
+ isnan
+ isnat
+ lcm
+ ldexp
+ left_shift
+ less
+ less_equal
+ little_endian
+ log
+ log10
+ log1p
+ log2
+ logaddexp
+ logaddexp2
+ logical_and
+ logical_not
+ logical_or
+ logical_xor
+ matmul
+ maximum
+ minimum
+ mod
+ modf
+ multiply
+ nan
+ negative
+ newaxis
+ nextafter
+ not_equal
+ pi
+ positive
+ power
+ rad2deg
+ radians
+ reciprocal
+ remainder
+ right_shift
+ rint
+ sctypeDict
+ sctypes
+ sign
+ signbit
+ sin
+ sinh
+ spacing
+ sqrt
+ square
+ subtract
+ tan
+ tanh
+ tracemalloc_domain
+ true_divide
+ trunc
+ typeDict
+ typecodes
+
diff --git a/docs/api/aria.core.JobManager.rst b/docs/api/aria.core.JobManager.rst
index fcfef227a7f7fcbe8ca6da58f7d402b9e1295f65..53815fcc52b8196160d40b93f83a3c1e06f76ee1 100644
--- a/docs/api/aria.core.JobManager.rst
+++ b/docs/api/aria.core.JobManager.rst
@@ -7,7 +7,7 @@ aria.core.JobManager module
.. currentmodule:: aria.core.JobManager
.. automodule:: aria.core.JobManager
- :members: HostSettings, HostSettingsXMLPickler, Job, JobManager, JobManagerXMLPickler, JobScheduler, JobSchedulerSettings, JobSettings, PartlyUsedNodesFinder
+ :members: ALWAYS, ARIA_ENV, ARRAY, BOOL, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, HostSettings, HostSettingsXMLPickler, INT, Job, JobManager, JobManagerXMLPickler, JobScheduler, JobSchedulerSettings, JobSettings, LIST, MODULE_NAME, NO, NONE, NOT_INIT, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, PartlyUsedNodesFinder, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -30,6 +30,39 @@ Classes:
JobSettings
PartlyUsedNodesFinder
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ NOT_INIT
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.Merger.rst b/docs/api/aria.core.Merger.rst
index ed8f360aec8ab9f8325af3f4473b0986d463e7c6..1285d0cc55395a048c3ea582c967375f1daef3ed 100644
--- a/docs/api/aria.core.Merger.rst
+++ b/docs/api/aria.core.Merger.rst
@@ -7,7 +7,7 @@ aria.core.Merger module
.. currentmodule:: aria.core.Merger
.. automodule:: aria.core.Merger
- :members: Merger, MergerSettings, MergerTextPickler, MergerXMLPickler
+ :members: LIST, Merger, MergerSettings, MergerTextPickler, MergerXMLPickler, REPORT_HEADER, TUPLE
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -25,6 +25,15 @@ Classes:
MergerTextPickler
MergerXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ LIST
+ REPORT_HEADER
+ TUPLE
+
diff --git a/docs/api/aria.core.MolMol.rst b/docs/api/aria.core.MolMol.rst
index 75d88798dff2872492d7f4d53a99bb43e2bef156..ad1211e7aad92f60172ee236ada8ee102c4ae902 100644
--- a/docs/api/aria.core.MolMol.rst
+++ b/docs/api/aria.core.MolMol.rst
@@ -7,7 +7,7 @@ aria.core.MolMol module
.. currentmodule:: aria.core.MolMol
.. automodule:: aria.core.MolMol
- :members: MolMolPickler, write_noe_restraints
+ :members: LIST, LOWER_BOUND_EXT, MolMolPickler, TUPLE, UPPER_BOUND_EXT, write_noe_restraints
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -29,6 +29,16 @@ Functions:
write_noe_restraints
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ LIST
+ LOWER_BOUND_EXT
+ TUPLE
+ UPPER_BOUND_EXT
+
diff --git a/docs/api/aria.core.Molecule.rst b/docs/api/aria.core.Molecule.rst
index d9f59de89df3f9820ac0d62de0a94027094af023..83ff32fa20d5a4411551bafc9bc790d6c752170b 100644
--- a/docs/api/aria.core.Molecule.rst
+++ b/docs/api/aria.core.Molecule.rst
@@ -7,7 +7,7 @@ aria.core.Molecule module
.. currentmodule:: aria.core.Molecule
.. automodule:: aria.core.Molecule
- :members: Molecule, MoleculeXMLPickler
+ :members: ALWAYS, ARIA_ENV, ARRAY, BOOL, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, Molecule, MoleculeXMLPickler, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -23,6 +23,38 @@ Classes:
Molecule
MoleculeXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.NOEModel.rst b/docs/api/aria.core.NOEModel.rst
index 07db14d226f41e57cb593eb6b5e7e1d611c9d5ce..1096ce1a77b966d7adbd31b0a9f0705369d80ad3 100644
--- a/docs/api/aria.core.NOEModel.rst
+++ b/docs/api/aria.core.NOEModel.rst
@@ -7,7 +7,7 @@ aria.core.NOEModel module
.. currentmodule:: aria.core.NOEModel
.. automodule:: aria.core.NOEModel
- :members: ISPA, NOEModel, SpinDiffusionCorrection
+ :members: ALLOW_THREADS, ALWAYS, ARIA_ENV, ARRAY, BOOL, BUFSIZE, CCPN_EXTENSION, CLIP, DICT, ERR_CALL, ERR_DEFAULT, ERR_IGNORE, ERR_LOG, ERR_PRINT, ERR_RAISE, ERR_WARN, FLOAT, FLOAT64, FLOATING_POINT_SUPPORT, FPE_DIVIDEBYZERO, FPE_INVALID, FPE_OVERFLOW, FPE_UNDERFLOW, False_, GZIP, INT, ISPA, Inf, Infinity, LIST, MAXDIMS, MAY_SHARE_BOUNDS, MAY_SHARE_EXACT, MODULE_NAME, NAN, NINF, NO, NOEModel, NONE, NZERO, NaN, ORDEREDICT, PATH_MODULES, PINF, PRINT_LOCK, PROJECT_TEMPLATE, PZERO, RAISE, SHIFT_DIVIDEBYZERO, SHIFT_INVALID, SHIFT_OVERFLOW, SHIFT_UNDERFLOW, STRING, ScalarType, SpinDiffusionCorrection, TUPLE, TYPES, True_, UFUNC_BUFSIZE_DEFAULT, UFUNC_PYVALS_NAME, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, WRAP, YES, absolute, add, arccos, arccosh, arcsin, arcsinh, arctan, arctan2, arctanh, bitwise_and, bitwise_not, bitwise_or, bitwise_xor, cbrt, ceil, conj, conjugate, copysign, cos, cosh, deg2rad, degrees, divide, divmod, e, equal, euler_gamma, exp, exp2, expm1, fabs, float_power, floor, floor_divide, fmax, fmin, fmod, frexp, gcd, greater, greater_equal, heaviside, hypot, inf, infty, invert, isfinite, isinf, isnan, isnat, lcm, ldexp, left_shift, less, less_equal, little_endian, log, log10, log1p, log2, logaddexp, logaddexp2, logical_and, logical_not, logical_or, logical_xor, matmul, maximum, minimum, mod, modf, multiply, nan, negative, newaxis, nextafter, not_equal, pi, positive, power, rad2deg, radians, reciprocal, remainder, right_shift, rint, sctypeDict, sctypes, sign, signbit, sin, sinh, spacing, sqrt, square, subtract, tan, tanh, tracemalloc_domain, true_divide, trunc, typeDict, typecodes
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -24,6 +24,178 @@ Classes:
NOEModel
SpinDiffusionCorrection
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALLOW_THREADS
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ BUFSIZE
+ CCPN_EXTENSION
+ CLIP
+ DICT
+ ERR_CALL
+ ERR_DEFAULT
+ ERR_IGNORE
+ ERR_LOG
+ ERR_PRINT
+ ERR_RAISE
+ ERR_WARN
+ FLOAT
+ FLOAT64
+ FLOATING_POINT_SUPPORT
+ FPE_DIVIDEBYZERO
+ FPE_INVALID
+ FPE_OVERFLOW
+ FPE_UNDERFLOW
+ False_
+ GZIP
+ INT
+ Inf
+ Infinity
+ LIST
+ MAXDIMS
+ MAY_SHARE_BOUNDS
+ MAY_SHARE_EXACT
+ MODULE_NAME
+ NAN
+ NINF
+ NO
+ NONE
+ NZERO
+ NaN
+ ORDEREDICT
+ PATH_MODULES
+ PINF
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ PZERO
+ RAISE
+ SHIFT_DIVIDEBYZERO
+ SHIFT_INVALID
+ SHIFT_OVERFLOW
+ SHIFT_UNDERFLOW
+ STRING
+ ScalarType
+ TUPLE
+ TYPES
+ True_
+ UFUNC_BUFSIZE_DEFAULT
+ UFUNC_PYVALS_NAME
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ WRAP
+ YES
+ absolute
+ add
+ arccos
+ arccosh
+ arcsin
+ arcsinh
+ arctan
+ arctan2
+ arctanh
+ bitwise_and
+ bitwise_not
+ bitwise_or
+ bitwise_xor
+ cbrt
+ ceil
+ conj
+ conjugate
+ copysign
+ cos
+ cosh
+ deg2rad
+ degrees
+ divide
+ divmod
+ e
+ equal
+ euler_gamma
+ exp
+ exp2
+ expm1
+ fabs
+ float_power
+ floor
+ floor_divide
+ fmax
+ fmin
+ fmod
+ frexp
+ gcd
+ greater
+ greater_equal
+ heaviside
+ hypot
+ inf
+ infty
+ invert
+ isfinite
+ isinf
+ isnan
+ isnat
+ lcm
+ ldexp
+ left_shift
+ less
+ less_equal
+ little_endian
+ log
+ log10
+ log1p
+ log2
+ logaddexp
+ logaddexp2
+ logical_and
+ logical_not
+ logical_or
+ logical_xor
+ matmul
+ maximum
+ minimum
+ mod
+ modf
+ multiply
+ nan
+ negative
+ newaxis
+ nextafter
+ not_equal
+ pi
+ positive
+ power
+ rad2deg
+ radians
+ reciprocal
+ remainder
+ right_shift
+ rint
+ sctypeDict
+ sctypes
+ sign
+ signbit
+ sin
+ sinh
+ spacing
+ sqrt
+ square
+ subtract
+ tan
+ tanh
+ tracemalloc_domain
+ true_divide
+ trunc
+ typeDict
+ typecodes
+
diff --git a/docs/api/aria.core.NOESYSpectrum.rst b/docs/api/aria.core.NOESYSpectrum.rst
index e8c60a000256bcb97b1b6f887a28a397eec11de4..319dd5dfae7f002471c335864fb33ee27f478892 100644
--- a/docs/api/aria.core.NOESYSpectrum.rst
+++ b/docs/api/aria.core.NOESYSpectrum.rst
@@ -7,7 +7,7 @@ aria.core.NOESYSpectrum module
.. currentmodule:: aria.core.NOESYSpectrum
.. automodule:: aria.core.NOESYSpectrum
- :members: ConstraintList, NOESYSpectrum, NOESYSpectrumXMLPickler
+ :members: ALWAYS, ARIA_ENV, ARRAY, BOOL, CCPN_EXTENSION, ConstraintList, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NOESYSpectrum, NOESYSpectrumXMLPickler, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -24,6 +24,38 @@ Classes:
NOESYSpectrum
NOESYSpectrumXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.NOESYSpectrumFilter.rst b/docs/api/aria.core.NOESYSpectrumFilter.rst
index dda45644fbe69cd3d869733869acec8d5585ea20..e6c210562835ca2790159d99d584a9a979c70f73 100644
--- a/docs/api/aria.core.NOESYSpectrumFilter.rst
+++ b/docs/api/aria.core.NOESYSpectrumFilter.rst
@@ -7,7 +7,7 @@ aria.core.NOESYSpectrumFilter module
.. currentmodule:: aria.core.NOESYSpectrumFilter
.. automodule:: aria.core.NOESYSpectrumFilter
- :members: NOESYSpectrumFilter, NOESYSpectrumFilterSettings, NOESYSpectrumFilterTextPickler
+ :members: ARRAY, BOOL, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, NO, NOESYSpectrumFilter, NOESYSpectrumFilterSettings, NOESYSpectrumFilterTextPickler, NONE, NOT_INIT, ORDEREDICT, STRING, TUPLE, TYPES, UNICODE, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -24,6 +24,29 @@ Classes:
NOESYSpectrumFilterSettings
NOESYSpectrumFilterTextPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ARRAY
+ BOOL
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ NO
+ NONE
+ NOT_INIT
+ ORDEREDICT
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ YES
+
diff --git a/docs/api/aria.core.Network.rst b/docs/api/aria.core.Network.rst
index cb629472b7005068d24bd568950c56bc5af576ba..0319002f934329042996b870d037c11c55353a1b 100644
--- a/docs/api/aria.core.Network.rst
+++ b/docs/api/aria.core.Network.rst
@@ -7,7 +7,7 @@ aria.core.Network module
.. currentmodule:: aria.core.Network
.. automodule:: aria.core.Network
- :members: CovalentConstraint, NetworkAnchoring, NetworkAnchoringTextPickler, NetworkPsPickler, NetworkScoreTextPickler, NetworkSettings, NetworkXMLPickler
+ :members: ALWAYS, ARIA_ENV, ARRAY, ASSIGNMENT_TYPE_DICT, BOOL, CCPN_EXTENSION, CovalentConstraint, DICT, FLOAT, FLOAT64, GZIP, HEADER_ABBREVIATIONS, HEADER_ALL, HEADER_ASSIGNMENT_TYPE, HEADER_DICT, HEADER_PROJECT, HEADER_RESTRAINT_ACTIVE, HEADER_RESTRAINT_DEFINITION, HEADER_SEQUENCE_SEPARATION, INT, LIST, MODULE_NAME, NA, NO, NONE, NetworkAnchoring, NetworkAnchoringTextPickler, NetworkPsPickler, NetworkScoreTextPickler, NetworkSettings, NetworkXMLPickler, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, TYPE_NONPOLYMER, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -28,6 +28,49 @@ Classes:
NetworkSettings
NetworkXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ ASSIGNMENT_TYPE_DICT
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ HEADER_ABBREVIATIONS
+ HEADER_ALL
+ HEADER_ASSIGNMENT_TYPE
+ HEADER_DICT
+ HEADER_PROJECT
+ HEADER_RESTRAINT_ACTIVE
+ HEADER_RESTRAINT_DEFINITION
+ HEADER_SEQUENCE_SEPARATION
+ INT
+ LIST
+ MODULE_NAME
+ NA
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ TYPE_NONPOLYMER
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.PDBReader.rst b/docs/api/aria.core.PDBReader.rst
index 3af4cf2dc213d4859b98bdb7abb29e985cd06485..da0e8627393b173318dbc877c6ba9039fb8a5761 100644
--- a/docs/api/aria.core.PDBReader.rst
+++ b/docs/api/aria.core.PDBReader.rst
@@ -7,7 +7,7 @@ aria.core.PDBReader module
.. currentmodule:: aria.core.PDBReader
.. automodule:: aria.core.PDBReader
- :members: PDBReader
+ :members: BASE_TYPES, CNS_CONVENTION, IUPAC_CONVENTION, PDBReader, TYPE_AMINO_ACID, TYPE_DNA, TYPE_DNA_BASE, TYPE_NONBASE, TYPE_NONPOLYMER, TYPE_PROTEIN, TYPE_RNA, TYPE_RNA_BASE
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -22,6 +22,23 @@ Classes:
PDBReader
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ BASE_TYPES
+ CNS_CONVENTION
+ IUPAC_CONVENTION
+ TYPE_AMINO_ACID
+ TYPE_DNA
+ TYPE_DNA_BASE
+ TYPE_NONBASE
+ TYPE_NONPOLYMER
+ TYPE_PROTEIN
+ TYPE_RNA
+ TYPE_RNA_BASE
+
diff --git a/docs/api/aria.core.PeakAssigner.rst b/docs/api/aria.core.PeakAssigner.rst
index a0fae07520db5ed25daf0955c47ab21966673bcc..a8ce19c48cc01e920d362124c33384d8eb86f277 100644
--- a/docs/api/aria.core.PeakAssigner.rst
+++ b/docs/api/aria.core.PeakAssigner.rst
@@ -7,7 +7,7 @@ aria.core.PeakAssigner module
.. currentmodule:: aria.core.PeakAssigner
.. automodule:: aria.core.PeakAssigner
- :members: PeakAssigner, PeakAssignerSettings, PeakAssignerTextPickler, PeakAssignerXMLPickler, peak_shape
+ :members: ALLOW_THREADS, ALWAYS, ARIA_ENV, ARRAY, ASSIGNMENT_METHODS, ASSIGNMENT_METHOD_EQUIVALENT, ASSIGNMENT_METHOD_FLOATING, ASSIGNMENT_METHOD_STEREO_SPECIFIC, AVERAGING_METHODS, AVERAGING_METHOD_FAST, AVERAGING_METHOD_NONE, AVERAGING_METHOD_SLOW, BOOL, BUFSIZE, CCPN_EXTENSION, CLIP, DICT, ERR_CALL, ERR_DEFAULT, ERR_IGNORE, ERR_LOG, ERR_PRINT, ERR_RAISE, ERR_WARN, FLOAT, FLOAT64, FLOATING_POINT_SUPPORT, FPE_DIVIDEBYZERO, FPE_INVALID, FPE_OVERFLOW, FPE_UNDERFLOW, False_, GZIP, INT, Inf, Infinity, LIST, MAXDIMS, MAY_SHARE_BOUNDS, MAY_SHARE_EXACT, MODULE_NAME, NAN, NINF, NO, NONE, NZERO, NaN, ORDEREDICT, PATH_MODULES, PINF, PRINT_LOCK, PROJECT_TEMPLATE, PZERO, PeakAssigner, PeakAssignerSettings, PeakAssignerTextPickler, PeakAssignerXMLPickler, RAISE, SHIFT_DIVIDEBYZERO, SHIFT_INVALID, SHIFT_OVERFLOW, SHIFT_UNDERFLOW, STRING, ScalarType, TUPLE, TYPES, True_, UFUNC_BUFSIZE_DEFAULT, UFUNC_PYVALS_NAME, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, WRAP, YES, absolute, add, arccos, arccosh, arcsin, arcsinh, arctan, arctan2, arctanh, bitwise_and, bitwise_not, bitwise_or, bitwise_xor, cbrt, ceil, conj, conjugate, copysign, cos, cosh, deg2rad, degrees, divide, divmod, e, equal, euler_gamma, exp, exp2, expm1, fabs, float_power, floor, floor_divide, fmax, fmin, fmod, frexp, gcd, greater, greater_equal, heaviside, hypot, inf, infty, invert, isfinite, isinf, isnan, isnat, lcm, ldexp, left_shift, less, less_equal, little_endian, log, log10, log1p, log2, logaddexp, logaddexp2, logical_and, logical_not, logical_or, logical_xor, matmul, maximum, minimum, mod, modf, multiply, nan, negative, newaxis, nextafter, not_equal, peak_shape, pi, positive, power, rad2deg, radians, reciprocal, remainder, right_shift, rint, sctypeDict, sctypes, sign, signbit, sin, sinh, spacing, sqrt, square, subtract, tan, tanh, tracemalloc_domain, true_divide, trunc, typeDict, typecodes
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -32,6 +32,186 @@ Functions:
peak_shape
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALLOW_THREADS
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ ASSIGNMENT_METHODS
+ ASSIGNMENT_METHOD_EQUIVALENT
+ ASSIGNMENT_METHOD_FLOATING
+ ASSIGNMENT_METHOD_STEREO_SPECIFIC
+ AVERAGING_METHODS
+ AVERAGING_METHOD_FAST
+ AVERAGING_METHOD_NONE
+ AVERAGING_METHOD_SLOW
+ BOOL
+ BUFSIZE
+ CCPN_EXTENSION
+ CLIP
+ DICT
+ ERR_CALL
+ ERR_DEFAULT
+ ERR_IGNORE
+ ERR_LOG
+ ERR_PRINT
+ ERR_RAISE
+ ERR_WARN
+ FLOAT
+ FLOAT64
+ FLOATING_POINT_SUPPORT
+ FPE_DIVIDEBYZERO
+ FPE_INVALID
+ FPE_OVERFLOW
+ FPE_UNDERFLOW
+ False_
+ GZIP
+ INT
+ Inf
+ Infinity
+ LIST
+ MAXDIMS
+ MAY_SHARE_BOUNDS
+ MAY_SHARE_EXACT
+ MODULE_NAME
+ NAN
+ NINF
+ NO
+ NONE
+ NZERO
+ NaN
+ ORDEREDICT
+ PATH_MODULES
+ PINF
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ PZERO
+ RAISE
+ SHIFT_DIVIDEBYZERO
+ SHIFT_INVALID
+ SHIFT_OVERFLOW
+ SHIFT_UNDERFLOW
+ STRING
+ ScalarType
+ TUPLE
+ TYPES
+ True_
+ UFUNC_BUFSIZE_DEFAULT
+ UFUNC_PYVALS_NAME
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ WRAP
+ YES
+ absolute
+ add
+ arccos
+ arccosh
+ arcsin
+ arcsinh
+ arctan
+ arctan2
+ arctanh
+ bitwise_and
+ bitwise_not
+ bitwise_or
+ bitwise_xor
+ cbrt
+ ceil
+ conj
+ conjugate
+ copysign
+ cos
+ cosh
+ deg2rad
+ degrees
+ divide
+ divmod
+ e
+ equal
+ euler_gamma
+ exp
+ exp2
+ expm1
+ fabs
+ float_power
+ floor
+ floor_divide
+ fmax
+ fmin
+ fmod
+ frexp
+ gcd
+ greater
+ greater_equal
+ heaviside
+ hypot
+ inf
+ infty
+ invert
+ isfinite
+ isinf
+ isnan
+ isnat
+ lcm
+ ldexp
+ left_shift
+ less
+ less_equal
+ little_endian
+ log
+ log10
+ log1p
+ log2
+ logaddexp
+ logaddexp2
+ logical_and
+ logical_not
+ logical_or
+ logical_xor
+ matmul
+ maximum
+ minimum
+ mod
+ modf
+ multiply
+ nan
+ negative
+ newaxis
+ nextafter
+ not_equal
+ pi
+ positive
+ power
+ rad2deg
+ radians
+ reciprocal
+ remainder
+ right_shift
+ rint
+ sctypeDict
+ sctypes
+ sign
+ signbit
+ sin
+ sinh
+ spacing
+ sqrt
+ square
+ subtract
+ tan
+ tanh
+ tracemalloc_domain
+ true_divide
+ trunc
+ typeDict
+ typecodes
+
diff --git a/docs/api/aria.core.Project.rst b/docs/api/aria.core.Project.rst
index e6daf3757fa7908667ca2188525c06afee956c60..1cc4466d43f946452b5a4d3f94a1153ad10215a3 100644
--- a/docs/api/aria.core.Project.rst
+++ b/docs/api/aria.core.Project.rst
@@ -7,7 +7,7 @@ aria.core.Project module
.. currentmodule:: aria.core.Project
.. automodule:: aria.core.Project
- :members: Project, ProjectSettings, ProjectSingleton, ProjectThread, ProjectXMLPickler, checksum
+ :members: ALWAYS, ARIA_ENV, ARRAY, BOOL, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, Project, ProjectSettings, ProjectSingleton, ProjectThread, ProjectXMLPickler, QUALITY_CHECKS_HEADER, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES, checksum
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -33,6 +33,39 @@ Functions:
checksum
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ QUALITY_CHECKS_HEADER
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.Protocol.rst b/docs/api/aria.core.Protocol.rst
index e944a9043f6a3a76eb0c7fb9e0a42a7fccd1e7a3..536a8ed8cd68696ccd3b2ad9afc6c5f9a33fbe59 100644
--- a/docs/api/aria.core.Protocol.rst
+++ b/docs/api/aria.core.Protocol.rst
@@ -7,7 +7,7 @@ aria.core.Protocol module
.. currentmodule:: aria.core.Protocol
.. automodule:: aria.core.Protocol
- :members: IterationSettings, IterationSettingsXMLPickler, Protocol, ProtocolSettings, ProtocolXMLPickler, dump_peaks_as_text, files_exist
+ :members: ALLOW_THREADS, ALWAYS, ARIA_ENV, ARRAY, BOOL, BUFSIZE, CCPN_EXTENSION, CLIP, DICT, ERR_CALL, ERR_DEFAULT, ERR_IGNORE, ERR_LOG, ERR_PRINT, ERR_RAISE, ERR_WARN, FLOAT, FLOAT64, FLOATING_POINT_SUPPORT, FPE_DIVIDEBYZERO, FPE_INVALID, FPE_OVERFLOW, FPE_UNDERFLOW, False_, GZIP, INT, Inf, Infinity, IterationSettings, IterationSettingsXMLPickler, KEYBOARD_INTERRUPT, LIST, MAXDIMS, MAY_SHARE_BOUNDS, MAY_SHARE_EXACT, MISSING_STRUCTURES, MODULE_NAME, NAN, NINF, NO, NONE, NZERO, NaN, ORDEREDICT, PATH_MODULES, PATH_MOLMOL, PINF, PRINT_LOCK, PROJECT_TEMPLATE, PZERO, Protocol, ProtocolSettings, ProtocolXMLPickler, RAISE, REPORT_NOE_RESTRAINTS, REPORT_SUMMARY, REPORT_UPDATED_SPECTRUM, SHIFT_DIVIDEBYZERO, SHIFT_INVALID, SHIFT_OVERFLOW, SHIFT_UNDERFLOW, STRING, ScalarType, TUPLE, TYPES, True_, UFUNC_BUFSIZE_DEFAULT, UFUNC_PYVALS_NAME, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, WRAP, YES, absolute, add, arccos, arccosh, arcsin, arcsinh, arctan, arctan2, arctanh, bitwise_and, bitwise_not, bitwise_or, bitwise_xor, cbrt, ceil, conj, conjugate, copysign, cos, cosh, deg2rad, degrees, divide, divmod, dump_peaks_as_text, e, equal, euler_gamma, exp, exp2, expm1, fabs, files_exist, float_power, floor, floor_divide, fmax, fmin, fmod, frexp, gcd, greater, greater_equal, heaviside, hypot, inf, infty, invert, isfinite, isinf, isnan, isnat, lcm, ldexp, left_shift, less, less_equal, little_endian, log, log10, log1p, log2, logaddexp, logaddexp2, logical_and, logical_not, logical_or, logical_xor, matmul, maximum, minimum, mod, modf, multiply, nan, negative, newaxis, nextafter, not_equal, pi, positive, power, rad2deg, radians, reciprocal, remainder, right_shift, rint, sctypeDict, sctypes, sign, signbit, sin, sinh, spacing, sqrt, square, subtract, tan, tanh, tracemalloc_domain, true_divide, trunc, typeDict, typecodes
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -34,6 +34,184 @@ Functions:
dump_peaks_as_text
files_exist
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALLOW_THREADS
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ BUFSIZE
+ CCPN_EXTENSION
+ CLIP
+ DICT
+ ERR_CALL
+ ERR_DEFAULT
+ ERR_IGNORE
+ ERR_LOG
+ ERR_PRINT
+ ERR_RAISE
+ ERR_WARN
+ FLOAT
+ FLOAT64
+ FLOATING_POINT_SUPPORT
+ FPE_DIVIDEBYZERO
+ FPE_INVALID
+ FPE_OVERFLOW
+ FPE_UNDERFLOW
+ False_
+ GZIP
+ INT
+ Inf
+ Infinity
+ KEYBOARD_INTERRUPT
+ LIST
+ MAXDIMS
+ MAY_SHARE_BOUNDS
+ MAY_SHARE_EXACT
+ MISSING_STRUCTURES
+ MODULE_NAME
+ NAN
+ NINF
+ NO
+ NONE
+ NZERO
+ NaN
+ ORDEREDICT
+ PATH_MODULES
+ PATH_MOLMOL
+ PINF
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ PZERO
+ RAISE
+ REPORT_NOE_RESTRAINTS
+ REPORT_SUMMARY
+ REPORT_UPDATED_SPECTRUM
+ SHIFT_DIVIDEBYZERO
+ SHIFT_INVALID
+ SHIFT_OVERFLOW
+ SHIFT_UNDERFLOW
+ STRING
+ ScalarType
+ TUPLE
+ TYPES
+ True_
+ UFUNC_BUFSIZE_DEFAULT
+ UFUNC_PYVALS_NAME
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ WRAP
+ YES
+ absolute
+ add
+ arccos
+ arccosh
+ arcsin
+ arcsinh
+ arctan
+ arctan2
+ arctanh
+ bitwise_and
+ bitwise_not
+ bitwise_or
+ bitwise_xor
+ cbrt
+ ceil
+ conj
+ conjugate
+ copysign
+ cos
+ cosh
+ deg2rad
+ degrees
+ divide
+ divmod
+ e
+ equal
+ euler_gamma
+ exp
+ exp2
+ expm1
+ fabs
+ float_power
+ floor
+ floor_divide
+ fmax
+ fmin
+ fmod
+ frexp
+ gcd
+ greater
+ greater_equal
+ heaviside
+ hypot
+ inf
+ infty
+ invert
+ isfinite
+ isinf
+ isnan
+ isnat
+ lcm
+ ldexp
+ left_shift
+ less
+ less_equal
+ little_endian
+ log
+ log10
+ log1p
+ log2
+ logaddexp
+ logaddexp2
+ logical_and
+ logical_not
+ logical_or
+ logical_xor
+ matmul
+ maximum
+ minimum
+ mod
+ modf
+ multiply
+ nan
+ negative
+ newaxis
+ nextafter
+ not_equal
+ pi
+ positive
+ power
+ rad2deg
+ radians
+ reciprocal
+ remainder
+ right_shift
+ rint
+ sctypeDict
+ sctypes
+ sign
+ signbit
+ sin
+ sinh
+ spacing
+ sqrt
+ square
+ subtract
+ tan
+ tanh
+ tracemalloc_domain
+ true_divide
+ trunc
+ typeDict
+ typecodes
+
diff --git a/docs/api/aria.core.Relaxation.rst b/docs/api/aria.core.Relaxation.rst
index f9b4b135bd83d23fe36dfd266f02ff4bf591b2cf..86935050b7a611348c84f8c3bc1379950d1eb94b 100644
--- a/docs/api/aria.core.Relaxation.rst
+++ b/docs/api/aria.core.Relaxation.rst
@@ -7,7 +7,7 @@ aria.core.Relaxation module
.. currentmodule:: aria.core.Relaxation
.. automodule:: aria.core.Relaxation
- :members: Relaxation
+ :members: ALLOW_THREADS, ALWAYS, ARIA_ENV, ARRAY, BOOL, BUFSIZE, CCPN_EXTENSION, CLIP, DICT, ERR_CALL, ERR_DEFAULT, ERR_IGNORE, ERR_LOG, ERR_PRINT, ERR_RAISE, ERR_WARN, FLOAT, FLOAT64, FLOATING_POINT_SUPPORT, FPE_DIVIDEBYZERO, FPE_INVALID, FPE_OVERFLOW, FPE_UNDERFLOW, False_, GZIP, INT, Inf, Infinity, LIST, MAXDIMS, MAY_SHARE_BOUNDS, MAY_SHARE_EXACT, MODULE_NAME, NAN, NINF, NO, NONE, NZERO, NaN, ORDEREDICT, PATH_MODULES, PINF, PRINT_LOCK, PROJECT_TEMPLATE, PZERO, RAISE, Relaxation, SHIFT_DIVIDEBYZERO, SHIFT_INVALID, SHIFT_OVERFLOW, SHIFT_UNDERFLOW, STRING, ScalarType, TUPLE, TYPES, True_, UFUNC_BUFSIZE_DEFAULT, UFUNC_PYVALS_NAME, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, WRAP, YES, absolute, add, arccos, arccosh, arcsin, arcsinh, arctan, arctan2, arctanh, bitwise_and, bitwise_not, bitwise_or, bitwise_xor, cbrt, ceil, conj, conjugate, copysign, cos, cosh, deg2rad, degrees, divide, divmod, e, equal, euler_gamma, exp, exp2, expm1, fabs, float_power, floor, floor_divide, fmax, fmin, fmod, frexp, gcd, greater, greater_equal, heaviside, hypot, inf, infty, invert, isfinite, isinf, isnan, isnat, lcm, ldexp, left_shift, less, less_equal, little_endian, log, log10, log1p, log2, logaddexp, logaddexp2, logical_and, logical_not, logical_or, logical_xor, matmul, maximum, minimum, mod, modf, multiply, nan, negative, newaxis, nextafter, not_equal, pi, positive, power, rad2deg, radians, reciprocal, remainder, right_shift, rint, sctypeDict, sctypes, sign, signbit, sin, sinh, spacing, sqrt, square, subtract, tan, tanh, tracemalloc_domain, true_divide, trunc, typeDict, typecodes
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -22,6 +22,178 @@ Classes:
Relaxation
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALLOW_THREADS
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ BUFSIZE
+ CCPN_EXTENSION
+ CLIP
+ DICT
+ ERR_CALL
+ ERR_DEFAULT
+ ERR_IGNORE
+ ERR_LOG
+ ERR_PRINT
+ ERR_RAISE
+ ERR_WARN
+ FLOAT
+ FLOAT64
+ FLOATING_POINT_SUPPORT
+ FPE_DIVIDEBYZERO
+ FPE_INVALID
+ FPE_OVERFLOW
+ FPE_UNDERFLOW
+ False_
+ GZIP
+ INT
+ Inf
+ Infinity
+ LIST
+ MAXDIMS
+ MAY_SHARE_BOUNDS
+ MAY_SHARE_EXACT
+ MODULE_NAME
+ NAN
+ NINF
+ NO
+ NONE
+ NZERO
+ NaN
+ ORDEREDICT
+ PATH_MODULES
+ PINF
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ PZERO
+ RAISE
+ SHIFT_DIVIDEBYZERO
+ SHIFT_INVALID
+ SHIFT_OVERFLOW
+ SHIFT_UNDERFLOW
+ STRING
+ ScalarType
+ TUPLE
+ TYPES
+ True_
+ UFUNC_BUFSIZE_DEFAULT
+ UFUNC_PYVALS_NAME
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ WRAP
+ YES
+ absolute
+ add
+ arccos
+ arccosh
+ arcsin
+ arcsinh
+ arctan
+ arctan2
+ arctanh
+ bitwise_and
+ bitwise_not
+ bitwise_or
+ bitwise_xor
+ cbrt
+ ceil
+ conj
+ conjugate
+ copysign
+ cos
+ cosh
+ deg2rad
+ degrees
+ divide
+ divmod
+ e
+ equal
+ euler_gamma
+ exp
+ exp2
+ expm1
+ fabs
+ float_power
+ floor
+ floor_divide
+ fmax
+ fmin
+ fmod
+ frexp
+ gcd
+ greater
+ greater_equal
+ heaviside
+ hypot
+ inf
+ infty
+ invert
+ isfinite
+ isinf
+ isnan
+ isnat
+ lcm
+ ldexp
+ left_shift
+ less
+ less_equal
+ little_endian
+ log
+ log10
+ log1p
+ log2
+ logaddexp
+ logaddexp2
+ logical_and
+ logical_not
+ logical_or
+ logical_xor
+ matmul
+ maximum
+ minimum
+ mod
+ modf
+ multiply
+ nan
+ negative
+ newaxis
+ nextafter
+ not_equal
+ pi
+ positive
+ power
+ rad2deg
+ radians
+ reciprocal
+ remainder
+ right_shift
+ rint
+ sctypeDict
+ sctypes
+ sign
+ signbit
+ sin
+ sinh
+ spacing
+ sqrt
+ square
+ subtract
+ tan
+ tanh
+ tracemalloc_domain
+ true_divide
+ trunc
+ typeDict
+ typecodes
+
diff --git a/docs/api/aria.core.Report.rst b/docs/api/aria.core.Report.rst
index 38c2655ea68a0a628411f29a6504b51e671f0743..63b10ae04c6be7be0015de5a87aef743135004b0 100644
--- a/docs/api/aria.core.Report.rst
+++ b/docs/api/aria.core.Report.rst
@@ -7,7 +7,7 @@ aria.core.Report module
.. currentmodule:: aria.core.Report
.. automodule:: aria.core.Report
- :members: CCPNSettings, CCPNSettingsXMLPickler, MolMolSettings, MolMolSettingsXMLPickler, NOEListSettings, NOEListSettingsXMLPickler, ReportBaseSettings, ReportBaseXMLPickler, ReportSettings, ReportXMLPickler, UpSpecSettings, UpSpecSettingsXMLPickler
+ :members: ALWAYS, ARIA_ENV, ARRAY, BOOL, CCPNSettings, CCPNSettingsXMLPickler, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, MolMolSettings, MolMolSettingsXMLPickler, NO, NOEListSettings, NOEListSettingsXMLPickler, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, ReportBaseSettings, ReportBaseXMLPickler, ReportSettings, ReportXMLPickler, STRING, TUPLE, TYPES, UNICODE, UpSpecSettings, UpSpecSettingsXMLPickler, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -33,6 +33,38 @@ Classes:
UpSpecSettings
UpSpecSettingsXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.Residue.rst b/docs/api/aria.core.Residue.rst
index dc991a8c07c69c30a39c6dc261f0fa3b0c462305..36529baacec8954367a32350b64c16a46fc02fd6 100644
--- a/docs/api/aria.core.Residue.rst
+++ b/docs/api/aria.core.Residue.rst
@@ -7,7 +7,7 @@ aria.core.Residue module
.. currentmodule:: aria.core.Residue
.. automodule:: aria.core.Residue
- :members: Residue, ResidueXMLPickler
+ :members: ARRAY, BOOL, DICT, FLOAT, FLOAT64, INT, LIST, NONE, ORDEREDICT, Residue, ResidueXMLPickler, STRING, TUPLE, TYPES, UNICODE
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -23,6 +23,25 @@ Classes:
Residue
ResidueXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ARRAY
+ BOOL
+ DICT
+ FLOAT
+ FLOAT64
+ INT
+ LIST
+ NONE
+ ORDEREDICT
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+
diff --git a/docs/api/aria.core.RmsReport.rst b/docs/api/aria.core.RmsReport.rst
index 51678e4f46d466459d683ad925dfa6a2a8c203e6..664ed145cb813fc85bd0a5c8eebee2d753be47a2 100644
--- a/docs/api/aria.core.RmsReport.rst
+++ b/docs/api/aria.core.RmsReport.rst
@@ -7,7 +7,7 @@ aria.core.RmsReport module
.. currentmodule:: aria.core.RmsReport
.. automodule:: aria.core.RmsReport
- :members: RmsReport
+ :members: RMS_PDF_REPORT, RMS_PS_MAP, RMS_PS_MAP_LEGEND, RMS_PS_PROFILE, RMS_PS_REPORT, RMS_TEXT_REPORT, RmsReport
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -22,6 +22,18 @@ Classes:
RmsReport
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ RMS_PDF_REPORT
+ RMS_PS_MAP
+ RMS_PS_MAP_LEGEND
+ RMS_PS_PROFILE
+ RMS_PS_REPORT
+ RMS_TEXT_REPORT
+
diff --git a/docs/api/aria.core.Settings.rst b/docs/api/aria.core.Settings.rst
index e6f176a583559f062190d70f9b356b2d3a68f15f..def7d639a98ff24d46b2d387d5ce89c5a28d9e9d 100644
--- a/docs/api/aria.core.Settings.rst
+++ b/docs/api/aria.core.Settings.rst
@@ -7,7 +7,7 @@ aria.core.Settings module
.. currentmodule:: aria.core.Settings
.. automodule:: aria.core.Settings
- :members: AbsolutePath, AutoFixChoice, AutoInteger, ChoiceEntity, Entity, EntityCastError, EntityError, EntityValueError, Float, FourLetterString, GZipChoice, Integer, MultiTypeEntity, NonEmptyString, NonNegativeFloat, NonNegativeInt, Path, PeakType, PositiveFloat, PositiveInteger, Settings, String, TrueFalseChoice, TypeEntity, Weight, YesNoChoice
+ :members: ARRAY, AbsolutePath, AutoFixChoice, AutoInteger, BOOL, ChoiceEntity, DICT, Entity, EntityCastError, EntityError, EntityValueError, FLOAT, FLOAT64, Float, FourLetterString, GZIP, GZipChoice, INT, Integer, LIST, MultiTypeEntity, NO, NONE, NOT_INIT, NonEmptyString, NonNegativeFloat, NonNegativeInt, ORDEREDICT, Path, PeakType, PositiveFloat, PositiveInteger, STRING, Settings, String, TUPLE, TYPES, TrueFalseChoice, TypeEntity, UNICODE, Weight, YES, YesNoChoice
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -53,6 +53,29 @@ Classes:
Weight
YesNoChoice
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ARRAY
+ BOOL
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ NO
+ NONE
+ NOT_INIT
+ ORDEREDICT
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ YES
+
diff --git a/docs/api/aria.core.ShiftAssignment.rst b/docs/api/aria.core.ShiftAssignment.rst
index 11c31b353b39c8bc2793bc923f63e5d34e42778a..7e098ca732a2a251f38937dc6a2e72de011bf027 100644
--- a/docs/api/aria.core.ShiftAssignment.rst
+++ b/docs/api/aria.core.ShiftAssignment.rst
@@ -7,7 +7,7 @@ aria.core.ShiftAssignment module
.. currentmodule:: aria.core.ShiftAssignment
.. automodule:: aria.core.ShiftAssignment
- :members: ShiftAssignment, ShiftAssignmentXMLPickler, SpinSystem, SpinSystem2XMLPickler, SpinSystemXMLPickler
+ :members: ALWAYS, ARIA_ENV, ARRAY, ASSIGNMENT_METHODS, ASSIGNMENT_METHOD_EQUIVALENT, ASSIGNMENT_METHOD_FLOATING, ASSIGNMENT_METHOD_STEREO_SPECIFIC, AVERAGING_METHODS, AVERAGING_METHOD_FAST, AVERAGING_METHOD_NONE, AVERAGING_METHOD_SLOW, BOOL, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, ShiftAssignment, ShiftAssignmentXMLPickler, SpinSystem, SpinSystem2XMLPickler, SpinSystemXMLPickler, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -26,6 +26,46 @@ Classes:
SpinSystem2XMLPickler
SpinSystemXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ ASSIGNMENT_METHODS
+ ASSIGNMENT_METHOD_EQUIVALENT
+ ASSIGNMENT_METHOD_FLOATING
+ ASSIGNMENT_METHOD_STEREO_SPECIFIC
+ AVERAGING_METHODS
+ AVERAGING_METHOD_FAST
+ AVERAGING_METHOD_NONE
+ AVERAGING_METHOD_SLOW
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.ShiftAssignmentFilter.rst b/docs/api/aria.core.ShiftAssignmentFilter.rst
index f1aaebf13d95e4a3f77081defce71928148e707f..a68bd79b43b40655b85a979a9d525f1c5157d901 100644
--- a/docs/api/aria.core.ShiftAssignmentFilter.rst
+++ b/docs/api/aria.core.ShiftAssignmentFilter.rst
@@ -7,7 +7,7 @@ aria.core.ShiftAssignmentFilter module
.. currentmodule:: aria.core.ShiftAssignmentFilter
.. automodule:: aria.core.ShiftAssignmentFilter
- :members: ChemicalShiftListFilter, ChemicalShiftListFilterSettings, ShiftAssignmentFilter, ShiftAssignmentFilterSettings, SpinSystemFilter, SpinSystemFilterSettings
+ :members: ChemicalShiftListFilter, ChemicalShiftListFilterSettings, EMPTY_SPIN_SYSTEM, INVALID_SHIFT_VALUES, ShiftAssignmentFilter, ShiftAssignmentFilterSettings, SpinSystemFilter, SpinSystemFilterSettings, TOO_MANY_SHIFTS
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -27,6 +27,15 @@ Classes:
SpinSystemFilter
SpinSystemFilterSettings
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ EMPTY_SPIN_SYSTEM
+ INVALID_SHIFT_VALUES
+ TOO_MANY_SHIFTS
+
diff --git a/docs/api/aria.core.SpinPair.rst b/docs/api/aria.core.SpinPair.rst
index 9c31a8085526e4320dbee482d05a6ce00f4a7e1c..c247814cf01b974f0cac04cbeacfa3953321a5ed 100644
--- a/docs/api/aria.core.SpinPair.rst
+++ b/docs/api/aria.core.SpinPair.rst
@@ -7,7 +7,7 @@ aria.core.SpinPair module
.. currentmodule:: aria.core.SpinPair
.. automodule:: aria.core.SpinPair
- :members: SpinPair, SpinPairXMLPickler
+ :members: ALWAYS, ARIA_ENV, ARRAY, BOOL, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, SpinPair, SpinPairXMLPickler, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -23,6 +23,38 @@ Classes:
SpinPair
SpinPairXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.StructureEnsemble.rst b/docs/api/aria.core.StructureEnsemble.rst
index 1b5392a2b5dbb411aae9de96360d4212cbfcbb57..7adbc347d0c0e842694ab912b6f75353bbbefd17 100644
--- a/docs/api/aria.core.StructureEnsemble.rst
+++ b/docs/api/aria.core.StructureEnsemble.rst
@@ -7,7 +7,7 @@ aria.core.StructureEnsemble module
.. currentmodule:: aria.core.StructureEnsemble
.. automodule:: aria.core.StructureEnsemble
- :members: NumberOfBestStructures, StructureEnsemble, StructureEnsembleSettings
+ :members: ARRAY, BOOL, CNS_CONVENTION, DICT, FLOAT, FLOAT64, INT, IUPAC_CONVENTION, LIST, NONE, NumberOfBestStructures, ORDEREDICT, STRING, StructureEnsemble, StructureEnsembleSettings, TUPLE, TYPES, UNICODE
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -24,6 +24,27 @@ Classes:
StructureEnsemble
StructureEnsembleSettings
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ARRAY
+ BOOL
+ CNS_CONVENTION
+ DICT
+ FLOAT
+ FLOAT64
+ INT
+ IUPAC_CONVENTION
+ LIST
+ NONE
+ ORDEREDICT
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+
diff --git a/docs/api/aria.core.SuperImposer.rst b/docs/api/aria.core.SuperImposer.rst
index 24b429ee47779cef16009b4fe2bdf1e6a9d07d14..515a0330f1702bda8ae2dea6c60a8b8468c13d6a 100644
--- a/docs/api/aria.core.SuperImposer.rst
+++ b/docs/api/aria.core.SuperImposer.rst
@@ -7,7 +7,7 @@ aria.core.SuperImposer module
.. currentmodule:: aria.core.SuperImposer
.. automodule:: aria.core.SuperImposer
- :members: SuperImposer
+ :members: ALLOW_THREADS, ARRAY, BOOL, BUFSIZE, CLIP, DICT, ERR_CALL, ERR_DEFAULT, ERR_IGNORE, ERR_LOG, ERR_PRINT, ERR_RAISE, ERR_WARN, FLOAT, FLOAT64, FLOATING_POINT_SUPPORT, FPE_DIVIDEBYZERO, FPE_INVALID, FPE_OVERFLOW, FPE_UNDERFLOW, False_, INT, Inf, Infinity, LIST, MAXDIMS, MAY_SHARE_BOUNDS, MAY_SHARE_EXACT, NAN, NINF, NONE, NZERO, NaN, ORDEREDICT, PINF, PZERO, RAISE, SHIFT_DIVIDEBYZERO, SHIFT_INVALID, SHIFT_OVERFLOW, SHIFT_UNDERFLOW, STRING, ScalarType, SuperImposer, TUPLE, TYPES, True_, UFUNC_BUFSIZE_DEFAULT, UFUNC_PYVALS_NAME, UNICODE, WRAP, absolute, add, arccos, arccosh, arcsin, arcsinh, arctan, arctan2, arctanh, bitwise_and, bitwise_not, bitwise_or, bitwise_xor, cbrt, ceil, conj, conjugate, copysign, cos, cosh, deg2rad, degrees, divide, divmod, e, equal, euler_gamma, exp, exp2, expm1, fabs, float_power, floor, floor_divide, fmax, fmin, fmod, frexp, gcd, greater, greater_equal, heaviside, hypot, inf, infty, invert, isfinite, isinf, isnan, isnat, lcm, ldexp, left_shift, less, less_equal, little_endian, log, log10, log1p, log2, logaddexp, logaddexp2, logical_and, logical_not, logical_or, logical_xor, matmul, maximum, minimum, mod, modf, multiply, nan, negative, newaxis, nextafter, not_equal, pi, positive, power, rad2deg, radians, reciprocal, remainder, right_shift, rint, sctypeDict, sctypes, sign, signbit, sin, sinh, spacing, sqrt, square, subtract, tan, tanh, tracemalloc_domain, true_divide, trunc, typeDict, typecodes
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -22,6 +22,165 @@ Classes:
SuperImposer
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALLOW_THREADS
+ ARRAY
+ BOOL
+ BUFSIZE
+ CLIP
+ DICT
+ ERR_CALL
+ ERR_DEFAULT
+ ERR_IGNORE
+ ERR_LOG
+ ERR_PRINT
+ ERR_RAISE
+ ERR_WARN
+ FLOAT
+ FLOAT64
+ FLOATING_POINT_SUPPORT
+ FPE_DIVIDEBYZERO
+ FPE_INVALID
+ FPE_OVERFLOW
+ FPE_UNDERFLOW
+ False_
+ INT
+ Inf
+ Infinity
+ LIST
+ MAXDIMS
+ MAY_SHARE_BOUNDS
+ MAY_SHARE_EXACT
+ NAN
+ NINF
+ NONE
+ NZERO
+ NaN
+ ORDEREDICT
+ PINF
+ PZERO
+ RAISE
+ SHIFT_DIVIDEBYZERO
+ SHIFT_INVALID
+ SHIFT_OVERFLOW
+ SHIFT_UNDERFLOW
+ STRING
+ ScalarType
+ TUPLE
+ TYPES
+ True_
+ UFUNC_BUFSIZE_DEFAULT
+ UFUNC_PYVALS_NAME
+ UNICODE
+ WRAP
+ absolute
+ add
+ arccos
+ arccosh
+ arcsin
+ arcsinh
+ arctan
+ arctan2
+ arctanh
+ bitwise_and
+ bitwise_not
+ bitwise_or
+ bitwise_xor
+ cbrt
+ ceil
+ conj
+ conjugate
+ copysign
+ cos
+ cosh
+ deg2rad
+ degrees
+ divide
+ divmod
+ e
+ equal
+ euler_gamma
+ exp
+ exp2
+ expm1
+ fabs
+ float_power
+ floor
+ floor_divide
+ fmax
+ fmin
+ fmod
+ frexp
+ gcd
+ greater
+ greater_equal
+ heaviside
+ hypot
+ inf
+ infty
+ invert
+ isfinite
+ isinf
+ isnan
+ isnat
+ lcm
+ ldexp
+ left_shift
+ less
+ less_equal
+ little_endian
+ log
+ log10
+ log1p
+ log2
+ logaddexp
+ logaddexp2
+ logical_and
+ logical_not
+ logical_or
+ logical_xor
+ matmul
+ maximum
+ minimum
+ mod
+ modf
+ multiply
+ nan
+ negative
+ newaxis
+ nextafter
+ not_equal
+ pi
+ positive
+ power
+ rad2deg
+ radians
+ reciprocal
+ remainder
+ right_shift
+ rint
+ sctypeDict
+ sctypes
+ sign
+ signbit
+ sin
+ sinh
+ spacing
+ sqrt
+ square
+ subtract
+ tan
+ tanh
+ tracemalloc_domain
+ true_divide
+ trunc
+ typeDict
+ typecodes
+
diff --git a/docs/api/aria.core.Topology.rst b/docs/api/aria.core.Topology.rst
index dd17b4f07ce5fe47e1cdfd3a48e8014e54d823df..f4b30abd8fa565aad3bd03b44135939c20dc572d 100644
--- a/docs/api/aria.core.Topology.rst
+++ b/docs/api/aria.core.Topology.rst
@@ -7,7 +7,7 @@ aria.core.Topology module
.. currentmodule:: aria.core.Topology
.. automodule:: aria.core.Topology
- :members: AtomGroup, AtomGroupSettings, AtomGroupXMLPickler, BaseAtom, BaseAtomSettings, BaseAtomXMLPickler, BaseResidue, BaseResidueSettings, BaseResidueXMLPickler, EquivalentGroup, EquivalentGroupSettings, EquivalentGroupXMLPickler, Terminus, TerminusSettings, TerminusXMLPickler, Topology, TopologyXMLPickler, load_topology
+ :members: ALWAYS, ARIA_ENV, ARRAY, ATOM_NOMENCLATURES, ATOM_TYPE_UNKNOWN, AtomGroup, AtomGroupSettings, AtomGroupXMLPickler, BOOL, BaseAtom, BaseAtomSettings, BaseAtomXMLPickler, BaseResidue, BaseResidueSettings, BaseResidueXMLPickler, CCPN_EXTENSION, DICT, EQUIV_AROMATIC, EQUIV_ISOPROPYL, EQUIV_METHYL, EQUIV_METHYLENE, EQUIV_NTERMINUS, EquivalentGroup, EquivalentGroupSettings, EquivalentGroupXMLPickler, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NOMENCLATURE_IUPAC, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TERMINUS_C3_PRIME_HYDROXYL, TERMINUS_C5_PRIME_HYDROXYL, TERMINUS_C5_PRIME_PHOSPHATE, TERMINUS_C_AMIDO, TERMINUS_C_CARBOXYL, TERMINUS_C_STANDARD, TERMINUS_N_AMINYL, TERMINUS_N_STANDARD, TOPOLOGY_IUPAC, TUPLE, TYPES, TYPE_AMINO_ACID, TYPE_DNA_BASE, TYPE_NONBASE, TYPE_RNA_BASE, Terminus, TerminusSettings, TerminusXMLPickler, Topology, TopologyXMLPickler, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES, load_topology
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -45,6 +45,59 @@ Functions:
load_topology
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ ATOM_NOMENCLATURES
+ ATOM_TYPE_UNKNOWN
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ EQUIV_AROMATIC
+ EQUIV_ISOPROPYL
+ EQUIV_METHYL
+ EQUIV_METHYLENE
+ EQUIV_NTERMINUS
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NOMENCLATURE_IUPAC
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TERMINUS_C3_PRIME_HYDROXYL
+ TERMINUS_C5_PRIME_HYDROXYL
+ TERMINUS_C5_PRIME_PHOSPHATE
+ TERMINUS_C_AMIDO
+ TERMINUS_C_CARBOXYL
+ TERMINUS_C_STANDARD
+ TERMINUS_N_AMINYL
+ TERMINUS_N_STANDARD
+ TOPOLOGY_IUPAC
+ TUPLE
+ TYPES
+ TYPE_AMINO_ACID
+ TYPE_DNA_BASE
+ TYPE_NONBASE
+ TYPE_RNA_BASE
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+
diff --git a/docs/api/aria.core.TypeChecking.rst b/docs/api/aria.core.TypeChecking.rst
index 1841aed61f2cbb07e8438063bf1a93faf4380cfe..c976f73e4279b406e82db86964bef307918399cb 100644
--- a/docs/api/aria.core.TypeChecking.rst
+++ b/docs/api/aria.core.TypeChecking.rst
@@ -7,7 +7,7 @@ aria.core.TypeChecking module
.. currentmodule:: aria.core.TypeChecking
.. automodule:: aria.core.TypeChecking
- :members: check_array, check_bool, check_dict, check_elements, check_file, check_float, check_int, check_list, check_string, check_tuple, check_type, is_type
+ :members: ARRAY, BOOL, DICT, FLOAT, FLOAT64, INT, LIST, NONE, ORDEREDICT, STRING, TUPLE, TYPES, UNICODE, check_array, check_bool, check_dict, check_elements, check_file, check_float, check_int, check_list, check_string, check_tuple, check_type, is_type
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -35,6 +35,19 @@ Data:
.. autosummary::
:nosignatures:
+ ARRAY
+ BOOL
+ DICT
+ FLOAT
+ FLOAT64
+ INT
+ LIST
+ NONE
+ ORDEREDICT
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
check_elements
check_type
is_type
diff --git a/docs/api/aria.core.ViolationAnalyser.rst b/docs/api/aria.core.ViolationAnalyser.rst
index e7ed2a9c84f4c12aa0775c36c9907b2787a481b4..653c4fe031710b93a2885033625bf180c95bac66 100644
--- a/docs/api/aria.core.ViolationAnalyser.rst
+++ b/docs/api/aria.core.ViolationAnalyser.rst
@@ -7,7 +7,7 @@ aria.core.ViolationAnalyser module
.. currentmodule:: aria.core.ViolationAnalyser
.. automodule:: aria.core.ViolationAnalyser
- :members: ViolationAnalyser, ViolationAnalyserSettings, ViolationAnalyserXMLPickler
+ :members: ALLOW_THREADS, ALWAYS, ARIA_ENV, ARRAY, BOOL, BUFSIZE, CCPN_EXTENSION, CLIP, DICT, ERR_CALL, ERR_DEFAULT, ERR_IGNORE, ERR_LOG, ERR_PRINT, ERR_RAISE, ERR_WARN, FLOAT, FLOAT64, FLOATING_POINT_SUPPORT, FPE_DIVIDEBYZERO, FPE_INVALID, FPE_OVERFLOW, FPE_UNDERFLOW, False_, GZIP, INT, Inf, Infinity, LIST, MAXDIMS, MAY_SHARE_BOUNDS, MAY_SHARE_EXACT, MODULE_NAME, NAN, NINF, NO, NONE, NZERO, NaN, ORDEREDICT, PATH_MODULES, PINF, PRINT_LOCK, PROJECT_TEMPLATE, PZERO, RAISE, SHIFT_DIVIDEBYZERO, SHIFT_INVALID, SHIFT_OVERFLOW, SHIFT_UNDERFLOW, STRING, ScalarType, TUPLE, TYPES, True_, UFUNC_BUFSIZE_DEFAULT, UFUNC_PYVALS_NAME, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, ViolationAnalyser, ViolationAnalyserSettings, ViolationAnalyserXMLPickler, WRAP, YES, absolute, add, arccos, arccosh, arcsin, arcsinh, arctan, arctan2, arctanh, bitwise_and, bitwise_not, bitwise_or, bitwise_xor, cbrt, ceil, conj, conjugate, copysign, cos, cosh, deg2rad, degrees, divide, divmod, e, equal, euler_gamma, exp, exp2, expm1, fabs, float_power, floor, floor_divide, fmax, fmin, fmod, frexp, gcd, greater, greater_equal, heaviside, hypot, inf, infty, invert, isfinite, isinf, isnan, isnat, lcm, ldexp, left_shift, less, less_equal, little_endian, log, log10, log1p, log2, logaddexp, logaddexp2, logical_and, logical_not, logical_or, logical_xor, matmul, maximum, minimum, mod, modf, multiply, nan, negative, newaxis, nextafter, not_equal, pi, positive, power, rad2deg, radians, reciprocal, remainder, right_shift, rint, sctypeDict, sctypes, sign, signbit, sin, sinh, spacing, sqrt, square, subtract, tan, tanh, tracemalloc_domain, true_divide, trunc, typeDict, typecodes
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -24,6 +24,178 @@ Classes:
ViolationAnalyserSettings
ViolationAnalyserXMLPickler
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALLOW_THREADS
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ BUFSIZE
+ CCPN_EXTENSION
+ CLIP
+ DICT
+ ERR_CALL
+ ERR_DEFAULT
+ ERR_IGNORE
+ ERR_LOG
+ ERR_PRINT
+ ERR_RAISE
+ ERR_WARN
+ FLOAT
+ FLOAT64
+ FLOATING_POINT_SUPPORT
+ FPE_DIVIDEBYZERO
+ FPE_INVALID
+ FPE_OVERFLOW
+ FPE_UNDERFLOW
+ False_
+ GZIP
+ INT
+ Inf
+ Infinity
+ LIST
+ MAXDIMS
+ MAY_SHARE_BOUNDS
+ MAY_SHARE_EXACT
+ MODULE_NAME
+ NAN
+ NINF
+ NO
+ NONE
+ NZERO
+ NaN
+ ORDEREDICT
+ PATH_MODULES
+ PINF
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ PZERO
+ RAISE
+ SHIFT_DIVIDEBYZERO
+ SHIFT_INVALID
+ SHIFT_OVERFLOW
+ SHIFT_UNDERFLOW
+ STRING
+ ScalarType
+ TUPLE
+ TYPES
+ True_
+ UFUNC_BUFSIZE_DEFAULT
+ UFUNC_PYVALS_NAME
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ WRAP
+ YES
+ absolute
+ add
+ arccos
+ arccosh
+ arcsin
+ arcsinh
+ arctan
+ arctan2
+ arctanh
+ bitwise_and
+ bitwise_not
+ bitwise_or
+ bitwise_xor
+ cbrt
+ ceil
+ conj
+ conjugate
+ copysign
+ cos
+ cosh
+ deg2rad
+ degrees
+ divide
+ divmod
+ e
+ equal
+ euler_gamma
+ exp
+ exp2
+ expm1
+ fabs
+ float_power
+ floor
+ floor_divide
+ fmax
+ fmin
+ fmod
+ frexp
+ gcd
+ greater
+ greater_equal
+ heaviside
+ hypot
+ inf
+ infty
+ invert
+ isfinite
+ isinf
+ isnan
+ isnat
+ lcm
+ ldexp
+ left_shift
+ less
+ less_equal
+ little_endian
+ log
+ log10
+ log1p
+ log2
+ logaddexp
+ logaddexp2
+ logical_and
+ logical_not
+ logical_or
+ logical_xor
+ matmul
+ maximum
+ minimum
+ mod
+ modf
+ multiply
+ nan
+ negative
+ newaxis
+ nextafter
+ not_equal
+ pi
+ positive
+ power
+ rad2deg
+ radians
+ reciprocal
+ remainder
+ right_shift
+ rint
+ sctypeDict
+ sctypes
+ sign
+ signbit
+ sin
+ sinh
+ spacing
+ sqrt
+ square
+ subtract
+ tan
+ tanh
+ tracemalloc_domain
+ true_divide
+ trunc
+ typeDict
+ typecodes
+
diff --git a/docs/api/aria.core.WhatifProfile.rst b/docs/api/aria.core.WhatifProfile.rst
index b1544afde27f84821818127d5b4a5d5cbc93fd61..6443035a9b4345819fb5380f54711c0f1893a5c6 100644
--- a/docs/api/aria.core.WhatifProfile.rst
+++ b/docs/api/aria.core.WhatifProfile.rst
@@ -7,7 +7,7 @@ aria.core.WhatifProfile module
.. currentmodule:: aria.core.WhatifProfile
.. automodule:: aria.core.WhatifProfile
- :members: WhatifProfile
+ :members: BAD, CHECK_LIST, FILENAME_WHATIF_PROFILE, FILENAME_WHATIF_PROFILE_EPS, FILENAME_WHATIF_PROFILE_PDF, FILENAME_WHATIF_PROFILE_PS, GOOD, LEGEND_LIST, LEGEND_LIST_I, OTHER, POOR, SCORES_THRE, WhatifProfile
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -22,6 +22,24 @@ Classes:
WhatifProfile
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ BAD
+ CHECK_LIST
+ FILENAME_WHATIF_PROFILE
+ FILENAME_WHATIF_PROFILE_EPS
+ FILENAME_WHATIF_PROFILE_PDF
+ FILENAME_WHATIF_PROFILE_PS
+ GOOD
+ LEGEND_LIST
+ LEGEND_LIST_I
+ OTHER
+ POOR
+ SCORES_THRE
+
diff --git a/docs/api/aria.core.ariabase.rst b/docs/api/aria.core.ariabase.rst
index b5e70dde5f6fe4ae96c9f7331a5abe410c9277d8..ea0864de121a3e2fbd4ad1fff9badee72e510c1a 100644
--- a/docs/api/aria.core.ariabase.rst
+++ b/docs/api/aria.core.ariabase.rst
@@ -7,7 +7,7 @@ aria.core.ariabase module
.. currentmodule:: aria.core.ariabase
.. automodule:: aria.core.ariabase
- :members: AriaBaseClass, get_aria_root, get_path
+ :members: ALWAYS, ARIA_ENV, ARRAY, AriaBaseClass, BOOL, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES, get_aria_root, get_path, safe_execute
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -29,6 +29,39 @@ Functions:
get_aria_root
get_path
+ safe_execute
+
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ CCPN_EXTENSION
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
diff --git a/docs/api/aria.core.ccpn_conversion.rst b/docs/api/aria.core.ccpn_conversion.rst
index fbf8fd68fd8640043777f20ec844b74c84eb3524..c163d2092d9a43c0268ef514cb280ef270a78383 100644
--- a/docs/api/aria.core.ccpn_conversion.rst
+++ b/docs/api/aria.core.ccpn_conversion.rst
@@ -7,7 +7,7 @@ aria.core.ccpn_conversion module
.. currentmodule:: aria.core.ccpn_conversion
.. automodule:: aria.core.ccpn_conversion
- :members: CCPNConverter, find_ccpn_atom, map_aria_atoms, map_dimensions
+ :members: CCPNConverter, TERMINUS_C3_PRIME_HYDROXYL, TERMINUS_C5_PRIME_HYDROXYL, TERMINUS_C5_PRIME_PHOSPHATE, TERMINUS_C_CARBOXYL, TERMINUS_C_STANDARD, TERMINUS_N_AMINYL, TERMINUS_N_STANDARD, TYPE_AMINO_ACID, TYPE_DNA, TYPE_DNA_BASE, TYPE_NONBASE, TYPE_NONPOLYMER, TYPE_PROTEIN, TYPE_RNA, TYPE_RNA_BASE, ccpn_path, find_ccpn_atom, map_aria_atoms, map_dimensions
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -31,6 +31,28 @@ Functions:
map_aria_atoms
map_dimensions
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ TERMINUS_C3_PRIME_HYDROXYL
+ TERMINUS_C5_PRIME_HYDROXYL
+ TERMINUS_C5_PRIME_PHOSPHATE
+ TERMINUS_C_CARBOXYL
+ TERMINUS_C_STANDARD
+ TERMINUS_N_AMINYL
+ TERMINUS_N_STANDARD
+ TYPE_AMINO_ACID
+ TYPE_DNA
+ TYPE_DNA_BASE
+ TYPE_NONBASE
+ TYPE_NONPOLYMER
+ TYPE_PROTEIN
+ TYPE_RNA
+ TYPE_RNA_BASE
+ ccpn_path
+
diff --git a/docs/api/aria.core.cns.rst b/docs/api/aria.core.cns.rst
index 3fb4d1149cd62073dc136f3a96a629b5fb819e21..412ee6c320978637c22680172445211bbf4b298b 100644
--- a/docs/api/aria.core.cns.rst
+++ b/docs/api/aria.core.cns.rst
@@ -7,7 +7,7 @@ aria.core.cns module
.. currentmodule:: aria.core.cns
.. automodule:: aria.core.cns
- :members: CNS, CNSSettings, CNSXMLPickler, StructureEngine
+ :members: ALWAYS, CNS, CNSSettings, CNSXMLPickler, CNS_FALSE, CNS_OUTPUT_PATH_NAME, CNS_TRUE, CONDOR_SCRIPT, CSH_SCRIPT_ANALYSIS, CSH_SCRIPT_CHECKPOINT, CSH_SCRIPT_REFINE, CSH_SCRIPT_REFINE_CONDOR, DICT, DIHEDRALS, DIHEDRALS_CSI, DIHEDRALS_TALOS, FILE_CNS_TEMPLATE, GZIP, HBONDS, HBONDS_CSI, INT, LIST, MODULE_NAME, NAME_NOE_RESTRAINTS_AMBIG, NAME_NOE_RESTRAINTS_UNAMBIG, NO, NONE, PLAN, PROTOCOLS_ANALYSIS, PROTOCOLS_CORE, RUN_CNS, SECONDARY_STRUCTURE, STRING, StructureEngine, TUPLE, VL_LOW, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -25,6 +25,45 @@ Classes:
CNSXMLPickler
StructureEngine
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ CNS_FALSE
+ CNS_OUTPUT_PATH_NAME
+ CNS_TRUE
+ CONDOR_SCRIPT
+ CSH_SCRIPT_ANALYSIS
+ CSH_SCRIPT_CHECKPOINT
+ CSH_SCRIPT_REFINE
+ CSH_SCRIPT_REFINE_CONDOR
+ DICT
+ DIHEDRALS
+ DIHEDRALS_CSI
+ DIHEDRALS_TALOS
+ FILE_CNS_TEMPLATE
+ GZIP
+ HBONDS
+ HBONDS_CSI
+ INT
+ LIST
+ MODULE_NAME
+ NAME_NOE_RESTRAINTS_AMBIG
+ NAME_NOE_RESTRAINTS_UNAMBIG
+ NO
+ NONE
+ PLAN
+ PROTOCOLS_ANALYSIS
+ PROTOCOLS_CORE
+ RUN_CNS
+ SECONDARY_STRUCTURE
+ STRING
+ TUPLE
+ VL_LOW
+ YES
+
diff --git a/docs/api/aria.core.conversion.rst b/docs/api/aria.core.conversion.rst
index 87e4ddfe37285cbde19574594bc27dc91fea2f35..e7e9b6c25c425fb403538bdb5f13415c9902fbb8 100644
--- a/docs/api/aria.core.conversion.rst
+++ b/docs/api/aria.core.conversion.rst
@@ -7,7 +7,7 @@ aria.core.conversion module
.. currentmodule:: aria.core.conversion
.. automodule:: aria.core.conversion
- :members: Base, ChainSettings, ChainSettingsXMLPickler, ChemicalShiftsSettings, ChemicalShiftsSettingsXMLPickler, Converter, ConverterSettings, ConverterSettingsXMLPickler, CrossPeaksSettings, CrossPeaksSettingsXMLPickler, MoleculeSettings, MoleculeSettingsXMLPickler, NoeList, PpmList, SequenceList, SpectrumSettings, SpectrumSettingsXMLPickler, abspath, convert_atomname, convert_value, is_pseudo, test_sparky
+ :members: ARRAY, BOOL, Base, CCPN_SPECTRUM_BLOCK, CCPN_XML_TEMPLATE, CHEMICAL_SHIFT_FORMATS, CNS_CONVENTION, CONVENTIONS, CROSSPEAK_FORMATS, ChainSettings, ChainSettingsXMLPickler, ChemicalShiftsSettings, ChemicalShiftsSettingsXMLPickler, Converter, ConverterSettings, ConverterSettingsXMLPickler, CrossPeaksSettings, CrossPeaksSettingsXMLPickler, DICT, DYANA_CONVENTION, FLOAT, FLOAT64, INT, IUPAC_CONVENTION, LIST, MoleculeSettings, MoleculeSettingsXMLPickler, NAMING_CONVENTIONS, NONE, NoeList, ORDEREDICT, PpmList, SEQUENCE_FORMATS, SPECTRUM_AMBIGUITIES, SPECTRUM_AMBIGUITY_ALL, SPECTRUM_AMBIGUITY_INTER, SPECTRUM_AMBIGUITY_INTRA, STRING, SequenceList, SpectrumSettings, SpectrumSettingsXMLPickler, TEMPLATE_XML, TUPLE, TYPES, TYPE_AMINO_ACID, TYPE_DNA, TYPE_DNA_BASE, TYPE_NONBASE, TYPE_NONPOLYMER, TYPE_PROTEIN, TYPE_RNA, TYPE_RNA_BASE, UNICODE, abspath, convert_atomname, convert_value, is_pseudo, test_sparky
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -49,6 +49,48 @@ Functions:
is_pseudo
test_sparky
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ARRAY
+ BOOL
+ CCPN_SPECTRUM_BLOCK
+ CCPN_XML_TEMPLATE
+ CHEMICAL_SHIFT_FORMATS
+ CNS_CONVENTION
+ CONVENTIONS
+ CROSSPEAK_FORMATS
+ DICT
+ DYANA_CONVENTION
+ FLOAT
+ FLOAT64
+ INT
+ IUPAC_CONVENTION
+ LIST
+ NAMING_CONVENTIONS
+ NONE
+ ORDEREDICT
+ SEQUENCE_FORMATS
+ SPECTRUM_AMBIGUITIES
+ SPECTRUM_AMBIGUITY_ALL
+ SPECTRUM_AMBIGUITY_INTER
+ SPECTRUM_AMBIGUITY_INTRA
+ STRING
+ TEMPLATE_XML
+ TUPLE
+ TYPES
+ TYPE_AMINO_ACID
+ TYPE_DNA
+ TYPE_DNA_BASE
+ TYPE_NONBASE
+ TYPE_NONPOLYMER
+ TYPE_PROTEIN
+ TYPE_RNA
+ TYPE_RNA_BASE
+ UNICODE
+
diff --git a/docs/api/aria.core.gui.decorators.rst b/docs/api/aria.core.gui.decorators.rst
index 105127cb1c427ed72c63fe8cde3aac6b2ce4c636..66407f31f49668454d67174daf0f82dcc03138c0 100644
--- a/docs/api/aria.core.gui.decorators.rst
+++ b/docs/api/aria.core.gui.decorators.rst
@@ -7,7 +7,7 @@ aria.core.gui.decorators module
.. currentmodule:: aria.core.gui.decorators
.. automodule:: aria.core.gui.decorators
- :members: CCPNProjectBrowser, DBrowseEntry, DCell, DCheckbutton, DComboBox, DEntry, DFileEntry, DIntOptionMenu, DLabelEntry, DListBox, DOptionMenu, DPathEntry, DTable, DText, WidgetDecorator, WidgetSaveError
+ :members: CCPNProjectBrowser, DBrowseEntry, DCell, DCheckbutton, DComboBox, DEntry, DFileEntry, DIntOptionMenu, DLabelEntry, DListBox, DOptionMenu, DPathEntry, DTable, DText, NO, NONE, PY3, WidgetDecorator, WidgetSaveError, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -43,6 +43,16 @@ Classes:
DText
WidgetDecorator
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ NO
+ NONE
+ PY3
+ YES
+
diff --git a/docs/api/aria.core.gui.gui.rst b/docs/api/aria.core.gui.gui.rst
index 0a9bfc758224d4a51816061aaf346fbd0f91d55c..f445c08e4fc5aa47e0f6dcf543f605344a08a87e 100644
--- a/docs/api/aria.core.gui.gui.rst
+++ b/docs/api/aria.core.gui.gui.rst
@@ -7,7 +7,7 @@ aria.core.gui.gui module
.. currentmodule:: aria.core.gui.gui
.. automodule:: aria.core.gui.gui
- :members: AboutBox, DiscardDialog, EntriesMissingDialog, GUI, GUISettings, NotSavedDialog, go, popup
+ :members: ACTIVE, ALL, ANCHOR, ARC, ARIA_ENV, AboutBox, BASELINE, BEVEL, BOTH, BOTTOM, BROWSE, BUTT, CANCEL, CASCADE, CENTER, CHAR, CHECKBUTTON, CHORD, COMMAND, CURRENT, DISABLED, DOTBOX, DiscardDialog, E, END, EW, EXTENDED, EntriesMissingDialog, FALSE, FIRST, FLAT, GROOVE, GUI, GUISettings, GUI_MODULES, GUI_SETTINGS_FILENAME, GUI_VERSION, HIDDEN, HORIZONTAL, INSERT, INSIDE, LAST, LEFT, LIST, MITER, MOVETO, MULTIPLE, N, NE, NO, NONE, NORMAL, NS, NSEW, NUMERIC, NW, NotSavedDialog, OFF, ON, OUTSIDE, PAGES, PATH_GUI_MODULES, PATH_MODULES, PIESLICE, PROJECTING, PROJECT_TEMPLATE, PY3, RADIOBUTTON, RAISED, RIDGE, RIGHT, ROUND, S, SCROLL, SE, SEL, SEL_FIRST, SEL_LAST, SEPARATOR, SINGLE, SOLID, SUNKEN, SW, TCL_ALL_EVENTS, TCL_DONT_WAIT, TCL_FILE_EVENTS, TCL_IDLE_EVENTS, TCL_TIMER_EVENTS, TCL_WINDOW_EVENTS, TK_OPTIONS_TEMPLATE, TOP, TRUE, UNDERLINE, UNITS, VERTICAL, W, WORD, X, Y, YES, go, popup
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -35,6 +35,106 @@ Functions:
go
popup
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ACTIVE
+ ALL
+ ANCHOR
+ ARC
+ ARIA_ENV
+ BASELINE
+ BEVEL
+ BOTH
+ BOTTOM
+ BROWSE
+ BUTT
+ CANCEL
+ CASCADE
+ CENTER
+ CHAR
+ CHECKBUTTON
+ CHORD
+ COMMAND
+ CURRENT
+ DISABLED
+ DOTBOX
+ E
+ END
+ EW
+ EXTENDED
+ FALSE
+ FIRST
+ FLAT
+ GROOVE
+ GUI_MODULES
+ GUI_SETTINGS_FILENAME
+ GUI_VERSION
+ HIDDEN
+ HORIZONTAL
+ INSERT
+ INSIDE
+ LAST
+ LEFT
+ LIST
+ MITER
+ MOVETO
+ MULTIPLE
+ N
+ NE
+ NO
+ NONE
+ NORMAL
+ NS
+ NSEW
+ NUMERIC
+ NW
+ OFF
+ ON
+ OUTSIDE
+ PAGES
+ PATH_GUI_MODULES
+ PATH_MODULES
+ PIESLICE
+ PROJECTING
+ PROJECT_TEMPLATE
+ PY3
+ RADIOBUTTON
+ RAISED
+ RIDGE
+ RIGHT
+ ROUND
+ S
+ SCROLL
+ SE
+ SEL
+ SEL_FIRST
+ SEL_LAST
+ SEPARATOR
+ SINGLE
+ SOLID
+ SUNKEN
+ SW
+ TCL_ALL_EVENTS
+ TCL_DONT_WAIT
+ TCL_FILE_EVENTS
+ TCL_IDLE_EVENTS
+ TCL_TIMER_EVENTS
+ TCL_WINDOW_EVENTS
+ TK_OPTIONS_TEMPLATE
+ TOP
+ TRUE
+ UNDERLINE
+ UNITS
+ VERTICAL
+ W
+ WORD
+ X
+ Y
+ YES
+
diff --git a/docs/api/aria.core.gui.panels.rst b/docs/api/aria.core.gui.panels.rst
index 99d9ea3442bcca2bf281a8c356b8da9917e096f0..06879d2a4c16151af18ffdce4262afa7452cfaed 100644
--- a/docs/api/aria.core.gui.panels.rst
+++ b/docs/api/aria.core.gui.panels.rst
@@ -7,7 +7,7 @@ aria.core.gui.panels module
.. currentmodule:: aria.core.gui.panels
.. automodule:: aria.core.gui.panels
- :members: AnalysisPanel, AnnealingAmbigPanel, AnnealingDihedralPanel, AnnealingFBHWPanel, AnnealingHBondPanel, AnnealingKarplusPanel, AnnealingRDCPanel, AnnealingSymmetryPanel, AnnealingUnambigPanel, CCPNPanel, CNSPanel, ChainCodeSelector, CisProPatchPanel, CmapOptionsPanel, ContactMapPanel, ContribPanel, ControlPanel, ControlPanelSettings, DataAmbigPanel, DataDihedralPanel, DataHBondPanel, DataIsoPeptidePatchPanel, DataKarplusPanel, DataOtherPanel, DataPanel, DataRDCPanel, DataSSBondPanel, DataSequencePanel, DataSpectrumPanel, DataTemplatePanel, DataUnambigPanel, DataZnPatchPanel, DynamicsPanel, HBDBPanel, HisPatchPanel, IterationPanel, JobManagerPanel, LogHarmonicPanel, Panel, PanelEx, PlotPanel, PreferencesPanel, ProjectPanel, ProtocolPanel, RamaPanel, ReportPanel, SSBridgePanel, SSBridgePanel2, SymmetryPanel, WaterRefinementPanel, file_and_format
+ :members: ALWAYS, ARIA_ENV, ARRAY, AnalysisPanel, AnnealingAmbigPanel, AnnealingDihedralPanel, AnnealingFBHWPanel, AnnealingHBondPanel, AnnealingKarplusPanel, AnnealingRDCPanel, AnnealingSymmetryPanel, AnnealingUnambigPanel, BOOL, BUTTON_WIDTH, CCPNPanel, CCPN_EXTENSION, CNSPanel, ChainCodeSelector, CisProPatchPanel, CmapOptionsPanel, ContactMapPanel, ContribPanel, ControlPanel, ControlPanelSettings, DATA_PDB, DATA_TEXT, DICT, DataAmbigPanel, DataDihedralPanel, DataHBondPanel, DataIsoPeptidePatchPanel, DataKarplusPanel, DataOtherPanel, DataPanel, DataRDCPanel, DataSSBondPanel, DataSequencePanel, DataSpectrumPanel, DataTemplatePanel, DataUnambigPanel, DataZnPatchPanel, DynamicsPanel, FLOAT, FLOAT64, GZIP, HBDBPanel, HisPatchPanel, INT, IterationPanel, JobManagerPanel, LIST, LogHarmonicPanel, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, PY3, Panel, PanelEx, PlotPanel, PreferencesPanel, ProjectPanel, ProtocolPanel, RamaPanel, ReportPanel, SSBridgePanel, SSBridgePanel2, STRING, SymmetryPanel, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, WaterRefinementPanel, YES, YES_NO_DICT, YES_NO_GZIP_DICT, file_and_format
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -78,6 +78,44 @@ Functions:
file_and_format
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALWAYS
+ ARIA_ENV
+ ARRAY
+ BOOL
+ BUTTON_WIDTH
+ CCPN_EXTENSION
+ DATA_PDB
+ DATA_TEXT
+ DICT
+ FLOAT
+ FLOAT64
+ GZIP
+ INT
+ LIST
+ MODULE_NAME
+ NO
+ NONE
+ ORDEREDICT
+ PATH_MODULES
+ PRINT_LOCK
+ PROJECT_TEMPLATE
+ PY3
+ STRING
+ TUPLE
+ TYPES
+ UNICODE
+ VL_LOW
+ VL_SETTINGS
+ VL_STANDARD
+ YES
+ YES_NO_DICT
+ YES_NO_GZIP_DICT
+
diff --git a/docs/api/aria.core.gui.widgets.rst b/docs/api/aria.core.gui.widgets.rst
index 1982aefd6a4285e9c839ad8e45e97c8d5be3374e..8a5561151dd0e35bbc6959ff8aea880939898e37 100644
--- a/docs/api/aria.core.gui.widgets.rst
+++ b/docs/api/aria.core.gui.widgets.rst
@@ -7,7 +7,7 @@ aria.core.gui.widgets module
.. currentmodule:: aria.core.gui.widgets
.. automodule:: aria.core.gui.widgets
- :members: BrowseEntry, Cell, DefaultButton, DefaultButtonBox, Dialog, DirChooser, Menu, MessageBox, MyPanedWindow, MyScrolledText, Node, OKDialog, Table, Tree, YesNoCancelDialog, YesNoDialog, ariaPopup
+ :members: ACTIVE, ALL, ANCHOR, ARC, BASELINE, BEVEL, BOTH, BOTTOM, BROWSE, BUTT, BUTTON_WIDTH, BrowseEntry, CASCADE, CENTER, CHAR, CHECKBUTTON, CHORD, COMMAND, CURRENT, Cell, DISABLED, DOTBOX, DefaultButton, DefaultButtonBox, Dialog, DirChooser, E, END, EW, EXCEPTION, EXTENDED, FALSE, FIRST, FLAT, GROOVE, HIDDEN, HORIZONTAL, INSERT, INSIDE, LAST, LEFT, MITER, MOVETO, MULTIPLE, Menu, MessageBox, MyPanedWindow, MyScrolledText, N, NE, NO, NONE, NORMAL, NS, NSEW, NUMERIC, NW, Node, OFF, OKDialog, ON, OUTSIDE, PAGES, PIESLICE, PROJECTING, PY3, RADIOBUTTON, RAISED, READABLE, RIDGE, RIGHT, ROUND, S, SCROLL, SE, SEL, SEL_FIRST, SEL_LAST, SEPARATOR, SINGLE, SOLID, SUNKEN, SW, StringTypes, TOP, TRUE, Table, TclVersion, TkVersion, Tree, UNDERLINE, UNITS, VERTICAL, W, WORD, WRITABLE, X, Y, YES, YesNoCancelDialog, YesNoDialog, ariaPopup, wantobjects
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -38,6 +38,98 @@ Classes:
YesNoDialog
ariaPopup
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ACTIVE
+ ALL
+ ANCHOR
+ ARC
+ BASELINE
+ BEVEL
+ BOTH
+ BOTTOM
+ BROWSE
+ BUTT
+ BUTTON_WIDTH
+ CASCADE
+ CENTER
+ CHAR
+ CHECKBUTTON
+ CHORD
+ COMMAND
+ CURRENT
+ DISABLED
+ DOTBOX
+ E
+ END
+ EW
+ EXCEPTION
+ EXTENDED
+ FALSE
+ FIRST
+ FLAT
+ GROOVE
+ HIDDEN
+ HORIZONTAL
+ INSERT
+ INSIDE
+ LAST
+ LEFT
+ MITER
+ MOVETO
+ MULTIPLE
+ N
+ NE
+ NO
+ NONE
+ NORMAL
+ NS
+ NSEW
+ NUMERIC
+ NW
+ OFF
+ ON
+ OUTSIDE
+ PAGES
+ PIESLICE
+ PROJECTING
+ PY3
+ RADIOBUTTON
+ RAISED
+ READABLE
+ RIDGE
+ RIGHT
+ ROUND
+ S
+ SCROLL
+ SE
+ SEL
+ SEL_FIRST
+ SEL_LAST
+ SEPARATOR
+ SINGLE
+ SOLID
+ SUNKEN
+ SW
+ StringTypes
+ TOP
+ TRUE
+ TclVersion
+ TkVersion
+ UNDERLINE
+ UNITS
+ VERTICAL
+ W
+ WORD
+ WRITABLE
+ X
+ Y
+ YES
+ wantobjects
+
diff --git a/docs/api/aria.core.legacy.Nomenclature.rst b/docs/api/aria.core.legacy.Nomenclature.rst
index 3f4f3cff41b76c894e3e6a92f1f1584f53865bef..ee4beac2eac384ad6883520b9e2430bb63bb61d8 100644
--- a/docs/api/aria.core.legacy.Nomenclature.rst
+++ b/docs/api/aria.core.legacy.Nomenclature.rst
@@ -7,7 +7,7 @@ aria.core.legacy.Nomenclature module
.. currentmodule:: aria.core.legacy.Nomenclature
.. automodule:: aria.core.legacy.Nomenclature
- :members: ConvertCnsProtonNames, ConvertCnsPseudoAtomNames
+ :members: AtomLib_Xplor_FileName, BaseDir, ConvertCnsProtonNames, ConvertCnsPseudoAtomNames
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -23,6 +23,14 @@ Functions:
ConvertCnsProtonNames
ConvertCnsPseudoAtomNames
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ AtomLib_Xplor_FileName
+ BaseDir
+
diff --git a/docs/api/aria.core.legacy.QualityChecks.Descriptive.rst b/docs/api/aria.core.legacy.QualityChecks.Descriptive.rst
index a1d6c209da0574eae396a5ba86cbc119991fcb48..ab69cb044a953f529df2d2852a9abe1fb19af879 100644
--- a/docs/api/aria.core.legacy.QualityChecks.Descriptive.rst
+++ b/docs/api/aria.core.legacy.QualityChecks.Descriptive.rst
@@ -7,7 +7,7 @@ aria.core.legacy.QualityChecks.Descriptive module
.. currentmodule:: aria.core.legacy.QualityChecks.Descriptive
.. automodule:: aria.core.legacy.QualityChecks.Descriptive
- :members: Descriptive
+ :members: ALLOW_THREADS, BUFSIZE, CLIP, Descriptive, ERR_CALL, ERR_DEFAULT, ERR_IGNORE, ERR_LOG, ERR_PRINT, ERR_RAISE, ERR_WARN, FLOATING_POINT_SUPPORT, FPE_DIVIDEBYZERO, FPE_INVALID, FPE_OVERFLOW, FPE_UNDERFLOW, False_, Inf, Infinity, MAXDIMS, MAY_SHARE_BOUNDS, MAY_SHARE_EXACT, NAN, NINF, NZERO, NaN, PINF, PZERO, RAISE, SHIFT_DIVIDEBYZERO, SHIFT_INVALID, SHIFT_OVERFLOW, SHIFT_UNDERFLOW, ScalarType, True_, UFUNC_BUFSIZE_DEFAULT, UFUNC_PYVALS_NAME, WRAP, absolute, add, arccos, arccosh, arcsin, arcsinh, arctan, arctan2, arctanh, bitwise_and, bitwise_not, bitwise_or, bitwise_xor, cbrt, ceil, conj, conjugate, copysign, cos, cosh, deg2rad, degrees, divide, divmod, e, equal, euler_gamma, exp, exp2, expm1, fabs, float_power, floor, floor_divide, fmax, fmin, fmod, frexp, gcd, greater, greater_equal, heaviside, hypot, inf, infty, invert, isfinite, isinf, isnan, isnat, lcm, ldexp, left_shift, less, less_equal, little_endian, log, log10, log1p, log2, logaddexp, logaddexp2, logical_and, logical_not, logical_or, logical_xor, matmul, maximum, minimum, mod, modf, multiply, nan, negative, newaxis, nextafter, not_equal, pi, positive, power, rad2deg, radians, reciprocal, remainder, right_shift, rint, sctypeDict, sctypes, sign, signbit, sin, sinh, spacing, sqrt, square, subtract, tan, tanh, tracemalloc_domain, true_divide, trunc, typeDict, typecodes
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -22,6 +22,152 @@ Classes:
Descriptive
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALLOW_THREADS
+ BUFSIZE
+ CLIP
+ ERR_CALL
+ ERR_DEFAULT
+ ERR_IGNORE
+ ERR_LOG
+ ERR_PRINT
+ ERR_RAISE
+ ERR_WARN
+ FLOATING_POINT_SUPPORT
+ FPE_DIVIDEBYZERO
+ FPE_INVALID
+ FPE_OVERFLOW
+ FPE_UNDERFLOW
+ False_
+ Inf
+ Infinity
+ MAXDIMS
+ MAY_SHARE_BOUNDS
+ MAY_SHARE_EXACT
+ NAN
+ NINF
+ NZERO
+ NaN
+ PINF
+ PZERO
+ RAISE
+ SHIFT_DIVIDEBYZERO
+ SHIFT_INVALID
+ SHIFT_OVERFLOW
+ SHIFT_UNDERFLOW
+ ScalarType
+ True_
+ UFUNC_BUFSIZE_DEFAULT
+ UFUNC_PYVALS_NAME
+ WRAP
+ absolute
+ add
+ arccos
+ arccosh
+ arcsin
+ arcsinh
+ arctan
+ arctan2
+ arctanh
+ bitwise_and
+ bitwise_not
+ bitwise_or
+ bitwise_xor
+ cbrt
+ ceil
+ conj
+ conjugate
+ copysign
+ cos
+ cosh
+ deg2rad
+ degrees
+ divide
+ divmod
+ e
+ equal
+ euler_gamma
+ exp
+ exp2
+ expm1
+ fabs
+ float_power
+ floor
+ floor_divide
+ fmax
+ fmin
+ fmod
+ frexp
+ gcd
+ greater
+ greater_equal
+ heaviside
+ hypot
+ inf
+ infty
+ invert
+ isfinite
+ isinf
+ isnan
+ isnat
+ lcm
+ ldexp
+ left_shift
+ less
+ less_equal
+ little_endian
+ log
+ log10
+ log1p
+ log2
+ logaddexp
+ logaddexp2
+ logical_and
+ logical_not
+ logical_or
+ logical_xor
+ matmul
+ maximum
+ minimum
+ mod
+ modf
+ multiply
+ nan
+ negative
+ newaxis
+ nextafter
+ not_equal
+ pi
+ positive
+ power
+ rad2deg
+ radians
+ reciprocal
+ remainder
+ right_shift
+ rint
+ sctypeDict
+ sctypes
+ sign
+ signbit
+ sin
+ sinh
+ spacing
+ sqrt
+ square
+ subtract
+ tan
+ tanh
+ tracemalloc_domain
+ true_divide
+ trunc
+ typeDict
+ typecodes
+
diff --git a/docs/api/aria.core.legacy.QualityChecks.QualityChecks.rst b/docs/api/aria.core.legacy.QualityChecks.QualityChecks.rst
index 696de296e81e1d67ad5e16186b04a1ad520c6d38..5e17c048463e98469e35f9a76771499711694ad5 100644
--- a/docs/api/aria.core.legacy.QualityChecks.QualityChecks.rst
+++ b/docs/api/aria.core.legacy.QualityChecks.QualityChecks.rst
@@ -7,7 +7,7 @@ aria.core.legacy.QualityChecks.QualityChecks module
.. currentmodule:: aria.core.legacy.QualityChecks.QualityChecks
.. automodule:: aria.core.legacy.QualityChecks.QualityChecks
- :members: copypdb_for_prosa, runChecks
+ :members: ARIA_VERSION, FILENAME_REPORT, FILENAME_REPORT_MP_CLASHSCORE, FILENAME_REPORT_PROCHECK, FILENAME_REPORT_PROSA, FILENAME_REPORT_TEX, FILENAME_REPORT_TEXT, FILENAME_REPORT_WHATIF, FILENAME_REPORT_WHATIF_FULL, copypdb_for_prosa, runChecks
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -23,6 +23,21 @@ Functions:
copypdb_for_prosa
runChecks
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ARIA_VERSION
+ FILENAME_REPORT
+ FILENAME_REPORT_MP_CLASHSCORE
+ FILENAME_REPORT_PROCHECK
+ FILENAME_REPORT_PROSA
+ FILENAME_REPORT_TEX
+ FILENAME_REPORT_TEXT
+ FILENAME_REPORT_WHATIF
+ FILENAME_REPORT_WHATIF_FULL
+
diff --git a/docs/api/aria.core.mathutils.rst b/docs/api/aria.core.mathutils.rst
index 66aae814d92b1a3f02d2bf39a2cd213abf3ffbfd..3db795df1a951ebd976439c26513d79907de8747 100644
--- a/docs/api/aria.core.mathutils.rst
+++ b/docs/api/aria.core.mathutils.rst
@@ -7,7 +7,7 @@ aria.core.mathutils module
.. currentmodule:: aria.core.mathutils
.. automodule:: aria.core.mathutils
- :members: average, confidenceInterval, standardDeviation, variance
+ :members: ALLOW_THREADS, BUFSIZE, CLIP, ERR_CALL, ERR_DEFAULT, ERR_IGNORE, ERR_LOG, ERR_PRINT, ERR_RAISE, ERR_WARN, FLOATING_POINT_SUPPORT, FPE_DIVIDEBYZERO, FPE_INVALID, FPE_OVERFLOW, FPE_UNDERFLOW, False_, Inf, Infinity, MAXDIMS, MAY_SHARE_BOUNDS, MAY_SHARE_EXACT, NAN, NINF, NZERO, NaN, PINF, PZERO, RAISE, SHIFT_DIVIDEBYZERO, SHIFT_INVALID, SHIFT_OVERFLOW, SHIFT_UNDERFLOW, ScalarType, True_, UFUNC_BUFSIZE_DEFAULT, UFUNC_PYVALS_NAME, WRAP, absolute, add, arccos, arccosh, arcsin, arcsinh, arctan, arctan2, arctanh, average, bitwise_and, bitwise_not, bitwise_or, bitwise_xor, cbrt, ceil, confidenceInterval, conj, conjugate, copysign, cos, cosh, deg2rad, degrees, divide, divmod, e, equal, euler_gamma, exp, exp2, expm1, fabs, float_power, floor, floor_divide, fmax, fmin, fmod, frexp, gcd, greater, greater_equal, heaviside, hypot, inf, infty, invert, isfinite, isinf, isnan, isnat, lcm, ldexp, left_shift, less, less_equal, little_endian, log, log10, log1p, log2, logaddexp, logaddexp2, logical_and, logical_not, logical_or, logical_xor, matmul, maximum, minimum, mod, modf, multiply, nan, negative, newaxis, nextafter, not_equal, pi, positive, power, rad2deg, radians, reciprocal, remainder, right_shift, rint, sctypeDict, sctypes, sign, signbit, sin, sinh, spacing, sqrt, square, standardDeviation, subtract, tan, tanh, tracemalloc_domain, true_divide, trunc, typeDict, typecodes, variance
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -25,6 +25,152 @@ Functions:
standardDeviation
variance
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ALLOW_THREADS
+ BUFSIZE
+ CLIP
+ ERR_CALL
+ ERR_DEFAULT
+ ERR_IGNORE
+ ERR_LOG
+ ERR_PRINT
+ ERR_RAISE
+ ERR_WARN
+ FLOATING_POINT_SUPPORT
+ FPE_DIVIDEBYZERO
+ FPE_INVALID
+ FPE_OVERFLOW
+ FPE_UNDERFLOW
+ False_
+ Inf
+ Infinity
+ MAXDIMS
+ MAY_SHARE_BOUNDS
+ MAY_SHARE_EXACT
+ NAN
+ NINF
+ NZERO
+ NaN
+ PINF
+ PZERO
+ RAISE
+ SHIFT_DIVIDEBYZERO
+ SHIFT_INVALID
+ SHIFT_OVERFLOW
+ SHIFT_UNDERFLOW
+ ScalarType
+ True_
+ UFUNC_BUFSIZE_DEFAULT
+ UFUNC_PYVALS_NAME
+ WRAP
+ absolute
+ add
+ arccos
+ arccosh
+ arcsin
+ arcsinh
+ arctan
+ arctan2
+ arctanh
+ bitwise_and
+ bitwise_not
+ bitwise_or
+ bitwise_xor
+ cbrt
+ ceil
+ conj
+ conjugate
+ copysign
+ cos
+ cosh
+ deg2rad
+ degrees
+ divide
+ divmod
+ e
+ equal
+ euler_gamma
+ exp
+ exp2
+ expm1
+ fabs
+ float_power
+ floor
+ floor_divide
+ fmax
+ fmin
+ fmod
+ frexp
+ gcd
+ greater
+ greater_equal
+ heaviside
+ hypot
+ inf
+ infty
+ invert
+ isfinite
+ isinf
+ isnan
+ isnat
+ lcm
+ ldexp
+ left_shift
+ less
+ less_equal
+ little_endian
+ log
+ log10
+ log1p
+ log2
+ logaddexp
+ logaddexp2
+ logical_and
+ logical_not
+ logical_or
+ logical_xor
+ matmul
+ maximum
+ minimum
+ mod
+ modf
+ multiply
+ nan
+ negative
+ newaxis
+ nextafter
+ not_equal
+ pi
+ positive
+ power
+ rad2deg
+ radians
+ reciprocal
+ remainder
+ right_shift
+ rint
+ sctypeDict
+ sctypes
+ sign
+ signbit
+ sin
+ sinh
+ spacing
+ sqrt
+ square
+ subtract
+ tan
+ tanh
+ tracemalloc_domain
+ true_divide
+ trunc
+ typeDict
+ typecodes
+
diff --git a/docs/api/aria.core.rst b/docs/api/aria.core.rst
index 8b937ad574e63fe1fa95b32d831525c60fd15a5d..bd7defbe4d3d8daa05aeb0498e35a112d3149a8f 100644
--- a/docs/api/aria.core.rst
+++ b/docs/api/aria.core.rst
@@ -5,9 +5,7 @@ aria.core package
=================
.. automodule:: aria.core
- :members: Analyser, AriaPeak, AriaXML, Assignment, AssignmentFilter, Atom, Calibrator, Chain, ChemicalShiftFilter, ChemicalShiftList, Cluster, Contribution, ContributionAssigner, ConversionTable, CovalentDistances, CrossPeak, CrossPeakFilter, DataContainer, Datum, Experiment, Factory, FloatFile, Infrastructure, Iteration, JobManager, Merger, MolMol, Molecule, Molprobity, NOEModel, NOESYSpectrum, NOESYSpectrumFilter, Network, OrderedDict, PDBReader, PeakAssigner, Project, Protocol, Relaxation, Report, Residue, RmsReport, Settings, ShiftAssignment, ShiftAssignmentFilter, Singleton, SpinPair, StructureEnsemble, SuperImposer, Topology, TypeChecking, ViolationAnalyser, WhatifProfile, ariabase, cns, conversion, mathutils, tools, xmlparser, xmlutils
- :undoc-members:
- :show-inheritance:
+
@@ -91,13 +89,7 @@ Subpackages:
aria.core.scientific
-Summary
--------
- ``__all__``: :mod:`Analyser <aria.core.Analyser>`, :mod:`AriaPeak <aria.core.AriaPeak>`, :mod:`AriaXML <aria.core.AriaXML>`, :mod:`Assignment <aria.core.Assignment>`, :mod:`AssignmentFilter <aria.core.AssignmentFilter>`, :mod:`Atom <aria.core.Atom>`, :mod:`Calibrator <aria.core.Calibrator>`, :mod:`Chain <aria.core.Chain>`, :mod:`ChemicalShiftFilter <aria.core.ChemicalShiftFilter>`, :mod:`ChemicalShiftList <aria.core.ChemicalShiftList>`, :mod:`Cluster <aria.core.Cluster>`, :mod:`Contribution <aria.core.Contribution>`, :mod:`ContributionAssigner <aria.core.ContributionAssigner>`, :mod:`ConversionTable <aria.core.ConversionTable>`, :mod:`CovalentDistances <aria.core.CovalentDistances>`, :mod:`CrossPeak <aria.core.CrossPeak>`, :mod:`CrossPeakFilter <aria.core.CrossPeakFilter>`, :mod:`DataContainer <aria.core.DataContainer>`, :mod:`Datum <aria.core.Datum>`, :mod:`Experiment <aria.core.Experiment>`, :mod:`Factory <aria.core.Factory>`, :mod:`FloatFile <aria.core.FloatFile>`, :mod:`Infrastructure <aria.core.Infrastructure>`, :mod:`Iteration <aria.core.Iteration>`, :mod:`JobManager <aria.core.JobManager>`, :mod:`Merger <aria.core.Merger>`, :mod:`MolMol <aria.core.MolMol>`, :mod:`Molecule <aria.core.Molecule>`, :mod:`Molprobity <aria.core.Molprobity>`, :mod:`NOEModel <aria.core.NOEModel>`, :mod:`NOESYSpectrum <aria.core.NOESYSpectrum>`, :mod:`NOESYSpectrumFilter <aria.core.NOESYSpectrumFilter>`, :mod:`Network <aria.core.Network>`, :mod:`OrderedDict <aria.core.OrderedDict>`, :mod:`PDBReader <aria.core.PDBReader>`, :mod:`PeakAssigner <aria.core.PeakAssigner>`, :mod:`Project <aria.core.Project>`, :mod:`Protocol <aria.core.Protocol>`, :mod:`Relaxation <aria.core.Relaxation>`, :mod:`Report <aria.core.Report>`, :mod:`Residue <aria.core.Residue>`, :mod:`RmsReport <aria.core.RmsReport>`, :mod:`Settings <aria.core.Settings>`, :mod:`ShiftAssignment <aria.core.ShiftAssignment>`, :mod:`ShiftAssignmentFilter <aria.core.ShiftAssignmentFilter>`, :mod:`Singleton <aria.core.Singleton>`, :mod:`SpinPair <aria.core.SpinPair>`, :mod:`StructureEnsemble <aria.core.StructureEnsemble>`, :mod:`SuperImposer <aria.core.SuperImposer>`, :mod:`Topology <aria.core.Topology>`, :mod:`TypeChecking <aria.core.TypeChecking>`, :mod:`ViolationAnalyser <aria.core.ViolationAnalyser>`, :mod:`WhatifProfile <aria.core.WhatifProfile>`, :mod:`ariabase <aria.core.ariabase>`, :mod:`cns <aria.core.cns>`, :mod:`conversion <aria.core.conversion>`, :mod:`mathutils <aria.core.mathutils>`, :mod:`tools <aria.core.tools>`, :mod:`xmlparser <aria.core.xmlparser>`, :mod:`xmlutils <aria.core.xmlutils>`
-
-Reference
----------
\ No newline at end of file
diff --git a/docs/api/aria.core.scientific.PDB.rst b/docs/api/aria.core.scientific.PDB.rst
index ad7ab08f6ddbae0dbab9f73e1c0065c7367e9bfb..7509269295d6b83ba0b777dac068fec046815051 100644
--- a/docs/api/aria.core.scientific.PDB.rst
+++ b/docs/api/aria.core.scientific.PDB.rst
@@ -7,7 +7,7 @@ aria.core.scientific.PDB module
.. currentmodule:: aria.core.scientific.PDB
.. automodule:: aria.core.scientific.PDB
- :members: AminoAcidResidue, Atom, Chain, DummyChain, Group, HetAtom, Molecule, NucleotideChain, NucleotideResidue, PDBFile, PeptideChain, Residue, ResidueNumber, Structure, defineAminoAcidResidue, defineNucleicAcidResidue
+ :members: AminoAcidResidue, Atom, Chain, DummyChain, Group, HetAtom, Molecule, NucleotideChain, NucleotideResidue, PDBFile, PeptideChain, Residue, ResidueNumber, Structure, amino_acids, defineAminoAcidResidue, defineNucleicAcidResidue, nucleic_acids
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -43,6 +43,14 @@ Functions:
defineAminoAcidResidue
defineNucleicAcidResidue
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ amino_acids
+ nucleic_acids
+
diff --git a/docs/api/aria.core.xmlparser.rst b/docs/api/aria.core.xmlparser.rst
index 5983bbad78f64b1fc75bb9783184399f7c861d95..6dc577209ada0a008e7adef8d3ac08f82b5805b2 100644
--- a/docs/api/aria.core.xmlparser.rst
+++ b/docs/api/aria.core.xmlparser.rst
@@ -7,7 +7,7 @@ aria.core.xmlparser module
.. currentmodule:: aria.core.xmlparser
.. automodule:: aria.core.xmlparser
- :members: SelfmadeXMLParser, quote
+ :members: ATTRIBUTE, ATTRIBUTE_VALUE, CHAR, CHAR_DATA, COMMENT, DECLARATION_SEPARATOR, DIGIT, DOCTYPE_DECLARATION, EMPTY_ELEMENT, ENCODING_DECLARATION, ENCODING_NAME, END_TAG, EQUALS, EXTERNAL_ID, ILLEGALCHARS, LETTER, MARKUP_DECLARATION, MISCELLANEOUS, NAME, NAMECHAR, NO, NOT_CHAR_DATA, OPTIONAL_SPACE, PROLOG, SPACE, STANDALONE_DECLARATION, START_TAG, SYSTEM_LITERAL, SelfmadeXMLParser, VERSION_INFO, VERSION_NUMBER, XML_DECLARATION, YES, quote
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -29,6 +29,44 @@ Functions:
quote
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ ATTRIBUTE
+ ATTRIBUTE_VALUE
+ CHAR
+ CHAR_DATA
+ COMMENT
+ DECLARATION_SEPARATOR
+ DIGIT
+ DOCTYPE_DECLARATION
+ EMPTY_ELEMENT
+ ENCODING_DECLARATION
+ ENCODING_NAME
+ END_TAG
+ EQUALS
+ EXTERNAL_ID
+ ILLEGALCHARS
+ LETTER
+ MARKUP_DECLARATION
+ MISCELLANEOUS
+ NAME
+ NAMECHAR
+ NO
+ NOT_CHAR_DATA
+ OPTIONAL_SPACE
+ PROLOG
+ SPACE
+ STANDALONE_DECLARATION
+ START_TAG
+ SYSTEM_LITERAL
+ VERSION_INFO
+ VERSION_NUMBER
+ XML_DECLARATION
+ YES
+
diff --git a/docs/api/aria.core.xmlutils.rst b/docs/api/aria.core.xmlutils.rst
index 2f62dc6c545d224d53c11801adbc3c204617bb3b..7335c756d74942c313336dfb69bebab816011fd5 100644
--- a/docs/api/aria.core.xmlutils.rst
+++ b/docs/api/aria.core.xmlutils.rst
@@ -7,7 +7,7 @@ aria.core.xmlutils module
.. currentmodule:: aria.core.xmlutils
.. automodule:: aria.core.xmlutils
- :members: BaseReader, ContentConverter, ContentHandler, XMLBasePickler, XMLContentHandler, XMLDocument, XMLElement, XMLPickler, XMLReader, XMLReaderError, XMLTagError
+ :members: BaseReader, ContentConverter, ContentHandler, XMLBasePickler, XMLContentHandler, XMLDocument, XMLElement, XMLPickler, XMLReader, XMLReaderError, XMLTagError, safe_elt
:undoc-members:
:show-inheritance:
:member-order: bysource
@@ -38,6 +38,13 @@ Classes:
XMLPickler
XMLReader
+Functions:
+
+.. autosummary::
+ :nosignatures:
+
+ safe_elt
+
diff --git a/docs/api/aria.rst b/docs/api/aria.rst
index 9b489fd23c436b067258265c36b517fc3347cf8d..491e2d46092809ef536556928117be8a51213712 100644
--- a/docs/api/aria.rst
+++ b/docs/api/aria.rst
@@ -5,7 +5,7 @@ aria package
============
.. automodule:: aria
- :members: get_version
+ :members: VERSION_RE, get_version
:undoc-members:
:show-inheritance:
@@ -37,6 +37,13 @@ Functions:
get_version
+Data:
+
+.. autosummary::
+ :nosignatures:
+
+ VERSION_RE
+
diff --git a/docs/changelog.rst b/docs/changelog.rst
index 4ccd5096370565eb279899ef8f2fc8a9671ef913..83d7eb5298269dbbad95019ca1772734b58bad5d 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -1,4 +1,4 @@
Changelog
=========
-.. include:: ../CHANGELOG
+.. mdinclude:: ../CHANGELOG.md
diff --git a/docs/conf.py b/docs/conf.py
index 480148574f440b0b225a0f8ce82d5513e3a45da1..f7335cb4022145b5521ff60d9a1a2514b5e09041 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -84,17 +84,26 @@ def get_version(full=True):
# -- Generate API documentation ------------------------------------------------
-def run_apidoc(_):
+def run_apidoc(app):
"""Generage API documentation"""
import better_apidoc
- better_apidoc.main(
- ['better-apidoc', '-t', './_templates', '--force', '--no-toc', '-E',
- '--separate', '-o', './api', '../aria', '../*test*',
- '../aria/aria2.py', '../aria/check.py'])
+ better_apidoc.APP = app
+ better_apidoc.main([
+ 'better-apidoc',
+ '-t',
+ os.path.join('.', '_templates'),
+ '--force',
+ '--no-toc',
+ '--separate',
+ '-o',
+ os.path.join('.', 'api'),
+ os.path.join('..', 'src', 'aria'),
+ ])
-def setup(app):
- app.connect('builder-inited', run_apidoc)
+# TODO: Doesnt works
+# def setup(app):
+# app.connect('builder-inited', run_apidoc)
# -- General configuration ------------------------------------------------
@@ -117,6 +126,7 @@ extensions = [
'sphinx.ext.inheritance_diagram',
'numpydoc',
'sphinx.ext.intersphinx',
+ 'm2r',
# 'sphinx.ext.nbsphinx'
]
@@ -131,9 +141,9 @@ autosummary_generate = True
# source_suffix = ['.rst', '.md']
source_suffix = ['.rst', '.md']
-source_parsers = {
- '.md': 'recommonmark.parser.CommonMarkParser',
-}
+# source_parsers = {
+# '.md': 'recommonmark.parser.CommonMarkParser',
+# }
# The master toctree document.
master_doc = 'index'
diff --git a/docs/configuration.rst b/docs/configuration.rst
index 7f57e85af769a40eede92a52c4ca1959ee0c3dbe..1f7a365a9a746ec3a0c3f79ee6e3b5f0c199a550 100644
--- a/docs/configuration.rst
+++ b/docs/configuration.rst
@@ -28,23 +28,23 @@ main
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Name | Type | Default | Description |
+==========================+======+==========================================================================================+=================================================================================================================================================================+
-| ss_dist_file | path | :download:`ss_dist.txt <../aria/conbox/data/ss_dist.txt>` | Distances between stable secondary structures. Those distances are used to make supplementary distance restraints related to secondary structure predictions. |
+| ss_dist_file | path | :download:`ss_dist.txt <../src/aria/conbox/data/ss_dist.txt>` | Distances between stable secondary structures. Those distances are used to make supplementary distance restraints related to secondary structure predictions. |
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| scsc_min_file | path | :download:`scsc_min.p <../aria/conbox/data/scsc_min.p>` | |
+| scsc_min_file | path | :download:`scsc_min.p <../src/aria/conbox/data/scsc_min.p>` | |
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| interlowerbounds_pdbstat | path | :download:`lowerbounds.inter.p <../aria/conbox/data/pdbdists/lowerbounds.inter.p>` | |
+| interlowerbounds_pdbstat | path | :download:`lowerbounds.inter.p <../src/aria/conbox/data/pdbdists/lowerbounds.inter.p>` | |
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| intertarget_pdbstat | path | :download:`targetdists.inter.p <../aria/conbox/data/pdbdists/targetdists.inter.p>` | |
+| intertarget_pdbstat | path | :download:`targetdists.inter.p <../src/aria/conbox/data/pdbdists/targetdists.inter.p>` | |
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| interupperbounds_pdbstat | path | :download:`upperbounds.inter.p <../aria/conbox/data/pdbdists/upperbounds.inter.p>` | |
+| interupperbounds_pdbstat | path | :download:`upperbounds.inter.p <../src/aria/conbox/data/pdbdists/upperbounds.inter.p>` | |
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| intralowerbounds_pdbstat | path | :download:`lowerbounds.intra.p <../aria/conbox/data/pdbdists/lowerbounds.intra.p>` | |
+| intralowerbounds_pdbstat | path | :download:`lowerbounds.intra.p <../src/aria/conbox/data/pdbdists/lowerbounds.intra.p>` | |
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| intratarget_pdbstat | path | :download:`targetdists.intra.p <../aria/conbox/data/pdbdists/targetdists.intra.p>` | |
+| intratarget_pdbstat | path | :download:`targetdists.intra.p <../src/aria/conbox/data/pdbdists/targetdists.intra.p>` | |
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| intraupperbounds_pdbstat | path | :download:`upperbounds.intra.p <../aria/conbox/data/pdbdists/upperbounds.intra.p>` | |
+| intraupperbounds_pdbstat | path | :download:`upperbounds.intra.p <../src/aria/conbox/data/pdbdists/upperbounds.intra.p>` | |
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ariaproject_template | str | :download:`2.3.6 <../aria/conbox/templates/aria_project_v2.3.6.xml>` | |
+| ariaproject_template | str | :download:`2.3.6 <../src/aria/conbox/templates/aria_project_v2.3.6.xml>` | |
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procheck_executable | path | ``None`` | |
+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
diff --git a/docs/contents.rst b/docs/contents.rst
index 52d2f28f5d8cde74bff524accae7a1052b7c8da0..4e7e833e11b4517781612af047571e69f1908b19 100644
--- a/docs/contents.rst
+++ b/docs/contents.rst
@@ -8,20 +8,11 @@
usage
contributing
-.. toctree::
- :maxdepth: 4
- :caption: API
-
- Core package <api/aria.core>
- Conbox package <api/aria.conbox>
-
.. toctree::
:maxdepth: 2
:caption: Tutorial
- tutorial/setup
- tutorial/run
- tutorial/analysis
+ tutorial
.. toctree::
:maxdepth: 2
@@ -29,3 +20,11 @@
examples/bpt1/bpt1
examples/malecoli/malecoli
+
+.. toctree::
+ :maxdepth: 4
+ :caption: API
+
+ Core package <api/aria.core>
+ Conbox package <api/aria.conbox>
+
diff --git a/docs/examples/bpt1/bpt1.rst b/docs/examples/bpt1/bpt1.rst
index 113342db06d7237236ec0a8613b2272ea77dab9f..4b327ffad95b70defe68ec3144f33d73549c0ddc 100644
--- a/docs/examples/bpt1/bpt1.rst
+++ b/docs/examples/bpt1/bpt1.rst
@@ -15,48 +15,50 @@ can be found in the ``docs`` folder or :download:`here <../../examples.tar.gz>`.
Contact map analysis
--------------------
+**Input**
+
.. code-block:: console
- > ariaec -o examples/bpt1/out maplot examples/bpt1/data/BPT1_BOVIN.fa examples/bpt1/data/BPT1_BOVIN.indextableplus examples/bpt1/data/BPT1_BOVIN.native.aligned.pdb examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out -t pdb gremlin
+ (venv) [user@host examples] > ariaec maplot bpt1/data/BPT1_BOVIN.fa bpt1/data/BPT1_BOVIN.indextableplus bpt1/data/BPT1_BOVIN.native.aligned.pdb bpt1/data/BPT1_BOVIN_contacts.gremlin.out -o bpt1/out -t pdb gremlin
**Output**
.. code-block:: console
- ================================================================================
-
- ARIA Evolutive Contact toolbox
-
- ================================================================================
+ ================================================================================
+
+ ARIA Evolutive Contact toolbox
+
+ ================================================================================
+
+ INFO Initialize settings
+ INFO Making output directories
+ INFO Reading fasta file /c7/home/fallain/tmp/bpt1/data/bpt1_bovin.fa
+ INFO Amino acid sequence: FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
+ INFO Checking if file /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
+ INFO Format type correct (indextableplus)
+ INFO Reading secondary structure file /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus]
+ INFO Loading ss dist file
+ INFO Reading distance file /c7/home/fallain/.conda/envs/aria/lib/python2.7/site-packages/aria/conbox/data/ss_dist.txt
+ INFO Align secondary structure sequence with protein sequence
+ INFO Reading /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN.native.aligned.pdb file
+ INFO Updating distance map with pdb file
+ INFO Generate contact map using contact definition defaultdict(None, {'default_cutoff': 8.0})
+ INFO Using default cutoff
+ INFO Reading /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file
+ INFO Pdb map set as reference
+ INFO Generate contact map plot (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN.maplot.pdf)
+ INFO Generate map report file (/c7/home/fallain/tmp/bpt1/out/mapreport)
+ INFO Generate roc file (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.csv)
+ INFO Generate roc plot (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.pdf)
+ INFO Generate precall file (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.csv)
+ INFO Generate precall plot (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.precall.pdf)
+ INFO Generate contact file (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN_contacts_gremlin.contact.txt)
+ INFO Generate stat file (/c7/home/fallain/tmp/bpt1/out/maplot.contactcmp.csv)
+ INFO Contact list: [(1, 39), (1, 42), (1, 51), (3, 22), (3, 25), (3, 45), (3, 47), (3, 51), (4, 23), (4, 38), (4, 39), (4, 42), (4, 49), (5, 23), (6, 19), (7, 37), (8, 12), (8, 31), (8, 33), (9, 19), (9, 34), (9, 37), (9, 41), (10, 33), (10, 36), (11, 33), (11, 35), (12, 8), (12, 20), (12, 31), (12, 33), (13, 33), (13, 34), (14, 31), (14, 33), (14, 36), (15, 31), (16, 29), (16, 31), (17, 41), (17, 43), (18, 28), (18, 29), (18, 45), (19, 6), (19, 9), (19, 28), (19, 29), (20, 12), (20, 25), (20, 27), (21, 28), (22, 3), (22, 25), (22, 28), (23, 4), (23, 5), (23, 26), (23, 29), (23, 43), (24, 28), (25, 3), (25, 20), (25, 22), (25, 28), (25, 46), (25, 53), (26, 23), (27, 20), (27, 48), (27, 52), (28, 18), (28, 19), (28, 21), (28, 22), (28, 24), (28, 25), (29, 16), (29, 18), (29, 19), (29, 23), (30, 33), (30, 37), (30, 38), (31, 8), (31, 12), (31, 14), (31, 15), (31, 16), (32, 37), (32, 38), (32, 40), (32, 41), (33, 8), (33, 10), (33, 11), (33, 12), (33, 13), (33, 14), (33, 30), (34, 9), (34, 13), (34, 37), (35, 11), (36, 10), (36, 14), (36, 39), (36, 50), (37, 7), (37, 9), (37, 30), (37, 32), (37, 34), (37, 41), (38, 4), (38, 30), (38, 32), (38, 41), (39, 1), (39, 4), (39, 36), (40, 32), (41, 9), (41, 17), (41, 32), (41, 37), (41, 38), (42, 1), (42, 4), (43, 17), (43, 23), (43, 47), (44, 47), (45, 3), (45, 18), (45, 49), (46, 25), (46, 49), (46, 50), (47, 3), (47, 43), (47, 44), (47, 51), (48, 27), (48, 52), (49, 4), (49, 45), (49, 46), (49, 53), (50, 36), (50, 46), (50, 53), (51, 1), (51, 3), (51, 47), (52, 27), (52, 48), (53, 25), (53, 49), (53, 50)]
+ INFO Generate contact map plot (/c7/home/fallain/tmp/bpt1/out/.maplot.pdf)
+ INFO Generate contact file (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN_native_aligned.contact.txt)
- INFO Initialize settings
- INFO Making output directories
- reading FASTA file examples/bpt1/data/BPT1_BOVIN.fa
- INFO Amino acid sequence: FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
- INFO Checking if file examples/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
- INFO Format type correct (indextableplus)
- INFO Reading secondary structure file examples/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus]
- INFO Loading ss dist file
- INFO Reading distance file ss_dist.txt
- INFO Align secondary structure sequence with protein sequence
- INFO Reader focused on file(s) ['examples/bpt1/data/BPT1_BOVIN.native.aligned.pdb', 'examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out'] ['pdb', 'gremlin']
- INFO Reading examples/bpt1/data/BPT1_BOVIN.native.aligned.pdb file
- INFO Updating distance map with pdb file
- INFO Generate contact map using contact definition defaultdict(None, {'bool': None, 'default_cutoff': 8.0})
- INFO Using default cutoff
- INFO Reading examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file
- INFO Pdb map set as reference
- INFO Generate contact map plot (examples/bpt1/out/BPT1_BOVIN.maplot.pdf)
- INFO Generate contact file (examples/bpt1/out/BPT1_BOVIN_native_aligned.contact.txt)
- INFO Generate map report file (examples/bpt1/out/mapreport)
- INFO Generate roc file (examples/bpt1/out/graphics/maplot.roc.csv)
- INFO Generate roc plot (examples/bpt1/out/graphics/maplot.roc.pdf)
- INFO Generate precall file (examples/bpt1/out/graphics/maplot.roc.csv)
- INFO Generate precall plot (examples/bpt1/out/graphics/maplot.precall.pdf)
- INFO Generate contact file (examples/bpt1/out/BPT1_BOVIN_contacts_gremlin.contact.txt)
- INFO Generate stat file (examples/bpt1/out/maplot.contactcmp.csv)
- INFO Contact list: [(1, 39), (1, 42), (1, 51), (3, 22), (3, 25), (3, 45), (3, 47), (3, 51), (4, 23), (4, 38), (4, 39), (4, 42), (4, 49), (5, 23), (6, 19), (7, 37), (8, 12), (8, 31), (8, 33), (9, 19), (9, 34), (9, 37), (9, 41), (10, 33), (10, 36), (11, 33), (11, 35), (12, 8), (12, 20), (12, 31), (12, 33), (13, 33), (13, 34), (14, 31), (14, 33), (14, 36), (15, 31), (16, 29), (16, 31), (17, 41), (17, 43), (18, 28), (18, 29), (18, 45), (19, 6), (19, 9), (19, 28), (19, 29), (20, 12), (20, 25), (20, 27), (21, 28), (22, 3), (22, 25), (22, 28), (23, 4), (23, 5), (23, 26), (23, 29), (23, 43), (24, 28), (25, 3), (25, 20), (25, 22), (25, 28), (25, 46), (25, 53), (26, 23), (27, 20), (27, 48), (27, 52), (28, 18), (28, 19), (28, 21), (28, 22), (28, 24), (28, 25), (29, 16), (29, 18), (29, 19), (29, 23), (30, 33), (30, 37), (30, 38), (31, 8), (31, 12), (31, 14), (31, 15), (31, 16), (32, 37), (32, 38), (32, 40), (32, 41), (33, 8), (33, 10), (33, 11), (33, 12), (33, 13), (33, 14), (33, 30), (34, 9), (34, 13), (34, 37), (35, 11), (36, 10), (36, 14), (36, 39), (36, 50), (37, 7), (37, 9), (37, 30), (37, 32), (37, 34), (37, 41), (38, 4), (38, 30), (38, 32), (38, 41), (39, 1), (39, 4), (39, 36), (40, 32), (41, 9), (41, 17), (41, 32), (41, 37), (41, 38), (42, 1), (42, 4), (43, 17), (43, 23), (43, 47), (44, 47), (45, 3), (45, 18), (45, 49), (46, 25), (46, 49), (46, 50), (47, 3), (47, 43), (47, 44), (47, 51), (48, 27), (48, 52), (49, 4), (49, 45), (49, 46), (49, 53), (50, 36), (50, 46), (50, 53), (51, 1), (51, 3), (51, 47), (52, 27), (52, 48), (53, 25), (53, 49), (53, 50)]
- INFO Generate contact map plot (examples/bpt1/out/.maplot.pdf)
Setup
diff --git a/docs/examples/malecoli/malecoli.rst b/docs/examples/malecoli/malecoli.rst
index 71339281ec4a6f9602d07fcfa44919913120c234..bbb9b2500f1e72be357b84fd300b7d2f9b7f9d04 100644
--- a/docs/examples/malecoli/malecoli.rst
+++ b/docs/examples/malecoli/malecoli.rst
@@ -18,7 +18,7 @@ Setup
.. code-block:: console
- > ariaec -o examples/malecoli/out -c examples/malecoli/data/config.ini setup examples/malecoli/data/MALE_ECOLI.fa examples/malecoli/data/MALE_ECOLI_contacts.evfold.out -t plmev -p examples/malecoli/data/ariaproject_nmr.xml
+ > ariaec setup examples/malecoli/data/MALE_ECOLI.fa examples/malecoli/data/MALE_ECOLI_contacts.evfold.out -t plmev -o examples/malecoli/out -c examples/malecoli/data/config.ini -p examples/malecoli/data/ariaproject_nmr.xml
**Output**
diff --git a/docs/index.rst b/docs/index.rst
index d513a86adebe4e1a43234ccab03170c5db80d14a..e411e4f21808cd44d29dd251983d969b39725a4e 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -40,13 +40,17 @@ Quick Start
Be sure to check if the following packages are correctly installed with
your python installation or virtual environment.
-* **pip** (>= 9.0)
-* **setuptools** (>= 18.0)
-* **numpy** (>= 1.11)
+* **pip** (>= 18.0)
+* **git** (>= 2.0)
+* **cns-solve** (1.21)
+* **ccpnmr analysis** (optional)
+* **ccpn data model** (optional)
Then the easiest solution is to call the **pip** command below :
- ``pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec``
+.. code-block:: shell
+
+ pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec
.. warning::
@@ -66,7 +70,7 @@ suggestions or bug report.
License
-------
-.. include:: ../COPYRIGHT
+.. mdinclude:: ../COPYRIGHT.md
.. include:: contents.rst
diff --git a/docs/installation.rst b/docs/installation.rst
index 3aec28e5e22aa3438a48da984ed898bfef009881..6512966d94aea58c010ce90deec656902c63adaa 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -1,10 +1,13 @@
-Linux installation
-==================
+============
+Installation
+============
.. note::
- Installation procedure may change in the future especially after the
- transition to Python 3 which should be the next major update.
+ For the moment, ``ariaec`` Command Line Interface (CLI) is only compatible
+ for **Python 2.7** but the transition to Python 3 is planned in the near
+ future. Installation procedure may change in the future especially after
+ the transition to **Python 3** which should be the next major update.
.. warning::
@@ -13,96 +16,136 @@ Linux installation
instruction before using ``aria2`` pipeline.
Dependencies
-------------
+============
Before starting the installation procedure, be sure to check if dependencies
-below are actually correctly installed in your environment.
+below are actually correctly installed.
-* **pip** (>= 9.0)
-* **setuptools** (>= 18.0)
-* **numpy**`` (>= 1.11)
+* **pip** (>= 18.0)
+* **git** (>= 2.0)
* **cns-solve** (1.21)
* **ccpnmr analysis** (optional)
* **ccpn data model** (optional)
CNS-solve
-+++++++++
-
-The only piece of Fortran code that needs to be compiled together with your
-CNS sources can be found in ./cns/src; only the code for floating
-chirality assignment is being used. The installation procedure has not
-changed since ARIA version 1.2:
-
-a) Academic users can obtain a free version of CNS from the CNS web site:
-
- http://cns.csb.yale.edu
-
- Commercial users need to purchase a CNX license from Accelrys (MSI).
-
-b) The ARIA fortran sources are located in the subdirectory ./cns/src of
- the distribution. Please copy all the files to the directory
- cns_solve_1.1/source of the unpacked cns_solve distribution (this will
- overwrite some files which is okay).
-
-c) Edit the file "cns_solve_env" in the directory cns_solve_1.1 to define the
- location of the CNSsolve directory.
-
-d) Go to directory cns_solve_1.1 and type "make install". This should start
- the compilation process.
+---------
+Academic users can obtain a free version of CNS from the `CNS web site
+<http://cns.csb.yale.edu>`_. Commercial users need to purchase a CNX license
+from Accelrys (MSI).
CCPNMR
-++++++
+------
In order to use the CCPN data model for import/export or data conversion, you
also need to install the CCPN data model, and the CCPNMR Analysis software in
case you want to export restraint lists, NOE assignments, and analyses of the
generated structures, e.g. the result of the violation analysis. The complete
CCPN distribution including the API, the FormatConverter, and CCPNMR Analysis
-can be obtained :ref:`here <http://www.ccpn.ac.uk/ccpn/software/downloads-v2/>`_
+can be obtained `here <http://www.ccpn.ac.uk/ccpn/software/downloads-v2/>`_.
The CCPN distribution provides scripts which guide you through the
installation process.
+Virtual environments
+====================
-Using pip
----------
+The usual installation process is to install the package inside a virtual
+environment for `Python <https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/>`_.
+In order to create a virtual environment, we need an environment manager like
+``virtualenv`` (or ``venv`` if we use Python 3) with the package manager
+``pip``. Another possibility is to use the `conda CLI
+<https://docs.conda.io/projects/conda/en/latest/commands.html#id2>`_ from the
+`Anaconda Python distribution <https://www.anaconda.com/distribution/>`_ which
+is a package and an environment manager.
-The recommended installation process is to use an up to date ``pip`` command with
-the last ``ariaec`` version. For the moment, the packages used Python 2.7 but
-the transition to Python 3 is planned in the near future.
+.. note::
-Then the easiest solution is to call the command below :
+ This step is optional but strongly recommended in order to avoid overlaps
+ between Python packages already installed in your global/local environment.
- ``pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec``
+virtualenv
+----------
-From source
------------
+To install the latest stable release, do the following steps on your terminal :
+
+1. Install or update `pip` and `virtualenv` in your current python environment
+
+.. code-block:: shell
+
+ python -m pip install --user --upgrade pip virtualenv
+
+2. Go to your project directory and create a virtual environment by giving the
+name of a directory to place the new virtual environment (e.g. `venv`).
+
+.. code-block:: shell
+
+ python -m virtualenv venv
+
+3. Activate the new environment.
+
+.. code-block:: shell
+
+ source venv/bin/activate
+
+.. note::
+ With this procedure, you will need to activate the environment before any
+ call to ``ariaec`` CLI with ``source venv/bin/activate``
+
+conda
+-----
+
+If you have Anaconda distribution instead of , you can use ``conda`` can perform the same operations as ``virtualenv``.
+
+1. Create an environment
+
+.. code-block:: shell
+
+ conda create --name ariaec python=2.7
+
+2. Activate the environment
+
+.. code-block:: shell
+
+ source activate ariaec
+
+
+Python Package Index
+====================
-Even though it is not recommanded, another possibility is to download the ZIP_
-or TAR_ version from Gitlab_, extract the files and run ``pip`` inside the new
-directory.
+Since ``ariaec`` is hosted on gitlab, we will use ``pip`` with ``git`` in order
+to install the package.
-Download
-++++++++
+.. code-block:: shell
+
+ pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec
+
+.. note::
+
+ If you don't use a virtual environment for Python, it is recommemded to use
+ the flag ``--user`` in order to install ``ariaec`` to the Python user
+ install directory (typically ``~/.local`` folder)
+
+From source
+===========
-ZIP_ or TAR_ version can be downloaded from Gitlab_ website or by command line
+Another possibility is to download the ZIP_ or TAR_ version from Gitlab_ and use
+the following steps to install the package.
+
+1. Download ZIP_ or TAR_ version from Gitlab_ website or through command line
.. code-block:: shell
wget -O ariaec-master.tar.gz https://gitlab.pasteur.fr/bis-aria/ariaec/repository/master/archive.tar.gz
mkdir ariaec-master && tar xzf ariaec-master.tar.gz -C ariaec-master --strip-components 1
-Local installation
-++++++++++++++++++
-
-You can then call ``pip`` locally to install the package in your environment.
+2. You can then call ``pip`` locally to install the package in your environment.
.. code-block:: shell
cd ariaec-master
- mkdir build_aria && cp -r aria setup.py PKG-INFO MANIFEST.in build_aria/
+ mkdir build_aria && cp -r src setup.py PKG-INFO MANIFEST.in build_aria/
cd build_aria
pip install --user .
@@ -112,13 +155,13 @@ You can then call ``pip`` locally to install the package in your environment.
Local pip install may lead to unexpected computation time if your directory
contains more than the ARIA package. In most cases, this is due to
virtualenv folders within the same directory. In those situations,
- the :command:`pip` command will also look into virtualenvs folders. A simple
+ the `pip` command will also look into virtualenvs folders. A simple
workaround to solve this issue is to create a empty folder for the
- installation as described below.
+ installation as described above.
Singularity
------------
+===========
For the sake of reproductibility, a Singularity_ recipe is also available
allowing cross platform and legacy OS support.
@@ -128,7 +171,7 @@ allowing cross platform and legacy OS support.
sudo singularity build aria.simg aria.shub
-The :abbr:`Command Line Interface (CLI)` described in :doc:`usage` section will
+The CLI described in [usage](usage.rst) section will
then be accessible by calling the generated singularity image.
.. code-block:: shell
@@ -136,25 +179,40 @@ then be accessible by calling the generated singularity image.
singularity run aria.simg COMMAND
Dockerfile
-----------
+==========
-Developers can also build their own Docker container using the ``Dockerfile``
-in the ``aria`` directory [1]_.
+Developers can also build their own Docker container using the Dockerfile_ [1]_.
Post installation instructions
==============================
+ARIA CNS
+--------
+
+The only piece of Fortran code that needs to be compiled together with your
+CNS sources can be found in `src/aria/cns/src`. Only the code for floating
+chirality assignment is being used. The procedure has not changed since ARIA
+version 1.2 :
+
+1. Please copy all the ARIA fortran files located in the subdirectory
+``src/aria/cns/src`` to the directory
+``cns_solve_1.1/source`` of the unpacked cns_solve distribution
+(this will overwrite some files which is okay).
+2. Edit the file ``cns_solve_env`` in the directory ``cns_solve_1.1`` to define
+the location of the CNSsolve directory.
+3. Go to the directory ``cns_solve_1.1`` and type ``make install``. This should
+start the compilation process.
-
.. Footnotes
.. [1] In order to build it, you have to be root on your computer.
.. Hyperlinks
+.. _Dockerfile: https://gitlab.pasteur.fr/bis-aria/ariaec/raw/master/Dockerfile?inline=false
.. _ZIP: https://gitlab.pasteur.fr/bis-aria/ariaec/repository/master/archive.zip
.. _TAR: https://gitlab.pasteur.fr/bis-aria/ariaec/repository/master/archive.tar
.. _Gitlab: https://gitlab.pasteur.fr/bis-aria/ariaec
diff --git a/docs/tutorial.rst b/docs/tutorial.rst
new file mode 100644
index 0000000000000000000000000000000000000000..35343ceec604a13f581592ac2e50e2346947bc05
--- /dev/null
+++ b/docs/tutorial.rst
@@ -0,0 +1,39 @@
+=========
+Workflows
+=========
+
+Structure calculation with EC restraints
+========================================
+
+The ``ariaec`` Command Line Interface (CLI) is the main tool for
+converting and analyze contact map information. The main command of this
+interface is ``ariaec setup`` which create an ARIA project XML file. Then we can
+follow the usual steps for an ARIA project.
+
+
+Configuration file
+------------------
+
+All the parameters for ``ariaec`` commands are encapsulated on a configuration
+file in INI format. Each time you need to overwrite the default parameters,
+another configuration file can be used with the updated parameters. There is
+no need to give all the parameters in order to have a correct configuration
+file.
+
+
+
+A more detailed description of the parameters is in :doc:`configuration`
+section.
+
+
+Restraints & project conversion
+-------------------------------
+
+
+Build infrastructure
+--------------------
+
+
+Running ARIA
+============
+
diff --git a/docs/usage.rst b/docs/usage.rst
index b8a21546c72d65ff67fe8da434325bb2a17b2214..9151d3e92933b1248c3314bccf764ac228a4022d 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -17,35 +17,38 @@ ARIAEC
.. code-block:: shell
- ariaec [-h] -o OUTPUT_DIRECTORY [-c CONF_FILE] [--nolog] [-d] COMMAND
+ ariaec COMMAND ARGS [OPTIONS]
**Commands**
.. rst-class:: table-hover
+.. list-table::
+ :header-rows: 1
+ :widths: 25 60
+
+ * - Name
+ - Short Description
+ * - `setup <Setup_>`_
+ - Setup ARIA project with EC data
+ * - `bbconv <BBconv_>`_
+ - Translate BBcontacts as distance restraints
+ * - `maplot <Maplot_>`_
+ - Contact map visualisation tool
+ * - `pdbqual <PDBQual_>`_
+ - Call PDB quality tools
+ * - `analysis <Analysis_>`_
+ - Analyze results from an ARIA project
+ * - `tbl2xml <TBL2XML_>`_
+ - Convert TBL restraints in ARIA XML format
+ * - `pdbdist <PDBDist_>`_
+ - Extract distance from a culled list of PDBs
+ * - `pdbstat <PDBStat_>`_
+ - Statistical analysis of ``pdbdist`` results
+ * - `iniconv <Iniconv_>`_
+ - Convert a INI file as csv for easy readability
-+-------------------------+-----------------------------------------------------+
-| Name | Short description |
-+=========================+=====================================================+
-| `setup <Setup_>`_ | Setup ARIA project with EC data |
-+-------------------------+-----------------------------------------------------+
-| `bbconv <BBconv_>`_ | Translate BBcontacts as distance restraints |
-+-------------------------+-----------------------------------------------------+
-| `maplot <Maplot_>`_ | Contact map visualisation tool |
-+-------------------------+-----------------------------------------------------+
-| `pdbqual <PDBQual_>`_ | Call PDB quality tools |
-+-------------------------+-----------------------------------------------------+
-| `analysis <Analysis_>`_ | Analyze results from an ARIA project |
-+-------------------------+-----------------------------------------------------+
-| `tbl2xml <TBL2XML_>`_ | Convert TBL restraints in ARIA XML format |
-+-------------------------+-----------------------------------------------------+
-| `pdbdist <PDBDist_>`_ | Extract distance from a culled list of PDBs |
-+-------------------------+-----------------------------------------------------+
-| `pdbstat <PDBStat_>`_ | Statistical analysis of ``pdbdist`` results |
-+-------------------------+-----------------------------------------------------+
-| `iniconv <Iniconv_>`_ | Convert a INI file as csv for easy readability |
-+-------------------------+-----------------------------------------------------+
**Options**
@@ -53,43 +56,38 @@ ARIAEC
.. rst-class:: table-hover
+.. list-table::
+ :header-rows: 1
+ :widths: 25 60
-+--------------------------------------------------------+-----------------------------------------------------+
-| Name | Description |
-+========================================================+=====================================================+
-| ``-h``, ``--help`` | show help message and exit |
-+--------------------------------------------------------+-----------------------------------------------------+
-| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None) |
-+--------------------------------------------------------+-----------------------------------------------------+
-| ``-c CONF_FILE``, ``--conf CONF_FILE`` | configuration file (default: None) |
-+--------------------------------------------------------+-----------------------------------------------------+
-| ``--nolog`` | Don't generate log files (default: False) |
-+--------------------------------------------------------+-----------------------------------------------------+
-| ``-d``, ``--debug`` | Increase output verbosity (default: False) |
-+--------------------------------------------------------+-----------------------------------------------------+
-
+ * - Name
+ - Short Description
+ * - ``-h``, ``--help``
+ - show help message and exit
Setup
+++++
-Translate contact maps as distance restraints and setup ARIA infrastructure.
+Translate contact maps as distance restraints and initialize a new ARIA XML project.
.. code-block:: shell
- ariaec setup [-options] seq infile [infile ...] -t intype [intype ...]
+ ariaec setup SEQFILE INFILE [INFILE ...] -o OUTPUT_DIRECTORY [OPTIONS] -t INTYPE [INTYPE ...]
**Arguments**
.. rst-class:: table-hover
+.. list-table::
+ :header-rows: 1
+ :widths: 25 60
-+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| Name | Short description |
-+=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
-| ``seq`` | Sequence file [``FASTA``] |
-+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``infile [infile ...]`` | Contact or pdb file(s) used to build aria distance restraints |
-+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+ * - Name
+ - Short Description
+ * - ``seq``
+ - Sequence file [``FASTA``]
+ * - ``infile [infile ...]``
+ - Contact or pdb file(s) used to build aria distance restraints
.. _ConKit: http://www.conkit.org/en/latest/
@@ -99,33 +97,49 @@ Translate contact maps as distance restraints and setup ARIA infrastructure.
.. rst-class:: table-hover
-
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| Name | Description |
-+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
-| ``-t intype [intype ...]`` | Contact Map file format:sup:`*` |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-d DISTFILE``, ``--distfile DISTFILE`` | Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-s SSPRED``, ``--ssfile SSPRED`` | Secondary structure prediction file |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-p ARIAPROJECT``, ``--ariaproject ARIAPROJECT`` | ARIA project file. This project will be updated with data generated during the ``ariaec setup`` call |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-r SEQRANGE``, ``--range SEQRANGE`` | Index range if we don't want tu use the whole sequence and map |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-n REF``, ``--native REF`` | Native pdb. Allow TP/FP detection |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``--hb HB`` | H-bonds contact file (eg: metapsicov.hb) |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``--ssidx`` | Use secondary structure index |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``--no-filter`` | Do not filter contact map |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``--extract-all`` | Extract data or all data and parameters if an ARIA project is defined with ``-p`` option |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| :sup:`*` Accepted contact map formats combining formats supported by ConKit_ with few supplementary formats: ``gremlin``, ``pconsc1``, ``pconsc3``, ``pconsc2``, ``bbcontacts``, ``metapsicov_stg1``, ``membrain``, ``metapsicovhb``, ``comsat``, ``casprr``, ``ccmpred``, ``plm``, ``bclcontact``, ``epcmap``, ``evfold``, ``native``, ``pconsc``, ``psicov``, ``freecontact``, ``genericstructure``, ``ncont``, ``plmc``, ``plmdca``, ``metapsicov_stg2``, ``native_full``, ``metapsicov``, ``evcoupling``, ``contactlist``, ``plmev``, ``mmcif``, ``casp``, ``pdb``, ``flib`` |
-+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-
+.. list-table::
+ :header-rows: 1
+ :widths: 25 60
+
+ * - Name
+ - Short Description
+ * - ``-h``, ``--help``
+ - show help message and exit
+ * - ``-d``, ``--debug``
+ - Increase output verbosity (default: False)
+ * - ``--nolog``
+ - Don't generate log files (default: False)
+ * - ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY``
+ - Output directory (default: None)
+ * - ``-c CONF_FILE``, ``--conf CONF_FILE``
+ - configuration file (default: None)
+ * - ``-t intype [intype ...]``
+ - Contact Map file format:sup:`*`
+ * - ``-d DISTFILE``, ``--distfile DISTFILE``
+ - Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints
+ * - ``-s SSPRED``, ``--ssfile SSPRED``
+ - Secondary structure prediction file. Supported formats are psipred, psipred2, psipred3, ss2 and indextableplus
+ * - ``-p ARIAPROJECT``, ``--ariaproject ARIAPROJECT``
+ - ARIA project file. This project will be updated with data generated during the ``ariaec setup`` call
+ * - ``-r SEQRANGE``, ``--range SEQRANGE``
+ - Index range if we don't want tu use the whole sequence and map
+ * - ``-n REF``, ``--native REF``
+ - Native pdb. Allow TP/FP detection
+ * - ``--hb HB``
+ - H-bonds contact file (eg: metapsicov.hb)
+ * - ``--no-filter``
+ - Do not filter contact map
+ * - ``--extract-all``
+ - Extract data or all data and parameters if an ARIA project is defined with ``-p`` option
+ * - ``--ssidx``
+ - :sup:`*` Accepted contact map formats combining formats supported by ConKit_ with few supplementary formats: ``gremlin``, ``pconsc1``, ``pconsc3``, ``pconsc2``, ``bbcontacts``, ``metapsicov_stg1``, ``membrain``, ``metapsicovhb``, ``comsat``, ``casprr``, ``ccmpred``, ``plm``, ``bclcontact``, ``epcmap``, ``evfold``, ``native``, ``pconsc``, ``psicov``, ``freecontact``, ``genericstructure``, ``ncont``, ``plmc``, ``plmdca``, ``metapsicov_stg2``, ``native_full``, ``metapsicov``, ``evcoupling``, ``contactlist``, ``plmev``, ``mmcif``, ``casp``, ``pdb``, ``flib``
+
+
+.. warning::
+
+ The contact map format option needs to have the same number of format that
+ the number of contact of pdb files. Since this is a greedy option, it needs
+ to be at the end of the command in order to work correctly.
Bbconv
++++++
@@ -134,7 +148,7 @@ Translate BBcontacts as distance restraints which can be used during
.. code-block:: shell
- ariaec bbconv [-h] contactfile sspred seq [msa] -t contactype
+ ariaec bbconv CONTACTFILE SSPRED SEQ [MSA] [OPTIONS] -t CONTACTYPE
**Arguments**
@@ -161,6 +175,14 @@ Translate BBcontacts as distance restraints which can be used during
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Name | Description |
+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
+| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-c CONF_FILE``, ``--conf CONF_FILE`` | configuration file (default: None) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``--nolog`` | Don't generate log files (default: False) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-d``, ``--debug`` | Increase output verbosity (default: False) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-t intype`` | Contact Map file format:sup:`*` |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| :sup:`*` Accepted contact map formats combining formats supported by ConKit_ with few supplementary formats: ``gremlin``, ``pconsc1``, ``pconsc3``, ``pconsc2``, ``bbcontacts``, ``metapsicov_stg1``, ``membrain``, ``metapsicovhb``, ``comsat``, ``casprr``, ``ccmpred``, ``plm``, ``bclcontact``, ``epcmap``, ``evfold``, ``native``, ``pconsc``, ``psicov``, ``freecontact``, ``genericstructure``, ``ncont``, ``plmc``, ``plmdca``, ``metapsicov_stg2``, ``native_full``, ``metapsicov``, ``evcoupling``, ``contactlist``, ``plmev``, ``mmcif``, ``casp``, ``pdb``, ``flib`` |
@@ -175,7 +197,7 @@ Contactmap analysis and visualisation tool.
.. code-block:: shell
- ariaec maplot [-h] [--filter] [--onlyreport] [--no-filter] [--ssidx] [--prefix] [--prefixname PREFIXNAME] seq sspred infile [infile ...] -t intype [intype ...] --merge mergetype [mergetype ...]
+ ariaec maplot SEQ SSPRED INFILE [INFILE ...] [OPTIONS] -t INTYPE [INTYPE ...] --merge MERGETYPE [MERGETYPE ...]
**Arguments**
@@ -198,6 +220,14 @@ Contactmap analysis and visualisation tool.
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Name | Description |
+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
+| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-c CONF_FILE``, ``--conf CONF_FILE`` | configuration file (default: None) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``--nolog`` | Don't generate log files (default: False) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-d``, ``--debug`` | Increase output verbosity (default: False) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-t intype [intype ...]`` | Contact Map file format:sup:`*` |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--merge mergetype [mergetype ...]`` | Merge given contact types with other maps |
@@ -249,6 +279,14 @@ Supplementary analysis results for a specific iteration from an ARIA project.
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Name | Description |
+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
+| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-c CONF_FILE``, ``--conf CONF_FILE`` | configuration file (default: None) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``--nolog`` | Don't generate log files (default: False) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-d``, ``--debug`` | Increase output verbosity (default: False) |
++--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-r REF, --ref REF`` | Native pdb. Allow TP/FP detection. |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-d RESTRAINT`` | Distance restraint file (XML) used for violation analysis. Otherwise, use restraints of the current iteration |
diff --git a/package.json b/package.json
index 903d2fd4183768b52d819d5e53f1f034c50514dc..a37f4ddd3b7433b047791e92c9f02b191a57f6b9 100644
--- a/package.json
+++ b/package.json
@@ -1,16 +1,15 @@
{
"name": "ariaec",
- "version": "0.0.18",
+ "version": "0.0.21",
"description": "===================================================== de Novo Ambiguous Restraints for Iterative Assignment =====================================================",
"main": "index.js",
"directories": {
"doc": "docs"
},
"scripts": {
- "precommit": "conventional-changelog -i CHANGELOG -s -r 0",
+ "precommit": "conventional-changelog -p angular -i CHANGELOG.md -s -r 0 && git add CHANGELOG.md",
"test": "echo \"Error: no test specified\" && exit 1",
- "commitmsg": "commitlint -e $GIT_PARAMS",
- "changelog": "conventional-changelog -i CHANGELOG -s -r 0"
+ "commitmsg": "commitlint -e $GIT_PARAMS"
},
"repository": {
"type": "git",
@@ -24,5 +23,9 @@
"husky": "^0.14.3",
"standard-version": "^4.3.0"
},
- "dependencies": {}
+ "dependencies": {
+ "@hutson/semantic-delivery-gitlab": "^9.0.4",
+ "conventional-changelog-angular": "^5.0.3",
+ "conventional-changelog-cli": "^2.0.21"
+ }
}
diff --git a/setup.py b/setup.py
index a8a07facc2f1cbb19f7ef3d1a34c1714892a8a82..96e990d6cf8b2c8cbd55241093016ab6bd4034d2 100644
--- a/setup.py
+++ b/setup.py
@@ -203,45 +203,57 @@ def setup_package():
},
classifiers=[_f for _f in CLASSIFIERS.split('\n') if _f],
platforms=["Linux", "Solaris", "Mac OS-X", "Unix"],
+ python_requires='>=2.7,<3.0.*',
setup_requires=[
# Setuptools 18.0 properly handles Cython extensions.
'setuptools>=18.0',
- 'cython',
- 'pytest-runner'
+ 'cython==0.28.2',
+ 'numpy==1.16.0',
+ 'biopython==1.73',
+ 'scipy<1.3.0',
+ 'matplotlib<3.0',
+ 'pytest-runner',
+ 'networkx==2.2',
+ ],
+ tests_requires=[
+ 'pytest<=4.6',
+ 'pytest-cov<=2.7'
],
- tests_requires=['pytest', 'pytest-cov'],
# Project uses reStructuredText, so ensure that the docutils get
# installed or upgraded on the target machine
install_requires=[
- 'future',
+ 'future==0.17.1',
'setuptools>=18.0',
- 'cython',
+ 'cython==0.28.2',
+ 'numpy==1.16.0',
+ 'matplotlib<3.0',
'docutils>=0.3',
'six>=1.10',
- 'Sphinx',
+ 'Sphinx<1.8',
'sphinx_rtd_theme',
+ 'm2r<=0.2.1',
# 'sphinx_bootstrap_theme',
# 'sphinxcontrib-napoleon',
'configparser',
'mako',
- 'biopython>=1.69',
- 'scipy>= 0.9',
- 'pandas',
+ 'pandas<=0.24',
'seaborn',
- 'sklearn',
+ 'scikit-learn<=0.20',
'colorlog',
'mako',
- 'pbxplore',
+ # TODO: Solve the issue with pbxplore
+ #'pbxplore',
'pathos',
'tqdm',
- 'hdbscan',
- 'conkit',
+ 'hdbscan==0.8.18',
+ 'conkit==0.11.2',
# 'nbsphinx',
'recommonmark',
'numpydoc',
'better_apidoc',
'requests[security]',
# 'scikit-bio' Doesn't works with python 2.7. Only 3.4 +
+ 'MDAnalysis<0.19'
],
entry_points={
'console_scripts': [
@@ -252,8 +264,8 @@ def setup_package():
},
# bin folder is normally for non python code that could be executed
# directly on terminal (bash scripts, ...)
- scripts=['aria/aria2.py',
- 'aria/check.py'],
+ scripts=['src/aria/aria2.py',
+ 'src/aria/check.py'],
# Force setuptools to unzip in order to access data files with pkgutil
# since pkg_resources don't like relative paths in zipped egg dir :/
# TODO: solution to enable zip_safe
@@ -266,7 +278,9 @@ def setup_package():
# to respect pep recommandations. Non data files can be includes outside
# the package with data_files key (non data files are not accessible by
# the package after the installation)
- # package_dir={
+ package_dir={
+ '': 'src'
+ },
# '': 'src/py',
# 'aria': 'src/py/aria',
# 'aria.cns': 'cns',
@@ -279,7 +293,9 @@ def setup_package():
# 'aria.src.xml': 'src/xml',
# 'aria.src.csh': 'src/csh'},
- packages=find_packages(exclude=("examples*",)),
+ packages=find_packages("src", exclude=("docs*",)),
+ # Line below works for Python 3 only
+ # packages=find_namespace_packages(where='src'),
# Install any data files found in the package
include_package_data=True,
@@ -317,7 +333,7 @@ def setup_package():
setup(**metadata)
-for package in ('pip>=9.0', 'setuptools>=18.0', 'numpy>=1.11.0', 'matplotlib'):
+for package in ('pip>=9.0', 'setuptools>=18.0', 'numpy>=1.11.0', 'matplotlib<3.0'):
if not is_installed(package):
print(textwrap.dedent("""
Installation needs {package}. You can install it via:
diff --git a/aria/__init__.py b/src/aria/__init__.py
similarity index 100%
rename from aria/__init__.py
rename to src/aria/__init__.py
diff --git a/aria/aria2.py b/src/aria/aria2.py
similarity index 98%
rename from aria/aria2.py
rename to src/aria/aria2.py
index 808524b38e29b6666ce24ee1e9b39fcfdbda783e..7d5a71225e8c66a47025bda3e389958614a0b6f6 100644
--- a/aria/aria2.py
+++ b/src/aria/aria2.py
@@ -29,10 +29,11 @@
"""
from __future__ import absolute_import, division, print_function
from future.builtins import input
-from aria.core.ariabase import get_aria_root, ARIA_ENV
+from aria.core.ariabase import get_aria_root, ARIA_ENV, LOG_CONF
import os
import sys
+import logging
# ARIA_ENV = 'ARIA2'
@@ -349,6 +350,8 @@ Conversion:
actual conversion.
'''
+LOG = logging.getLogger(__name__)
+
def print_sequence(data):
"""
@@ -517,9 +520,8 @@ def welcome():
"""
import aria.core.ariabase as ariabase
- message = \
- """
-ARIA Version %s. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
+ message = """\
+ARIA Version {0}. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.
If you use this software, please quote the following reference(s):
@@ -527,8 +529,8 @@ If you use this software, please quote the following reference(s):
Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR
structure calculation. Bioinformatics 23:381-382
-"""
- print(message % ariabase.AriaBaseClass().get_version_string())
+""".format(ariabase.AriaBaseClass().get_version_string())
+ return message
def check_python():
@@ -1011,13 +1013,16 @@ def run_aria(project_file, log_file=None, debug=0, test_commands=1,
try:
log_file = os.path.expanduser(log_file)
- f = open(log_file, 'w')
+ # f = open(log_file, 'w')
except Exception as msg:
- print(msg)
- print('Could not create log-file: %s', log_file)
- f = None
-
- AriaBaseClass.log_file = f
+ LOG.exception(msg)
+ # print(msg)
+ # print('Could not create log-file: %s', log_file)
+ # f = None
+
+ # AriaBaseClass.log_file = f
+ # Update logging out files
+ LOG_CONF.up_outfiles(log_file)
if debug:
from aria.core.TypeChecking import check_type
diff --git a/aria/ariacns.py b/src/aria/ariacns.py
similarity index 100%
rename from aria/ariacns.py
rename to src/aria/ariacns.py
diff --git a/aria/check.py b/src/aria/check.py
similarity index 100%
rename from aria/check.py
rename to src/aria/check.py
diff --git a/aria/cns/protocols/analysis/cop.inp b/src/aria/cns/protocols/analysis/cop.inp
similarity index 100%
rename from aria/cns/protocols/analysis/cop.inp
rename to src/aria/cns/protocols/analysis/cop.inp
diff --git a/aria/cns/protocols/analysis/energy.inp b/src/aria/cns/protocols/analysis/energy.inp
similarity index 100%
rename from aria/cns/protocols/analysis/energy.inp
rename to src/aria/cns/protocols/analysis/energy.inp
diff --git a/aria/cns/protocols/analysis/ensemble_rmsd.inp b/src/aria/cns/protocols/analysis/ensemble_rmsd.inp
similarity index 100%
rename from aria/cns/protocols/analysis/ensemble_rmsd.inp
rename to src/aria/cns/protocols/analysis/ensemble_rmsd.inp
diff --git a/aria/cns/protocols/analysis/minimize.inp b/src/aria/cns/protocols/analysis/minimize.inp
similarity index 100%
rename from aria/cns/protocols/analysis/minimize.inp
rename to src/aria/cns/protocols/analysis/minimize.inp
diff --git a/aria/cns/protocols/analysis/noe_violations.inp b/src/aria/cns/protocols/analysis/noe_violations.inp
similarity index 100%
rename from aria/cns/protocols/analysis/noe_violations.inp
rename to src/aria/cns/protocols/analysis/noe_violations.inp
diff --git a/aria/cns/protocols/analysis/print_coup.inp b/src/aria/cns/protocols/analysis/print_coup.inp
similarity index 100%
rename from aria/cns/protocols/analysis/print_coup.inp
rename to src/aria/cns/protocols/analysis/print_coup.inp
diff --git a/aria/cns/protocols/analysis/print_dih.inp b/src/aria/cns/protocols/analysis/print_dih.inp
similarity index 100%
rename from aria/cns/protocols/analysis/print_dih.inp
rename to src/aria/cns/protocols/analysis/print_dih.inp
diff --git a/aria/cns/protocols/analysis/print_geom.inp b/src/aria/cns/protocols/analysis/print_geom.inp
similarity index 100%
rename from aria/cns/protocols/analysis/print_geom.inp
rename to src/aria/cns/protocols/analysis/print_geom.inp
diff --git a/aria/cns/protocols/analysis/print_noes.inp b/src/aria/cns/protocols/analysis/print_noes.inp
similarity index 100%
rename from aria/cns/protocols/analysis/print_noes.inp
rename to src/aria/cns/protocols/analysis/print_noes.inp
diff --git a/aria/cns/protocols/analysis/print_sani.inp b/src/aria/cns/protocols/analysis/print_sani.inp
similarity index 100%
rename from aria/cns/protocols/analysis/print_sani.inp
rename to src/aria/cns/protocols/analysis/print_sani.inp
diff --git a/aria/cns/protocols/analysis/rmsave.inp b/src/aria/cns/protocols/analysis/rmsave.inp
similarity index 100%
rename from aria/cns/protocols/analysis/rmsave.inp
rename to src/aria/cns/protocols/analysis/rmsave.inp
diff --git a/aria/cns/protocols/analysis/rmsd.inp b/src/aria/cns/protocols/analysis/rmsd.inp
similarity index 100%
rename from aria/cns/protocols/analysis/rmsd.inp
rename to src/aria/cns/protocols/analysis/rmsd.inp
diff --git a/aria/cns/protocols/analysis/rotares.cns b/src/aria/cns/protocols/analysis/rotares.cns
similarity index 100%
rename from aria/cns/protocols/analysis/rotares.cns
rename to src/aria/cns/protocols/analysis/rotares.cns
diff --git a/aria/cns/protocols/analysis/wellordered.inp b/src/aria/cns/protocols/analysis/wellordered.inp
similarity index 100%
rename from aria/cns/protocols/analysis/wellordered.inp
rename to src/aria/cns/protocols/analysis/wellordered.inp
diff --git a/aria/cns/protocols/boxtyp20.pdb b/src/aria/cns/protocols/boxtyp20.pdb
similarity index 100%
rename from aria/cns/protocols/boxtyp20.pdb
rename to src/aria/cns/protocols/boxtyp20.pdb
diff --git a/aria/cns/protocols/define_methyls_all.cns b/src/aria/cns/protocols/define_methyls_all.cns
similarity index 100%
rename from aria/cns/protocols/define_methyls_all.cns
rename to src/aria/cns/protocols/define_methyls_all.cns
diff --git a/aria/cns/protocols/define_methyls_ini.cns b/src/aria/cns/protocols/define_methyls_ini.cns
similarity index 100%
rename from aria/cns/protocols/define_methyls_ini.cns
rename to src/aria/cns/protocols/define_methyls_ini.cns
diff --git a/aria/cns/protocols/dmso.pdb b/src/aria/cns/protocols/dmso.pdb
similarity index 100%
rename from aria/cns/protocols/dmso.pdb
rename to src/aria/cns/protocols/dmso.pdb
diff --git a/aria/cns/protocols/era_2.dat b/src/aria/cns/protocols/era_2.dat
similarity index 100%
rename from aria/cns/protocols/era_2.dat
rename to src/aria/cns/protocols/era_2.dat
diff --git a/aria/cns/protocols/era_3.dat b/src/aria/cns/protocols/era_3.dat
similarity index 100%
rename from aria/cns/protocols/era_3.dat
rename to src/aria/cns/protocols/era_3.dat
diff --git a/aria/cns/protocols/era_4.dat b/src/aria/cns/protocols/era_4.dat
similarity index 100%
rename from aria/cns/protocols/era_4.dat
rename to src/aria/cns/protocols/era_4.dat
diff --git a/aria/cns/protocols/era_5.dat b/src/aria/cns/protocols/era_5.dat
similarity index 100%
rename from aria/cns/protocols/era_5.dat
rename to src/aria/cns/protocols/era_5.dat
diff --git a/aria/cns/protocols/expected_newdb.tbl b/src/aria/cns/protocols/expected_newdb.tbl
similarity index 100%
rename from aria/cns/protocols/expected_newdb.tbl
rename to src/aria/cns/protocols/expected_newdb.tbl
diff --git a/aria/cns/protocols/flags_new.cns b/src/aria/cns/protocols/flags_new.cns
similarity index 100%
rename from aria/cns/protocols/flags_new.cns
rename to src/aria/cns/protocols/flags_new.cns
diff --git a/aria/cns/protocols/force_newdb.tbl b/src/aria/cns/protocols/force_newdb.tbl
similarity index 100%
rename from aria/cns/protocols/force_newdb.tbl
rename to src/aria/cns/protocols/force_newdb.tbl
diff --git a/aria/cns/protocols/freezn.cns b/src/aria/cns/protocols/freezn.cns
similarity index 100%
rename from aria/cns/protocols/freezn.cns
rename to src/aria/cns/protocols/freezn.cns
diff --git a/aria/cns/protocols/generate.inp b/src/aria/cns/protocols/generate.inp
similarity index 100%
rename from aria/cns/protocols/generate.inp
rename to src/aria/cns/protocols/generate.inp
diff --git a/aria/cns/protocols/generate_dmso.cns b/src/aria/cns/protocols/generate_dmso.cns
similarity index 100%
rename from aria/cns/protocols/generate_dmso.cns
rename to src/aria/cns/protocols/generate_dmso.cns
diff --git a/aria/cns/protocols/generate_rigid_template.inp b/src/aria/cns/protocols/generate_rigid_template.inp
similarity index 100%
rename from aria/cns/protocols/generate_rigid_template.inp
rename to src/aria/cns/protocols/generate_rigid_template.inp
diff --git a/aria/cns/protocols/generate_template.inp b/src/aria/cns/protocols/generate_template.inp
similarity index 100%
rename from aria/cns/protocols/generate_template.inp
rename to src/aria/cns/protocols/generate_template.inp
diff --git a/aria/cns/protocols/generate_water.cns b/src/aria/cns/protocols/generate_water.cns
similarity index 100%
rename from aria/cns/protocols/generate_water.cns
rename to src/aria/cns/protocols/generate_water.cns
diff --git a/aria/cns/protocols/hbdb_files.dat b/src/aria/cns/protocols/hbdb_files.dat
similarity index 100%
rename from aria/cns/protocols/hbdb_files.dat
rename to src/aria/cns/protocols/hbdb_files.dat
diff --git a/aria/cns/protocols/hbdb_files.datbis b/src/aria/cns/protocols/hbdb_files.datbis
similarity index 100%
rename from aria/cns/protocols/hbdb_files.datbis
rename to src/aria/cns/protocols/hbdb_files.datbis
diff --git a/aria/cns/protocols/hbpot_xyz2_left.dat b/src/aria/cns/protocols/hbpot_xyz2_left.dat
similarity index 100%
rename from aria/cns/protocols/hbpot_xyz2_left.dat
rename to src/aria/cns/protocols/hbpot_xyz2_left.dat
diff --git a/aria/cns/protocols/hbpot_xyz2_right.dat b/src/aria/cns/protocols/hbpot_xyz2_right.dat
similarity index 100%
rename from aria/cns/protocols/hbpot_xyz2_right.dat
rename to src/aria/cns/protocols/hbpot_xyz2_right.dat
diff --git a/aria/cns/protocols/hbpot_xyz3_left.dat b/src/aria/cns/protocols/hbpot_xyz3_left.dat
similarity index 100%
rename from aria/cns/protocols/hbpot_xyz3_left.dat
rename to src/aria/cns/protocols/hbpot_xyz3_left.dat
diff --git a/aria/cns/protocols/hbpot_xyz3_right.dat b/src/aria/cns/protocols/hbpot_xyz3_right.dat
similarity index 100%
rename from aria/cns/protocols/hbpot_xyz3_right.dat
rename to src/aria/cns/protocols/hbpot_xyz3_right.dat
diff --git a/aria/cns/protocols/hbpot_xyz4_centN.dat b/src/aria/cns/protocols/hbpot_xyz4_centN.dat
similarity index 100%
rename from aria/cns/protocols/hbpot_xyz4_centN.dat
rename to src/aria/cns/protocols/hbpot_xyz4_centN.dat
diff --git a/aria/cns/protocols/hbpot_xyz4_isolC.dat b/src/aria/cns/protocols/hbpot_xyz4_isolC.dat
similarity index 100%
rename from aria/cns/protocols/hbpot_xyz4_isolC.dat
rename to src/aria/cns/protocols/hbpot_xyz4_isolC.dat
diff --git a/aria/cns/protocols/hbpot_xyz5_beta_anti_cent.dat b/src/aria/cns/protocols/hbpot_xyz5_beta_anti_cent.dat
similarity index 100%
rename from aria/cns/protocols/hbpot_xyz5_beta_anti_cent.dat
rename to src/aria/cns/protocols/hbpot_xyz5_beta_anti_cent.dat
diff --git a/aria/cns/protocols/hbpot_xyz5_beta_anti_edge.dat b/src/aria/cns/protocols/hbpot_xyz5_beta_anti_edge.dat
similarity index 100%
rename from aria/cns/protocols/hbpot_xyz5_beta_anti_edge.dat
rename to src/aria/cns/protocols/hbpot_xyz5_beta_anti_edge.dat
diff --git a/aria/cns/protocols/hbpot_xyz5_beta_para_cent.dat b/src/aria/cns/protocols/hbpot_xyz5_beta_para_cent.dat
similarity index 100%
rename from aria/cns/protocols/hbpot_xyz5_beta_para_cent.dat
rename to src/aria/cns/protocols/hbpot_xyz5_beta_para_cent.dat
diff --git a/aria/cns/protocols/hbpot_xyz5_beta_para_edge.dat b/src/aria/cns/protocols/hbpot_xyz5_beta_para_edge.dat
similarity index 100%
rename from aria/cns/protocols/hbpot_xyz5_beta_para_edge.dat
rename to src/aria/cns/protocols/hbpot_xyz5_beta_para_edge.dat
diff --git a/aria/cns/protocols/hbpot_xyz5_non_beta.dat b/src/aria/cns/protocols/hbpot_xyz5_non_beta.dat
similarity index 100%
rename from aria/cns/protocols/hbpot_xyz5_non_beta.dat
rename to src/aria/cns/protocols/hbpot_xyz5_non_beta.dat
diff --git a/aria/cns/protocols/logn_auto_weight.cns b/src/aria/cns/protocols/logn_auto_weight.cns
similarity index 100%
rename from aria/cns/protocols/logn_auto_weight.cns
rename to src/aria/cns/protocols/logn_auto_weight.cns
diff --git a/aria/cns/protocols/newsymmetry.cns b/src/aria/cns/protocols/newsymmetry.cns
similarity index 100%
rename from aria/cns/protocols/newsymmetry.cns
rename to src/aria/cns/protocols/newsymmetry.cns
diff --git a/aria/cns/protocols/print_coorheader.cns b/src/aria/cns/protocols/print_coorheader.cns
similarity index 100%
rename from aria/cns/protocols/print_coorheader.cns
rename to src/aria/cns/protocols/print_coorheader.cns
diff --git a/aria/cns/protocols/print_coorheader_auto.cns b/src/aria/cns/protocols/print_coorheader_auto.cns
similarity index 100%
rename from aria/cns/protocols/print_coorheader_auto.cns
rename to src/aria/cns/protocols/print_coorheader_auto.cns
diff --git a/aria/cns/protocols/read_data.cns b/src/aria/cns/protocols/read_data.cns
similarity index 100%
rename from aria/cns/protocols/read_data.cns
rename to src/aria/cns/protocols/read_data.cns
diff --git a/aria/cns/protocols/refine.inp b/src/aria/cns/protocols/refine.inp
similarity index 100%
rename from aria/cns/protocols/refine.inp
rename to src/aria/cns/protocols/refine.inp
diff --git a/aria/cns/protocols/refine_OLD.inp b/src/aria/cns/protocols/refine_OLD.inp
similarity index 100%
rename from aria/cns/protocols/refine_OLD.inp
rename to src/aria/cns/protocols/refine_OLD.inp
diff --git a/aria/cns/protocols/refine_dmso.inp b/src/aria/cns/protocols/refine_dmso.inp
similarity index 100%
rename from aria/cns/protocols/refine_dmso.inp
rename to src/aria/cns/protocols/refine_dmso.inp
diff --git a/aria/cns/protocols/refine_water.inp b/src/aria/cns/protocols/refine_water.inp
similarity index 100%
rename from aria/cns/protocols/refine_water.inp
rename to src/aria/cns/protocols/refine_water.inp
diff --git a/aria/cns/protocols/sa_l_cool1.cns b/src/aria/cns/protocols/sa_l_cool1.cns
similarity index 100%
rename from aria/cns/protocols/sa_l_cool1.cns
rename to src/aria/cns/protocols/sa_l_cool1.cns
diff --git a/aria/cns/protocols/sa_l_hightemp.cns b/src/aria/cns/protocols/sa_l_hightemp.cns
similarity index 100%
rename from aria/cns/protocols/sa_l_hightemp.cns
rename to src/aria/cns/protocols/sa_l_hightemp.cns
diff --git a/aria/cns/protocols/sa_l_randomchain.cns b/src/aria/cns/protocols/sa_l_randomchain.cns
similarity index 100%
rename from aria/cns/protocols/sa_l_randomchain.cns
rename to src/aria/cns/protocols/sa_l_randomchain.cns
diff --git a/aria/cns/protocols/sa_l_reduced.cns b/src/aria/cns/protocols/sa_l_reduced.cns
similarity index 100%
rename from aria/cns/protocols/sa_l_reduced.cns
rename to src/aria/cns/protocols/sa_l_reduced.cns
diff --git a/aria/cns/protocols/sa_ls_cool2.cns b/src/aria/cns/protocols/sa_ls_cool2.cns
similarity index 100%
rename from aria/cns/protocols/sa_ls_cool2.cns
rename to src/aria/cns/protocols/sa_ls_cool2.cns
diff --git a/aria/cns/protocols/sa_ltad_cool1.cns b/src/aria/cns/protocols/sa_ltad_cool1.cns
similarity index 100%
rename from aria/cns/protocols/sa_ltad_cool1.cns
rename to src/aria/cns/protocols/sa_ltad_cool1.cns
diff --git a/aria/cns/protocols/sa_ltad_hightemp4.cns b/src/aria/cns/protocols/sa_ltad_hightemp4.cns
similarity index 100%
rename from aria/cns/protocols/sa_ltad_hightemp4.cns
rename to src/aria/cns/protocols/sa_ltad_hightemp4.cns
diff --git a/aria/cns/protocols/sa_rc_hightemp.cns b/src/aria/cns/protocols/sa_rc_hightemp.cns
similarity index 100%
rename from aria/cns/protocols/sa_rc_hightemp.cns
rename to src/aria/cns/protocols/sa_rc_hightemp.cns
diff --git a/aria/cns/protocols/setup_newdb2.tbl b/src/aria/cns/protocols/setup_newdb2.tbl
similarity index 100%
rename from aria/cns/protocols/setup_newdb2.tbl
rename to src/aria/cns/protocols/setup_newdb2.tbl
diff --git a/aria/cns/protocols/setup_swap_init.cns b/src/aria/cns/protocols/setup_swap_init.cns
similarity index 100%
rename from aria/cns/protocols/setup_swap_init.cns
rename to src/aria/cns/protocols/setup_swap_init.cns
diff --git a/aria/cns/protocols/swap.cns b/src/aria/cns/protocols/swap.cns
similarity index 100%
rename from aria/cns/protocols/swap.cns
rename to src/aria/cns/protocols/swap.cns
diff --git a/aria/cns/protocols/torsiontop.cns b/src/aria/cns/protocols/torsiontop.cns
similarity index 100%
rename from aria/cns/protocols/torsiontop.cns
rename to src/aria/cns/protocols/torsiontop.cns
diff --git a/aria/cns/protocols/write_symnoe.cns b/src/aria/cns/protocols/write_symnoe.cns
similarity index 100%
rename from aria/cns/protocols/write_symnoe.cns
rename to src/aria/cns/protocols/write_symnoe.cns
diff --git a/aria/cns/protocols/write_symnoe2.cns b/src/aria/cns/protocols/write_symnoe2.cns
similarity index 100%
rename from aria/cns/protocols/write_symnoe2.cns
rename to src/aria/cns/protocols/write_symnoe2.cns
diff --git a/aria/cns/protocols/xplortodiana3.inp b/src/aria/cns/protocols/xplortodiana3.inp
similarity index 100%
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rename to src/aria/cns/protocols/xplortodiana3.inp
diff --git a/aria/cns/src/README b/src/aria/cns/src/README
similarity index 100%
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rename to src/aria/cns/src/README
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similarity index 100%
rename from aria/cns/src/aria.f
rename to src/aria/cns/src/aria.f
diff --git a/aria/cns/src/aria.inc b/src/aria/cns/src/aria.inc
similarity index 100%
rename from aria/cns/src/aria.inc
rename to src/aria/cns/src/aria.inc
diff --git a/aria/cns/src/ariass.f b/src/aria/cns/src/ariass.f
similarity index 100%
rename from aria/cns/src/ariass.f
rename to src/aria/cns/src/ariass.f
diff --git a/aria/cns/src/aribac.f b/src/aria/cns/src/aribac.f
similarity index 100%
rename from aria/cns/src/aribac.f
rename to src/aria/cns/src/aribac.f
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similarity index 100%
rename from aria/cns/src/arical.f
rename to src/aria/cns/src/arical.f
diff --git a/aria/cns/src/arivio.f b/src/aria/cns/src/arivio.f
similarity index 100%
rename from aria/cns/src/arivio.f
rename to src/aria/cns/src/arivio.f
diff --git a/aria/cns/src/bonded.f b/src/aria/cns/src/bonded.f
similarity index 100%
rename from aria/cns/src/bonded.f
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rename to src/aria/cns/src/cns.f
diff --git a/aria/cns/src/ener.inc b/src/aria/cns/src/ener.inc
similarity index 100%
rename from aria/cns/src/ener.inc
rename to src/aria/cns/src/ener.inc
diff --git a/aria/cns/src/energy.f b/src/aria/cns/src/energy.f
similarity index 100%
rename from aria/cns/src/energy.f
rename to src/aria/cns/src/energy.f
diff --git a/aria/cns/src/hbdb.f b/src/aria/cns/src/hbdb.f
similarity index 100%
rename from aria/cns/src/hbdb.f
rename to src/aria/cns/src/hbdb.f
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rename from aria/cns/src/hbdb.inc
rename to src/aria/cns/src/hbdb.inc
diff --git a/aria/cns/src/helplib/cns b/src/aria/cns/src/helplib/cns
similarity index 100%
rename from aria/cns/src/helplib/cns
rename to src/aria/cns/src/helplib/cns
diff --git a/aria/cns/src/helplib/cns-aria b/src/aria/cns/src/helplib/cns-aria
similarity index 100%
rename from aria/cns/src/helplib/cns-aria
rename to src/aria/cns/src/helplib/cns-aria
diff --git a/aria/cns/src/helplib/cns-aria-analyse b/src/aria/cns/src/helplib/cns-aria-analyse
similarity index 100%
rename from aria/cns/src/helplib/cns-aria-analyse
rename to src/aria/cns/src/helplib/cns-aria-analyse
diff --git a/aria/cns/src/helplib/cns-aria-calibrate b/src/aria/cns/src/helplib/cns-aria-calibrate
similarity index 100%
rename from aria/cns/src/helplib/cns-aria-calibrate
rename to src/aria/cns/src/helplib/cns-aria-calibrate
diff --git a/aria/cns/src/helplib/cns-aria-countviolations b/src/aria/cns/src/helplib/cns-aria-countviolations
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rename to src/aria/cns/src/helplib/cns-aria-countviolations
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similarity index 100%
rename from aria/cns/src/helplib/cns-aria-do
rename to src/aria/cns/src/helplib/cns-aria-do
diff --git a/aria/cns/src/helplib/cns-aria-equivalent b/src/aria/cns/src/helplib/cns-aria-equivalent
similarity index 100%
rename from aria/cns/src/helplib/cns-aria-equivalent
rename to src/aria/cns/src/helplib/cns-aria-equivalent
diff --git a/aria/cns/src/noe.f b/src/aria/cns/src/noe.f
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diff --git a/aria/cns/src/print.f b/src/aria/cns/src/print.f
similarity index 100%
rename from aria/cns/src/print.f
rename to src/aria/cns/src/print.f
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rename to src/aria/cns/src/susc_anis.f
diff --git a/aria/cns/src/vectangl.f b/src/aria/cns/src/vectangl.f
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diff --git a/aria/cns/toppar/carbohydrate.param b/src/aria/cns/toppar/carbohydrate.param
similarity index 100%
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rename to src/aria/cns/toppar/carbohydrate.param
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similarity index 100%
rename from aria/cns/toppar/carbohydrate.top
rename to src/aria/cns/toppar/carbohydrate.top
diff --git a/aria/cns/toppar/dna-rna-allatom.param b/src/aria/cns/toppar/dna-rna-allatom.param
similarity index 100%
rename from aria/cns/toppar/dna-rna-allatom.param
rename to src/aria/cns/toppar/dna-rna-allatom.param
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rename to src/aria/cns/toppar/dna-rna-allatom.top
diff --git a/aria/cns/toppar/dna-rna-pho.link b/src/aria/cns/toppar/dna-rna-pho.link
similarity index 100%
rename from aria/cns/toppar/dna-rna-pho.link
rename to src/aria/cns/toppar/dna-rna-pho.link
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similarity index 100%
rename from aria/cns/toppar/dna-rna.link
rename to src/aria/cns/toppar/dna-rna.link
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similarity index 100%
rename from aria/cns/toppar/dna-rna.param
rename to src/aria/cns/toppar/dna-rna.param
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similarity index 100%
rename from aria/cns/toppar/dna-rna.top
rename to src/aria/cns/toppar/dna-rna.top
diff --git a/aria/cns/toppar/dna-rna_rep.param b/src/aria/cns/toppar/dna-rna_rep.param
similarity index 100%
rename from aria/cns/toppar/dna-rna_rep.param
rename to src/aria/cns/toppar/dna-rna_rep.param
diff --git a/aria/cns/toppar/ions.link b/src/aria/cns/toppar/ions.link
similarity index 100%
rename from aria/cns/toppar/ions.link
rename to src/aria/cns/toppar/ions.link
diff --git a/aria/cns/toppar/par_axis.pro b/src/aria/cns/toppar/par_axis.pro
similarity index 100%
rename from aria/cns/toppar/par_axis.pro
rename to src/aria/cns/toppar/par_axis.pro
diff --git a/aria/cns/toppar/parallhdg5.0.pro b/src/aria/cns/toppar/parallhdg5.0.pro
similarity index 100%
rename from aria/cns/toppar/parallhdg5.0.pro
rename to src/aria/cns/toppar/parallhdg5.0.pro
diff --git a/aria/cns/toppar/parallhdg5.1.pro b/src/aria/cns/toppar/parallhdg5.1.pro
similarity index 100%
rename from aria/cns/toppar/parallhdg5.1.pro
rename to src/aria/cns/toppar/parallhdg5.1.pro
diff --git a/aria/cns/toppar/parallhdg5.2.pro b/src/aria/cns/toppar/parallhdg5.2.pro
similarity index 100%
rename from aria/cns/toppar/parallhdg5.2.pro
rename to src/aria/cns/toppar/parallhdg5.2.pro
diff --git a/aria/cns/toppar/parallhdg5.3.pro b/src/aria/cns/toppar/parallhdg5.3.pro
similarity index 100%
rename from aria/cns/toppar/parallhdg5.3.pro
rename to src/aria/cns/toppar/parallhdg5.3.pro
diff --git a/aria/cns/toppar/parallhdg5.3.sol b/src/aria/cns/toppar/parallhdg5.3.sol
similarity index 100%
rename from aria/cns/toppar/parallhdg5.3.sol
rename to src/aria/cns/toppar/parallhdg5.3.sol
diff --git a/aria/cns/toppar/parallhdg5.3softbig.pro b/src/aria/cns/toppar/parallhdg5.3softbig.pro
similarity index 100%
rename from aria/cns/toppar/parallhdg5.3softbig.pro
rename to src/aria/cns/toppar/parallhdg5.3softbig.pro
diff --git a/aria/cns/toppar/protein-allhdg-dih-ucl-uu.top b/src/aria/cns/toppar/protein-allhdg-dih-ucl-uu.top
similarity index 100%
rename from aria/cns/toppar/protein-allhdg-dih-ucl-uu.top
rename to src/aria/cns/toppar/protein-allhdg-dih-ucl-uu.top
diff --git a/aria/cns/toppar/protein-allhdg-ucl-uu.param b/src/aria/cns/toppar/protein-allhdg-ucl-uu.param
similarity index 100%
rename from aria/cns/toppar/protein-allhdg-ucl-uu.param
rename to src/aria/cns/toppar/protein-allhdg-ucl-uu.param
diff --git a/aria/cns/toppar/protein-allhdg-ucl.param b/src/aria/cns/toppar/protein-allhdg-ucl.param
similarity index 100%
rename from aria/cns/toppar/protein-allhdg-ucl.param
rename to src/aria/cns/toppar/protein-allhdg-ucl.param
diff --git a/aria/cns/toppar/protein-allhdg-ucl.top b/src/aria/cns/toppar/protein-allhdg-ucl.top
similarity index 100%
rename from aria/cns/toppar/protein-allhdg-ucl.top
rename to src/aria/cns/toppar/protein-allhdg-ucl.top
diff --git a/aria/cns/toppar/protein-allhdg_dih_ucl.top b/src/aria/cns/toppar/protein-allhdg_dih_ucl.top
similarity index 100%
rename from aria/cns/toppar/protein-allhdg_dih_ucl.top
rename to src/aria/cns/toppar/protein-allhdg_dih_ucl.top
diff --git a/aria/cns/toppar/tensor.pdb b/src/aria/cns/toppar/tensor.pdb
similarity index 100%
rename from aria/cns/toppar/tensor.pdb
rename to src/aria/cns/toppar/tensor.pdb
diff --git a/aria/cns/toppar/tensor.psf b/src/aria/cns/toppar/tensor.psf
similarity index 100%
rename from aria/cns/toppar/tensor.psf
rename to src/aria/cns/toppar/tensor.psf
diff --git a/aria/cns/toppar/tensor2.pdb b/src/aria/cns/toppar/tensor2.pdb
similarity index 100%
rename from aria/cns/toppar/tensor2.pdb
rename to src/aria/cns/toppar/tensor2.pdb
diff --git a/aria/cns/toppar/tensor2.psf b/src/aria/cns/toppar/tensor2.psf
similarity index 100%
rename from aria/cns/toppar/tensor2.psf
rename to src/aria/cns/toppar/tensor2.psf
diff --git a/aria/cns/toppar/top_axis.pro b/src/aria/cns/toppar/top_axis.pro
similarity index 100%
rename from aria/cns/toppar/top_axis.pro
rename to src/aria/cns/toppar/top_axis.pro
diff --git a/aria/cns/toppar/topallhdg.pep b/src/aria/cns/toppar/topallhdg.pep
similarity index 100%
rename from aria/cns/toppar/topallhdg.pep
rename to src/aria/cns/toppar/topallhdg.pep
diff --git a/aria/cns/toppar/topallhdg5.0.pro b/src/aria/cns/toppar/topallhdg5.0.pro
similarity index 100%
rename from aria/cns/toppar/topallhdg5.0.pro
rename to src/aria/cns/toppar/topallhdg5.0.pro
diff --git a/aria/cns/toppar/topallhdg5.1.pro b/src/aria/cns/toppar/topallhdg5.1.pro
similarity index 100%
rename from aria/cns/toppar/topallhdg5.1.pro
rename to src/aria/cns/toppar/topallhdg5.1.pro
diff --git a/aria/cns/toppar/topallhdg5.2.pro b/src/aria/cns/toppar/topallhdg5.2.pro
similarity index 100%
rename from aria/cns/toppar/topallhdg5.2.pro
rename to src/aria/cns/toppar/topallhdg5.2.pro
diff --git a/aria/cns/toppar/topallhdg5.3.pep b/src/aria/cns/toppar/topallhdg5.3.pep
similarity index 100%
rename from aria/cns/toppar/topallhdg5.3.pep
rename to src/aria/cns/toppar/topallhdg5.3.pep
diff --git a/aria/cns/toppar/topallhdg5.3.pro b/src/aria/cns/toppar/topallhdg5.3.pro
similarity index 100%
rename from aria/cns/toppar/topallhdg5.3.pro
rename to src/aria/cns/toppar/topallhdg5.3.pro
diff --git a/aria/cns/toppar/topallhdg5.3.sol b/src/aria/cns/toppar/topallhdg5.3.sol
similarity index 100%
rename from aria/cns/toppar/topallhdg5.3.sol
rename to src/aria/cns/toppar/topallhdg5.3.sol
diff --git a/aria/conbox/__init__.py b/src/aria/conbox/__init__.py
similarity index 100%
rename from aria/conbox/__init__.py
rename to src/aria/conbox/__init__.py
diff --git a/aria/conbox/analysis.py b/src/aria/conbox/analysis.py
similarity index 99%
rename from aria/conbox/analysis.py
rename to src/aria/conbox/analysis.py
index f4ddf524f9c82635d5eea7921ef6e3aebf9ca561..637faa0b1a15188d227e86c0fda4fc2a627ed05a 100644
--- a/aria/conbox/analysis.py
+++ b/src/aria/conbox/analysis.py
@@ -191,6 +191,7 @@ class EnsembleAnalysis(object):
dref = None
if dists_ref:
+ # TODO: prendre en compte un gap dans les matrices
try:
dref = [dists_ref(*sp.getAtoms()) for sp in contrib]
dref = np.power(np.sum(np.power(dref, -6.), axis=0),
diff --git a/aria/conbox/commands.py b/src/aria/conbox/commands.py
similarity index 76%
rename from aria/conbox/commands.py
rename to src/aria/conbox/commands.py
index 0fafbb4b4a31b85f79b8462425558f0b5f1ac491..850dcada99824f856db1de73f83c3ecfd473350b 100644
--- a/aria/conbox/commands.py
+++ b/src/aria/conbox/commands.py
@@ -16,7 +16,8 @@ from .maplot import AriaEcContactMap
from .converter import AriaEcBbConverter, AriaEcXMLConverter, \
AriaEcConfigConverter
from .reader import MapFile
-from .pdbdist import PDBDist
+## TODO: Solve dependencie issue with mdanalysis and pbxplore
+#from .pdbdist import PDBDist
from .pdbstat import PDBStat
from .setup import AriaEcSetup
from .pdbqual import AriaEcPdbqual
@@ -156,13 +157,7 @@ class CLI(object):
"""
parser = argp.ArgumentParser(
formatter_class=argp.ArgumentDefaultsHelpFormatter)
- parser.add_argument("-o", "--output", dest="output_directory", type=str,
- help="Output directory", required=True, action=ReadableDir)
- parser.add_argument("--nolog", action="store_true",
- default=False, help="Don't generate log files")
- parser.add_argument("-d", "--debug", dest="verbose", default=False,
- action='store_true',
- help="Increase output verbosity")
+
return parser
# TODO: should be called in child classes .....
@@ -240,7 +235,7 @@ class AriaEcCommands(CLI):
u"Convert configuration files into a unique csv file")
contact_types = set(MapFile.types).union(
- set(CONTACT_FILE_PARSERS))
+ set(CONTACT_FILE_PARSERS)).union(set(MapFile.conkit_alias))
default_confile = "conf/config.ini"
def __init__(self):
@@ -251,9 +246,17 @@ class AriaEcCommands(CLI):
Update default CLI in order to add the confi
"""
parser = super(AriaEcCommands, self)._create_argparser()
- parser.add_argument("-c", "--conf", action=ReadableFile,
- dest="conf_file",
- default=None, help="configuration file")
+ # parser.add_argument("-c", "--conf", action=ReadableFile,
+ # dest="conf_file",
+ # default=None, help="configuration file")
+ # parser.add_argument("-o", "--output", dest="output_directory", type=str,
+ # help="Output directory", required=True,
+ # action=ReadableDir)
+ # parser.add_argument("--nolog", action="store_true",
+ # default=False, help="Don't generate log files")
+ # parser.add_argument("-d", "--debug", dest="verbose", default=False,
+ # action='store_true',
+ # help="Increase output verbosity")
# TODO: not really practical, we HAVE to call line below since every
# subcommand argparser have to be defined in the same scope
self.add_subparsers(parser.add_subparsers(dest="command"))
@@ -279,13 +282,24 @@ class AriaEcCommands(CLI):
# Args
group = parser.add_argument_group('required arguments')
group.add_argument("seq", action=ReadableFile,
- help="sequence file [FASTA]")
+ help="Sequence file [FASTA]")
# group.add_argument("sspred", action=ReadableFile,
# help="secondary structure prediction file")
group.add_argument("infiles", nargs="*", metavar="infile",
action=ReadableFile,
- help="contact or pdb file(s) used to build aria "
+ help="Contact or PDB file(s) used to build ARIA "
"distance restraints")
+ parser.add_argument("-c", "--conf", action=ReadableFile,
+ dest="conf_file",
+ default=None, help="Configuration file")
+ parser.add_argument("-o", "--output", dest="output_directory", type=str,
+ help="Output directory", required=True,
+ action=ReadableDir)
+ parser.add_argument("--nolog", action="store_true",
+ default=False, help="Don't generate log files")
+ parser.add_argument("--debug", dest="verbose", default=False,
+ action='store_true',
+ help="Increase output verbosity")
group.add_argument("-d", "--distfile", dest="distfile",
help="Pdb or distance matrix iif distance_type "
"set to distfile in conf file, "
@@ -298,7 +312,7 @@ class AriaEcCommands(CLI):
action=ReadableFile,
help="ARIA project file used to initialize a new "
"project with contact map data.")
- group.add_argument("-t", "--type",
+ group.add_argument("-t", "--type", required=True,
nargs="*", dest="contact_types",
choices=self.contact_types, help="Infile(s) contact "
"type(s)")
@@ -348,6 +362,17 @@ class AriaEcCommands(CLI):
parser.add_argument("-t", "--type", required=True, dest="contact_type",
choices=self.contact_types, help="Infile contact "
"type")
+ parser.add_argument("-c", "--conf", action=ReadableFile,
+ dest="conf_file",
+ default=None, help="configuration file")
+ parser.add_argument("-o", "--output", dest="output_directory", type=str,
+ help="Output directory", required=True,
+ action=ReadableDir)
+ parser.add_argument("--nolog", action="store_true",
+ default=False, help="Don't generate log files")
+ parser.add_argument("--debug", dest="verbose", default=False,
+ action='store_true',
+ help="Increase output verbosity")
return parser
def _iniconv_argparser(self, desc=None):
@@ -369,6 +394,17 @@ class AriaEcCommands(CLI):
# args
parser.add_argument("confiles", nargs='+',
type=str, help="config files")
+ parser.add_argument("-c", "--conf", action=ReadableFile,
+ dest="conf_file",
+ default=None, help="configuration file")
+ parser.add_argument("-o", "--output", dest="output_directory", type=str,
+ help="Output directory", required=True,
+ action=ReadableDir)
+ parser.add_argument("--nolog", action="store_true",
+ default=False, help="Don't generate log files")
+ parser.add_argument("--debug", dest="verbose", default=False,
+ action='store_true',
+ help="Increase output verbosity")
return parser
def _maplot_argparser(self, desc=None):
@@ -420,6 +456,17 @@ class AriaEcCommands(CLI):
parser.add_argument("--prefixname", dest="prefixname",
default="",
help="Prefix name for file names")
+ parser.add_argument("-c", "--conf", action=ReadableFile,
+ dest="conf_file",
+ default=None, help="configuration file")
+ parser.add_argument("-o", "--output", dest="output_directory", type=str,
+ help="Output directory", required=True,
+ action=ReadableDir)
+ parser.add_argument("--nolog", action="store_true",
+ default=False, help="Don't generate log files")
+ parser.add_argument("--debug", dest="verbose", default=False,
+ action='store_true',
+ help="Increase output verbosity")
return parser
def _pdbqual_argparser(self, desc=None):
@@ -429,6 +476,17 @@ class AriaEcCommands(CLI):
action=ReadableFile,
help="PDB file(s) used to run quality tools with "
"aria API")
+ parser.add_argument("-c", "--conf", action=ReadableFile,
+ dest="conf_file",
+ default=None, help="configuration file")
+ parser.add_argument("-o", "--output", dest="output_directory", type=str,
+ help="Output directory", required=True,
+ action=ReadableDir)
+ parser.add_argument("--nolog", action="store_true",
+ default=False, help="Don't generate log files")
+ parser.add_argument("--debug", dest="verbose", default=False,
+ action='store_true',
+ help="Increase output verbosity")
return parser
def _analysis_argparser(self, desc=None):
@@ -451,6 +509,17 @@ class AriaEcCommands(CLI):
parser.add_argument("-p", "--prefixname", dest="prefixname",
default=None,
help="Prefix name for file names")
+ parser.add_argument("-c", "--conf", action=ReadableFile,
+ dest="conf_file",
+ default=None, help="configuration file")
+ parser.add_argument("-o", "--output", dest="output_directory", type=str,
+ help="Output directory", required=True,
+ action=ReadableDir)
+ parser.add_argument("--nolog", action="store_true",
+ default=False, help="Don't generate log files")
+ parser.add_argument("--debug", dest="verbose", default=False,
+ action='store_true',
+ help="Increase output verbosity")
return parser
def _tbl2xml_argparser(self, desc=None):
@@ -477,6 +546,17 @@ class AriaEcCommands(CLI):
parser.add_argument("infiles", nargs="+", metavar="infile.tbl",
action=ReadableFile,
help="TBL distance restraint file(s)")
+ parser.add_argument("-c", "--conf", action=ReadableFile,
+ dest="conf_file",
+ default=None, help="configuration file")
+ parser.add_argument("-o", "--output", dest="output_directory", type=str,
+ help="Output directory", required=True,
+ action=ReadableDir)
+ parser.add_argument("--nolog", action="store_true",
+ default=False, help="Don't generate log files")
+ parser.add_argument("--debug", dest="verbose", default=False,
+ action='store_true',
+ help="Increase output verbosity")
return parser
def _pdbdist_argparser(self, desc=None):
@@ -510,6 +590,17 @@ class AriaEcCommands(CLI):
"--pdbdir", dest="pdbdir", default='',
metavar="PDB_FOLDER",
help="Folder containing pdb file entries")
+ parser.add_argument("-c", "--conf", action=ReadableFile,
+ dest="conf_file",
+ default=None, help="configuration file")
+ parser.add_argument("-o", "--output", dest="output_directory", type=str,
+ help="Output directory", required=True,
+ action=ReadableDir)
+ parser.add_argument("--nolog", action="store_true",
+ default=False, help="Don't generate log files")
+ parser.add_argument("--debug", dest="verbose", default=False,
+ action='store_true',
+ help="Increase output verbosity")
return parser
def _pdbstat_argparser(self, desc=None):
@@ -545,6 +636,17 @@ class AriaEcCommands(CLI):
"--min", dest="minflag", action="store_true", default=False,
help="Compute stats only on a minimized list of atom (CA, CB and 1 "
"SC)")
+ parser.add_argument("-c", "--conf", action=ReadableFile,
+ dest="conf_file",
+ default=None, help="configuration file")
+ parser.add_argument("-o", "--output", dest="output_directory", type=str,
+ help="Output directory", required=True,
+ action=ReadableDir)
+ parser.add_argument("--nolog", action="store_true",
+ default=False, help="Don't generate log files")
+ parser.add_argument("--debug", dest="verbose", default=False,
+ action='store_true',
+ help="Increase output verbosity")
return parser
def create_settings(self):
@@ -596,8 +698,9 @@ class AriaEcCommands(CLI):
def pdbdist(self):
"""Extract pdb distance distributions"""
- inst = PDBDist(self.create_settings())
- inst.run()
+ # TODO: See todo at the beginning of this file
+ #inst = PDBDist(self.create_settings())
+ #inst.run()
def pdbstat(self):
"""Analyse pdb distance distribution"""
diff --git a/aria/conbox/common.py b/src/aria/conbox/common.py
similarity index 86%
rename from aria/conbox/common.py
rename to src/aria/conbox/common.py
index 8ef02a22c82371665779ee30f646d55583dc3b2a..2b3a6df561d0e3ef31374f710fa36e1ac2a77039 100644
--- a/aria/conbox/common.py
+++ b/src/aria/conbox/common.py
@@ -424,7 +424,26 @@ def tickrot(axes, figure, rotype='horizontal', xaxis=True, yaxis=True):
figure.canvas.draw()
-# TODO: Add another level when we use verbose options instead of displaying debug messages
+class AbcLogFilter(logging.Filter):
+
+ abc_words = ("abc_funcName", "abc_lineno")
+
+ def filter(self, record):
+ """Set default values for abc attributes according to the
+ original attribute in LogRecord object"""
+ reg = re.compile(r"(?P<prefix>[A-Za-z0-9]*(?=_))?_?(?P<name>\w+)")
+
+ for abc_word in self.abc_words:
+ if not hasattr(record, abc_word):
+ prefix, name = [reg.match(abc_word).groupdict()[_]
+ for _ in ('prefix', 'name')]
+ setattr(record, abc_word, getattr(record, name))
+
+ return True
+
+
+# TODO: Add another level when we use verbose options instead of displaying
+# debug messages
class CustomLogging(object):
"""
Customized python logging config
@@ -433,7 +452,8 @@ class CustomLogging(object):
# "conf/logging.json")
default_file = "conf/logging.json"
- def __init__(self, level=logging.INFO, desc=None):
+ def __init__(self, level=logging.INFO, desc=None, welcome=True,
+ decorator=True):
"""
Parameters
@@ -445,12 +465,11 @@ class CustomLogging(object):
"""
# TODO: detect path log filenames and makedirs if not exists
logging.basicConfig(level=level)
- if desc:
- self.msg = desc.strip()
- else:
- self.msg = ""
- self.config = self.default_config()
- self.welcome()
+ self.msg = desc.strip() if desc else ""
+ self.config = self.load_config()
+ self.update_log()
+ if welcome:
+ self.welcome(decorator=decorator)
def update_msg(self, desc):
"""
@@ -470,15 +489,39 @@ class CustomLogging(object):
elif isinstance(self.msg, str):
self.msg = " - ".join((self.msg, desc.capitalize()))
- def default_config(self):
- """:return:"""
+ def update_log(self):
+ """
+ Update logging config with config attribute
+ """
+ logging.config.dictConfig(self.config)
+
+ def load_config(self, abc=False):
+ """
+ Build default configuration from default json file
+
+ Returns
+ -------
+ config: dict
+ default configuration for logging
+ """
# with open(self.default_file, 'rt') as f:
conf = pkgr.resource_stream(__name__, self.default_file).read().decode()
config = json.loads(conf)
- logging.config.dictConfig(config)
+
return config
- def set_outdir(self, outdir):
+ def up_outfiles(self, outfile):
+ base = os.path.splitext(outfile)[0]
+ for hand in self.config["handlers"]:
+ if "filename" in self.config["handlers"][hand]:
+ oldpath = self.config["handlers"][hand]["filename"]
+ old_ext = os.path.splitext(oldpath)[1]
+ newpath = os.path.abspath(base + old_ext)
+ self.config["handlers"][hand]["filename"] = newpath
+ shutil.copy2(oldpath, newpath)
+ self.update_log()
+
+ def set_outdir(self, outdir, logdir=True):
"""
Create log directory and change log files location
@@ -492,13 +535,11 @@ class CustomLogging(object):
"""
outdir = os.path.join(outdir,
- "log") if "log" not in outdir else outdir
- if not os.path.exists(os.path.abspath(outdir)):
- os.makedirs(outdir)
- else:
- # Trick to avoid overwriting files with w mode after copy2 call
+ "log") if "log" not in outdir and logdir else outdir
+ if os.path.exists(os.path.abspath(outdir)):
+ # Avoid overwriting files with w mode after copy2 call
shutil.rmtree(os.path.abspath(outdir))
- os.makedirs(outdir)
+ os.makedirs(outdir)
if outdir and "handlers" in self.config:
for hand in self.config["handlers"]:
if "filename" in self.config["handlers"][hand]:
@@ -508,22 +549,22 @@ class CustomLogging(object):
self.config["handlers"][hand]["filename"])))
self.config["handlers"][hand]["filename"] = newpath
shutil.copy2(oldpath, newpath)
- logging.config.dictConfig(self.config)
+ self.update_log()
- def welcome(self):
+ def welcome(self, decorator=True):
"""
Returns
-------
"""
- desc = '''
+ desc = '''\
================================================================================
{:^80}
================================================================================
-'''.format(self.msg)
+'''.format(self.msg) if decorator else self.msg
for hand in self.config.get("handlers"):
if "filename" in self.config["handlers"][hand]:
with open(self.config["handlers"][hand]["filename"],
diff --git a/aria/conbox/conf/config.ini b/src/aria/conbox/conf/config.ini
similarity index 96%
rename from aria/conbox/conf/config.ini
rename to src/aria/conbox/conf/config.ini
index 74f24c0bb5c9016f23f132a84b26842835a52daf..eef6ec94b5f61b769ae811529c339e8396c1afe5 100644
--- a/aria/conbox/conf/config.ini
+++ b/src/aria/conbox/conf/config.ini
@@ -36,7 +36,7 @@ default_cutoff: 8.0
;ca_ca:
;cb_cb:
;sc_sc:
-bool
+
[setup]
; ------------------------------ TBL parameters ------------------------------ #
; longrange_hb : True, False [False]
@@ -184,6 +184,15 @@ logharmonic_potential_weight_hbond: 25.0
rama_potential_enabled: yes
hbdb_potential_enabled: no
scoring_method: standard
+md_parameters_dynamics: torsion
+md_parameters_tad_temp_high: 10000.0
+md_parameters_tad_timestep_factor: 9.0
+md_parameters_cartesian_temp_high: 2000.0
+md_parameters_cartesian_first_iteration: 0
+md_parameters_timestep: 0.003
+md_parameters_temp_cool1_final: 1000.0
+md_parameters_temp_cool2_final: 50.0
+md_parameters_steps_refine: 4000
md_parameters_random_seed: 89764443
md_parameters_steps_high: 10000
md_parameters_steps_cool1: 5000
@@ -192,6 +201,7 @@ water_refinement_solvent: water
water_refinement_n_structures: 10
water_refinement_enabled: no
water_refinement_write_solvent_molecules: no
+structure_analysis_enabled: yes
procheck_executable:
procheck_enabled: yes
prosa_executable:
@@ -199,7 +209,7 @@ prosa_enabled: yes
whatif_executable:
whatif_enabled: yes
clashlist_executable:
-clahlist_enabled: no
+clashlist_enabled: no
pickle_output: no
; --------------------------- Iteration parameters --------------------------- #
; /!\ Parameters below can be formatted as a list if we want different values
@@ -256,7 +266,6 @@ L:
[pdbqual]
trash_directory: /tmp
-prosa: False
skip_prefix: fitted
csh_executable: csh
diff --git a/aria/conbox/conf/logging.json b/src/aria/conbox/conf/logging.json
similarity index 66%
rename from aria/conbox/conf/logging.json
rename to src/aria/conbox/conf/logging.json
index f4eea3defb2521b08188573539665aad74dece6d..795c8ff51e8f518f07b7eba57b79e890697039d0 100644
--- a/aria/conbox/conf/logging.json
+++ b/src/aria/conbox/conf/logging.json
@@ -6,7 +6,7 @@
"format": "%(levelname)-8s %(message)s"
},
"detail": {
- "format": "[%(asctime)s] --- %(levelname)-8s --- %(message)s (%(filename)s:%(lineno)s)",
+ "format": "[%(asctime)s] --- %(levelname)s --- %(message)s (%(name)s.%(abc_funcName)s:%(abc_lineno)s)",
"datefmt": "%m/%d/%Y %I:%M:%S %p"
},
"colored": {
@@ -14,7 +14,11 @@
"format": "%(log_color)s%(levelname)-8s%(reset)s %(message)s"
}
},
-
+ "filters": {
+ "abc_filter": {
+ "()": "aria.conbox.common.AbcLogFilter"
+ }
+ },
"handlers": {
"console": {
"class": "logging.StreamHandler",
@@ -22,38 +26,40 @@
"formatter": "colored",
"stream": "ext://sys.stdout"
},
-
"info_file_handler": {
"class": "logging.handlers.RotatingFileHandler",
"level": "INFO",
"formatter": "simple",
- "filename": "/tmp/ariaec.log",
+ "filename": "/tmp/aria.log",
"mode": "a",
"encoding": "utf8"
},
-
"debug_file_handler": {
"class": "logging.handlers.RotatingFileHandler",
"level": "DEBUG",
"formatter": "detail",
- "filename": "/tmp/ariaec.debug",
+ "filename": "/tmp/aria.debug",
"mode": "a",
- "encoding": "utf8"
+ "encoding": "utf8",
+ "filters": ["abc_filter"]
},
-
"error_file_handler": {
"class": "logging.handlers.RotatingFileHandler",
"level": "ERROR",
"formatter": "detail",
- "filename": "/tmp/ariaec.error",
+ "filename": "/tmp/aria.error",
"mode": "a",
- "encoding": "utf8"
+ "encoding": "utf8",
+ "filters": ["abc_filter"]
}
},
-
"root": {
"level": "INFO",
- "handlers": ["console", "info_file_handler", "error_file_handler",
- "debug_file_handler"]
+ "handlers": [
+ "console",
+ "info_file_handler",
+ "error_file_handler",
+ "debug_file_handler"
+ ]
}
}
\ No newline at end of file
diff --git a/aria/conbox/converter.py b/src/aria/conbox/converter.py
similarity index 100%
rename from aria/conbox/converter.py
rename to src/aria/conbox/converter.py
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res1.6_R0.25_d160427_chains2932 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res1.6_R0.25_d160427_chains2932
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc20_res1.6_R0.25_d160427_chains2932
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res1.6_R0.25_d160427_chains2932
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res1.8_R0.25_d160427_chains4479 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res1.8_R0.25_d160427_chains4479
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc20_res1.8_R0.25_d160427_chains4479
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res1.8_R0.25_d160427_chains4479
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res100_R100_inclNOTXRAY_d160427_chains11139 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res100_R100_inclNOTXRAY_d160427_chains11139
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc20_res100_R100_inclNOTXRAY_d160427_chains11139
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res100_R100_inclNOTXRAY_d160427_chains11139
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res100_R100_inclNOTXRAY_inclCA_d160427_chains11205 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res100_R100_inclNOTXRAY_inclCA_d160427_chains11205
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc20_res100_R100_inclNOTXRAY_inclCA_d160427_chains11205
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res100_R100_inclNOTXRAY_inclCA_d160427_chains11205
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.0_R0.25_d160427_chains6089 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.0_R0.25_d160427_chains6089
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.0_R0.25_d160427_chains6089
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.0_R0.25_d160427_chains6089
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.2_R1.0_d160427_chains7039 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.2_R1.0_d160427_chains7039
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.2_R1.0_d160427_chains7039
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.2_R1.0_d160427_chains7039
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.5_R1.0_d160427_chains8112 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.5_R1.0_d160427_chains8112
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.5_R1.0_d160427_chains8112
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res2.5_R1.0_d160427_chains8112
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res3.0_R1.0_d160427_chains9088 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res3.0_R1.0_d160427_chains9088
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc20_res3.0_R1.0_d160427_chains9088
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc20_res3.0_R1.0_d160427_chains9088
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res1.6_R0.25_d160427_chains3743 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res1.6_R0.25_d160427_chains3743
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc25_res1.6_R0.25_d160427_chains3743
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res1.6_R0.25_d160427_chains3743
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res1.8_R0.25_d160427_chains5983 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res1.8_R0.25_d160427_chains5983
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc25_res1.8_R0.25_d160427_chains5983
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res1.8_R0.25_d160427_chains5983
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res100_R100_inclNOTXRAY_d160427_chains15029 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res100_R100_inclNOTXRAY_d160427_chains15029
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc25_res100_R100_inclNOTXRAY_d160427_chains15029
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res100_R100_inclNOTXRAY_d160427_chains15029
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res100_R100_inclNOTXRAY_inclCA_d160427_chains15094 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res100_R100_inclNOTXRAY_inclCA_d160427_chains15094
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc25_res100_R100_inclNOTXRAY_inclCA_d160427_chains15094
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res100_R100_inclNOTXRAY_inclCA_d160427_chains15094
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.0_R0.25_d160427_chains8302 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.0_R0.25_d160427_chains8302
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.0_R0.25_d160427_chains8302
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.0_R0.25_d160427_chains8302
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.2_R1.0_d160427_chains9719 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.2_R1.0_d160427_chains9719
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.2_R1.0_d160427_chains9719
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.2_R1.0_d160427_chains9719
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.5_R1.0_d160427_chains11250 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.5_R1.0_d160427_chains11250
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.5_R1.0_d160427_chains11250
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res2.5_R1.0_d160427_chains11250
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res3.0_R1.0_d160427_chains12553 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res3.0_R1.0_d160427_chains12553
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc25_res3.0_R1.0_d160427_chains12553
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc25_res3.0_R1.0_d160427_chains12553
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc30_res1.6_R0.25_d160427_chains4285 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc30_res1.6_R0.25_d160427_chains4285
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc30_res1.6_R0.25_d160427_chains4285
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc30_res1.6_R0.25_d160427_chains4285
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc30_res1.8_R0.25_d160427_chains7108 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc30_res1.8_R0.25_d160427_chains7108
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rename from aria/conbox/data/cullpdb/160427/cullpdb_pc80_res1.6_R0.25_d160427_chains6362
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res1.6_R0.25_d160427_chains6362
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res1.8_R0.25_d160427_chains11423 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res1.8_R0.25_d160427_chains11423
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc80_res1.8_R0.25_d160427_chains11423
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res1.8_R0.25_d160427_chains11423
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res100_R100_inclNOTXRAY_d160427_chains36361 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res100_R100_inclNOTXRAY_d160427_chains36361
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc80_res100_R100_inclNOTXRAY_d160427_chains36361
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res100_R100_inclNOTXRAY_d160427_chains36361
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res100_R100_inclNOTXRAY_inclCA_d160427_chains36464 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res100_R100_inclNOTXRAY_inclCA_d160427_chains36464
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc80_res100_R100_inclNOTXRAY_inclCA_d160427_chains36464
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res100_R100_inclNOTXRAY_inclCA_d160427_chains36464
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.0_R0.25_d160427_chains17319 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.0_R0.25_d160427_chains17319
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.0_R0.25_d160427_chains17319
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.0_R0.25_d160427_chains17319
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.2_R1.0_d160427_chains21376 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.2_R1.0_d160427_chains21376
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.2_R1.0_d160427_chains21376
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.2_R1.0_d160427_chains21376
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.5_R1.0_d160427_chains25811 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.5_R1.0_d160427_chains25811
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.5_R1.0_d160427_chains25811
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res2.5_R1.0_d160427_chains25811
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res3.0_R1.0_d160427_chains29601 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res3.0_R1.0_d160427_chains29601
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc80_res3.0_R1.0_d160427_chains29601
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc80_res3.0_R1.0_d160427_chains29601
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res1.6_R0.25_d160427_chains6615 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res1.6_R0.25_d160427_chains6615
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc90_res1.6_R0.25_d160427_chains6615
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res1.6_R0.25_d160427_chains6615
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res1.8_R0.25_d160427_chains12015 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res1.8_R0.25_d160427_chains12015
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc90_res1.8_R0.25_d160427_chains12015
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res1.8_R0.25_d160427_chains12015
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res100_R100_inclNOTXRAY_d160427_chains39511 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res100_R100_inclNOTXRAY_d160427_chains39511
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc90_res100_R100_inclNOTXRAY_d160427_chains39511
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res100_R100_inclNOTXRAY_d160427_chains39511
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res100_R100_inclNOTXRAY_inclCA_d160427_chains39636 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res100_R100_inclNOTXRAY_inclCA_d160427_chains39636
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc90_res100_R100_inclNOTXRAY_inclCA_d160427_chains39636
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res100_R100_inclNOTXRAY_inclCA_d160427_chains39636
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.0_R0.25_d160427_chains18357 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.0_R0.25_d160427_chains18357
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.0_R0.25_d160427_chains18357
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.0_R0.25_d160427_chains18357
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.2_R1.0_d160427_chains22765 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.2_R1.0_d160427_chains22765
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.2_R1.0_d160427_chains22765
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.2_R1.0_d160427_chains22765
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.5_R1.0_d160427_chains27666 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.5_R1.0_d160427_chains27666
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.5_R1.0_d160427_chains27666
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res2.5_R1.0_d160427_chains27666
diff --git a/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res3.0_R1.0_d160427_chains31953 b/src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res3.0_R1.0_d160427_chains31953
similarity index 100%
rename from aria/conbox/data/cullpdb/160427/cullpdb_pc90_res3.0_R1.0_d160427_chains31953
rename to src/aria/conbox/data/cullpdb/160427/cullpdb_pc90_res3.0_R1.0_d160427_chains31953
diff --git a/aria/conbox/data/cullpdb/170315/cullpdb_pc25_res1.6_R0.25_d170315_chains3901.18206 b/src/aria/conbox/data/cullpdb/170315/cullpdb_pc25_res1.6_R0.25_d170315_chains3901.18206
similarity index 100%
rename from aria/conbox/data/cullpdb/170315/cullpdb_pc25_res1.6_R0.25_d170315_chains3901.18206
rename to src/aria/conbox/data/cullpdb/170315/cullpdb_pc25_res1.6_R0.25_d170315_chains3901.18206
diff --git a/aria/conbox/data/pdbdists/lowerbounds.inter.p b/src/aria/conbox/data/pdbdists/lowerbounds.inter.p
similarity index 100%
rename from aria/conbox/data/pdbdists/lowerbounds.inter.p
rename to src/aria/conbox/data/pdbdists/lowerbounds.inter.p
diff --git a/aria/conbox/data/pdbdists/lowerbounds.intra.p b/src/aria/conbox/data/pdbdists/lowerbounds.intra.p
similarity index 100%
rename from aria/conbox/data/pdbdists/lowerbounds.intra.p
rename to src/aria/conbox/data/pdbdists/lowerbounds.intra.p
diff --git a/aria/conbox/data/pdbdists/targetdists.inter.p b/src/aria/conbox/data/pdbdists/targetdists.inter.p
similarity index 100%
rename from aria/conbox/data/pdbdists/targetdists.inter.p
rename to src/aria/conbox/data/pdbdists/targetdists.inter.p
diff --git a/aria/conbox/data/pdbdists/targetdists.intra.p b/src/aria/conbox/data/pdbdists/targetdists.intra.p
similarity index 100%
rename from aria/conbox/data/pdbdists/targetdists.intra.p
rename to src/aria/conbox/data/pdbdists/targetdists.intra.p
diff --git a/aria/conbox/data/pdbdists/upperbounds.inter.p b/src/aria/conbox/data/pdbdists/upperbounds.inter.p
similarity index 100%
rename from aria/conbox/data/pdbdists/upperbounds.inter.p
rename to src/aria/conbox/data/pdbdists/upperbounds.inter.p
diff --git a/aria/conbox/data/pdbdists/upperbounds.intra.p b/src/aria/conbox/data/pdbdists/upperbounds.intra.p
similarity index 100%
rename from aria/conbox/data/pdbdists/upperbounds.intra.p
rename to src/aria/conbox/data/pdbdists/upperbounds.intra.p
diff --git a/aria/conbox/data/scsc_min.p b/src/aria/conbox/data/scsc_min.p
similarity index 100%
rename from aria/conbox/data/scsc_min.p
rename to src/aria/conbox/data/scsc_min.p
diff --git a/aria/conbox/data/ss_dist.txt b/src/aria/conbox/data/ss_dist.txt
similarity index 100%
rename from aria/conbox/data/ss_dist.txt
rename to src/aria/conbox/data/ss_dist.txt
diff --git a/aria/conbox/data/topallhdg5.3.pro b/src/aria/conbox/data/topallhdg5.3.pro
similarity index 100%
rename from aria/conbox/data/topallhdg5.3.pro
rename to src/aria/conbox/data/topallhdg5.3.pro
diff --git a/aria/conbox/maplot.py b/src/aria/conbox/maplot.py
similarity index 96%
rename from aria/conbox/maplot.py
rename to src/aria/conbox/maplot.py
index 4d624485912f479584f2b471681f307b63df5303..3b3d3fda35514bd3cb010901ef9545bffa8669ba 100644
--- a/aria/conbox/maplot.py
+++ b/src/aria/conbox/maplot.py
@@ -128,7 +128,7 @@ class AriaEcContactMap(object):
mergecontactmap = mergemaps.get("maplot")
for mapname, mapt in self.allresmap.keys():
if mapt != self.reftype:
- # TODO: DON'T WORK !!!!
+ # TODO: DOESN'T WORK !!!!
LOG.info("Merging %s with %s map",
mergetype, mapt)
up_map = self.allresmap[mapt]["maplot"]
@@ -191,11 +191,14 @@ class AriaEcContactMap(object):
cmpmap.write_contacts(mapname,
scoremap=scoremap,
outdir=outdir)
- cmpmap.compare_contactmap(refmap, cmplist, prefix,
+ cmpmap.compare_contactmap(refmap, cmplist,
+ prefix if prefix else "cmp",
distmap=self.refmap["distmap"],
human_idx=True,
outdir=outdir)
- refmap.compareplot(cmpmap, outprefix=prefix,
+ LOG.info(prefix)
+ refmap.compareplot(cmpmap,
+ outprefix=prefix if prefix else "ref",
outdir=outdir,
save_fig=self.settings.maplot.config.get(
"save_fig"),
diff --git a/aria/conbox/ndconv.py b/src/aria/conbox/ndconv.py
similarity index 100%
rename from aria/conbox/ndconv.py
rename to src/aria/conbox/ndconv.py
diff --git a/aria/conbox/pdbdist.py b/src/aria/conbox/pdbdist.py
similarity index 100%
rename from aria/conbox/pdbdist.py
rename to src/aria/conbox/pdbdist.py
diff --git a/aria/conbox/pdbqual.py b/src/aria/conbox/pdbqual.py
similarity index 67%
rename from aria/conbox/pdbqual.py
rename to src/aria/conbox/pdbqual.py
index f63b7469bc4aaa161ee3a721f1aee99b4cf14f91..10e09e5d61eaca75ecbf7c4810e34ccd2810dc0c 100644
--- a/aria/conbox/pdbqual.py
+++ b/src/aria/conbox/pdbqual.py
@@ -9,7 +9,7 @@ import logging
import os
import shutil
-from ..core.legacy import QualityChecks
+from ..core.legacy.QualityChecks.QualityChecks import runChecks, FILENAME_REPORT
from .common import CommandProtocol
LOG = logging.getLogger(__name__)
@@ -29,14 +29,17 @@ class AriaEcPdbqual(CommandProtocol):
if os.path.abspath(infile) != os.path.abspath(self.settings.pdbqual["output_directory"]):
shutil.copy(infile, self.settings.pdbqual["output_directory"])
LOG.info(self.settings.pdbqual["output_directory"])
- QualityChecks.runChecks(
+ runChecks(
workingDirectory=self.settings.pdbqual["output_directory"],
trashDirectory=self.settings.pdbqual["trash_directory"],
- prosaOnOff=1 if self.settings.pdbqual["prosa"] else 0,
- procheckExe=self.settings.main["procheck_executable"],
- whatIfExe=self.settings.main["whatif_executable"],
- clashlistExe=self.settings.main["clashlist_executable"],
- prosaExe=self.settings.main["prosa_executable"] if self.settings.main["prosa_executable"] else "",
+ procheckExe=self.settings.setup["procheck_executable"],
+ procheckOnOff=1 if self.settings.setup["procheck_enabled"] in ("yes", True, "True") else 0,
+ whatIfExe=self.settings.setup["whatif_executable"],
+ whatifOnOff=1 if self.settings.setup["whatif_enabled"] in ("yes", True, "True") else 0,
+ clashlistExe=self.settings.setup["clashlist_executable"],
+ clashlistOnOff=1 if self.settings.setup["clashlist_enabled"] in ("yes", True, "True") else 0,
+ prosaExe=self.settings.setup["prosa_executable"] if self.settings.main["prosa_executable"] else "",
+ prosaOnOff=1 if self.settings.setup["prosa_enabled"] in ("yes", True, "True") else 0,
cshExe=self.settings.pdbqual["csh_executable"],
howManyPdb=len(self.settings.pdbqual["infiles"]),
verbose=1,
@@ -45,7 +48,7 @@ class AriaEcPdbqual(CommandProtocol):
)
LOG.info("%s generated",
os.path.join(self.settings.pdbqual["output_directory"],
- QualityChecks.FILENAME_REPORT))
+ FILENAME_REPORT))
LOG.info("Removing infile(s) in output directory %s", self.settings.pdbqual["output_directory"])
[os.remove(
os.path.join(self.settings.pdbqual["output_directory"],
diff --git a/aria/conbox/pdbstat.py b/src/aria/conbox/pdbstat.py
similarity index 100%
rename from aria/conbox/pdbstat.py
rename to src/aria/conbox/pdbstat.py
diff --git a/aria/conbox/protein.py b/src/aria/conbox/protein.py
similarity index 98%
rename from aria/conbox/protein.py
rename to src/aria/conbox/protein.py
index b0e0a01e88d8c5353829c0b7b0035b0d8ba124d8..49e805a1a52d29aa440174baf1635dcaac4bf075 100644
--- a/aria/conbox/protein.py
+++ b/src/aria/conbox/protein.py
@@ -15,9 +15,8 @@ import re
import sys
from six import iteritems, text_type
from copy import copy
-
from ..core.legacy import AminoAcid as AmnAcd
-from .common import (reg_load, ppdict)
+from .common import (reg_load, ppdict, Capturing)
# import skbio.Protein as skprot
# TODO: interface skbio ??
@@ -46,9 +45,9 @@ class SsList(object):
r'\s+(?P<up_residue>[AC-IK-NP-TVWYZ])'
r'\s+(?P<ss_pred>[HEC])'
r'\s+(?P<ss_conf>\d?)'),
- 'ss3': re.compile(r'^\s*(?P<up_index>\d+)'
+ 'ss2': re.compile(r'^\s*(?P<up_index>\d+)'
r'\s+(?P<up_residue>[AC-IK-NP-TVWYZ])'
- r'\s+(?P<ss_pred>[HEC])'
+ r'\s+(?P<ss_pred>[HECBTG])'
r'\s+(?P<h_conf>\d?\.?\d*)'
r'\s+(?P<e_conf>\d?\.?\d*)'
r'\s+(?P<c_conf>\d?\.?\d*)'),
@@ -583,10 +582,12 @@ class AminoAcidSequence(SequenceList.SequenceList, object):
# TODO: smarter reader checking type of file (fasta, etc ...)
# TODO: capturing has some troubles with unicode ...
# with Capturing() as output:
- if os.path.splitext(filename)[1] == '.seq':
- self.ReadSeq(text_type(filename))
- else:
- self.ReadFasta(text_type(filename))
+ with Capturing() as output:
+ if os.path.splitext(filename)[1] == '.seq':
+ self.ReadSeq(text_type(filename))
+ else:
+ self.ReadFasta(text_type(filename))
+ LOG.info("".join(output).capitalize())
self.sequence = "".join(
(AmnAcd.AminoAcid(str(_))[0]
for _ in self.aalist))
diff --git a/aria/conbox/protmap.py b/src/aria/conbox/protmap.py
similarity index 99%
rename from aria/conbox/protmap.py
rename to src/aria/conbox/protmap.py
index e2f6a3e6f4a31f603626d4150db7470ab069e687..5bae9d02197b657a8cc1c965f5384fa520e55bb3 100644
--- a/aria/conbox/protmap.py
+++ b/src/aria/conbox/protmap.py
@@ -490,7 +490,7 @@ class ProteinMap(Map):
Parameters
----------
outdir :
- param outprefix: (Default value = '')
+ param outprefix: (Default value = 'protein')
size_fig :
param plot_ext: (Default value = 10)
plot_dpi :
@@ -2184,7 +2184,9 @@ class MapFilter(object):
start_list = [ss_start_end[elm][0] for elm in ss_start_end]
end_list = [ss_start_end[elm][1] for elm in ss_start_end]
-
+ LOG.debug("Checking secondary structures clashes for contact list {0} "
+ "[{1}] with secondary structure list {2} [{3}]".format(
+ str(contact_list), len(contact_list), str(ss_list), len(ss_list)))
for icontact, contact in enumerate(contact_list):
# For each res-res contact
outcontact = str(hum_contact(contact))
@@ -2468,16 +2470,6 @@ class MapFilter(object):
"""
# TODO: utiliser self.clash_dict au lieu de meta_clash
- """
-
- :param clash_dict:
- :param desc_dict:
- :param contactlist:
- :param outdir:
- :param outprefix:
- :param clashlist:
- :param human_idx:
- """
meta_clash = {
"cons": {
"flag": 888, "msg": "", "warn": "",
diff --git a/aria/conbox/reader.py b/src/aria/conbox/reader.py
similarity index 95%
rename from aria/conbox/reader.py
rename to src/aria/conbox/reader.py
index 304ffd813240c61ef38f48765f65b7460c990c87..a4c570214ee2f02581bcbaedbf6f410fc8410a1d 100644
--- a/aria/conbox/reader.py
+++ b/src/aria/conbox/reader.py
@@ -19,7 +19,6 @@ from conkit.core.sequencefile import SequenceFile
from .common import sort_2dict
from .protmap import (ResMap, ResAtmMap)
-
LOG = logging.getLogger(__name__)
# TODO: check if Atom is still used ...
Atom = collections.namedtuple("Atom", ["name", "coords"])
@@ -161,6 +160,9 @@ class MapFile(RegexFile):
# sort_field allow sorting lines with values into this field
# TODO: wrong regex for native_full ?
# TODO: smarter dict ...
+ conkit_alias = {
+ "raptorx": "casprr",
+ }
types = {
"plmdca": {
"regex": re.compile(r"^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+"
@@ -339,8 +341,11 @@ class MapFile(RegexFile):
self.checkflag = kwargs.pop("check_type") \
if "check_type" in kwargs else True
super(MapFile, self).__init__(*args, **kwargs)
+ self.filetype = self.filetype if self.filetype not in self.conkit_alias else \
+ self.conkit_alias[self.filetype]
if not self.conioflag and self.checkflag:
- LOG.info("Conkit doesn't support {ftype}".format(
+ LOG.info("The file format {ftype} is not supported by the conkit "
+ "plugin. Switching to homemade parsers.".format(
ftype=self.filetype))
LOG.debug("Using {module}".format(module=__name__))
self.regex, self.filetype, self.sort = self.check_maptype()
@@ -398,8 +403,10 @@ class MapFile(RegexFile):
-------
"""
- LOG.info("Checking if file %s correspond to %s format", self.filepath,
- self.filetype)
+ LOG.info(
+ "Checking if file %s correspond to our definition of %s format",
+ self.filepath,
+ self.filetype)
# Check if given type is supported
# TODO: report this check into commands section
if os.stat(self.filepath).st_size == 0:
@@ -415,10 +422,11 @@ class MapFile(RegexFile):
if self.filetype in self.types:
match = self.types[self.filetype].get("regex").match(line)
else:
- LOG.error("Format %s not supported !", self.filetype)
+ LOG.error("Format %s not supported. Please refer"
+ " to the documentation for supported files",
+ self.filetype)
match = None
if match:
- LOG.info("Format type correct")
return [
self.types[self.filetype].get("regex"),
self.filetype,
@@ -441,7 +449,8 @@ class MapFile(RegexFile):
# Stop checking after second line
LOG.error("Can't read %s file.", self.filetype)
break
- LOG.error("Wrong format type given ...")
+ LOG.error("Wrong format type given. Please refer to the "
+ "documentation to check if the given format is correct.")
return [None] * 3
def load(self, *args):
@@ -594,7 +603,8 @@ class ContactMapFile(MapFile):
path=kwargs.get("path"),
desc=self.filetype) if self.sort else None
distmap = ResMap(protein.aa_sequence.sequence, mtype='distance',
- seqidx=protein.index, idxnames=idxnames, path=kwargs.get("path"),
+ seqidx=protein.index, idxnames=idxnames,
+ path=kwargs.get("path"),
colnames=colnames, sym=kwargs['sym'],
desc=self.filetype) if self.filetype == "metapsicovhb" else None
@@ -655,7 +665,7 @@ class ContactMapFile(MapFile):
if self.filetype == "metapsicovhb":
self.distlist.append(self.lines[contact].get("res_dist"))
- if self.filetype in ("evfold", "plmdca", "plm", "plmev"):
+ if self.filetype in ("evcoupling", "plmdca", "plm", "plmev"):
self.clashlist.append(next(
(el for el in (
self.lines[contact].get("ss_filter"),
@@ -683,8 +693,12 @@ class ContactMapFile(MapFile):
alignment = pairwise2.align.localxs(
seq, protein.aa_sequence.sequence, -1, -1,
one_alignment_only=True)[0]
- LOG.info('Alignment of amino acid sequence with contact file\n'
- '%s' % pairwise2.format_alignment(*alignment))
+ LOG.info(
+ 'Alignment of sequence in contact file ({0})'
+ ' with reference ({1})\n{2}'.format(
+ self.filetype,
+ os.path.basename(protein.aa_sequence.fileName),
+ pairwise2.format_alignment(*alignment)))
shift = re.match(r'^-*', alignment[1])
shift = len(shift.group(0)) if shift else 0
if shift:
@@ -823,16 +837,19 @@ class PDBFile(MapFile):
float(self.lines[atomy]['z']))
dist = distance.euclidean(coordx, coordy)
- if indx[0] in list(resmap.index.get_level_values("residuex"))\
- and indy[0] in list(resmap.index.get_level_values("residuex")):
+ if indx[0] in list(resmap.index.get_level_values("residuex")) \
+ and indy[0] in list(
+ resmap.index.get_level_values("residuex")):
LOG.debug("Update distance value (%s, %s)", indx, indy)
newmap.at[indx, indy] = dist
if sym:
# If symmetric matrix
newmap.at[indy, indx] = dist
- elif indx[0] not in list(resmap.index.get_level_values("residuex")):
+ elif indx[0] not in list(
+ resmap.index.get_level_values("residuex")):
error_list.add(indx[0])
- elif indy[0] not in list(resmap.index.get_level_values("residuex")):
+ elif indy[0] not in list(
+ resmap.index.get_level_values("residuex")):
error_list.add(indy[0])
if error_list:
# Listing related humanidx in the initial df
@@ -851,6 +868,7 @@ class PDBFile(MapFile):
class DistanceMapFile(MapFile):
"""Distance matrix file"""
+
def __init__(self, filepath, filetype):
super(MapFile).__init__(filepath, filetype)
raise NotImplementedError
@@ -936,8 +954,8 @@ class MapFileListReader(object):
maptypes = [maptypes] if type(maptypes) != list else maptypes
if not maptypes or len(maps) != len(maptypes):
maptypes = [os.path.splitext(_)[1][1:] for _ in maps]
- LOG.info("Reader focused on file(s) %s %s", maps,
- maptypes)
+ # LOG.info("Analyzing input file(s) %s %s", maps,
+ # maptypes)
for i, filepath in enumerate(maps):
if os.path.exists(filepath):
# TODO: check_type functionstr
diff --git a/aria/conbox/settings.py b/src/aria/conbox/settings.py
similarity index 98%
rename from aria/conbox/settings.py
rename to src/aria/conbox/settings.py
index 9024bd150f6123272841fe2ad5852f3c09a7d471..5f2f808cf58cc668db8bb4cee3fe93e975a9b49e 100644
--- a/aria/conbox/settings.py
+++ b/src/aria/conbox/settings.py
@@ -33,6 +33,10 @@ class Setting(object):
else:
raise KeyError(item)
+ def get(self, key, default=None):
+ return self.config[key] if key in self.config else self.args[key] \
+ if key in self.args else default
+
def __repr__(self):
return "Setting object\n config: %s\n args : %s" % (self.config,
self.args)
@@ -146,6 +150,7 @@ class AriaEcSettings(Settings):
SECTIONS = ("main", "setup", "maplot", "bbconv", "contactdef",
"pdbqual", "pdbdist", "analysis", "tbl2xml", "pdbstat",
"iniconv")
+
# TODO: options in main section should be accessible from all sections ! DO
# not use this a other section as it is done actually
diff --git a/aria/conbox/setup.py b/src/aria/conbox/setup.py
similarity index 100%
rename from aria/conbox/setup.py
rename to src/aria/conbox/setup.py
diff --git a/aria/conbox/templates/aria_project_v2.3.0.xml b/src/aria/conbox/templates/aria_project_v2.3.0.xml
similarity index 99%
rename from aria/conbox/templates/aria_project_v2.3.0.xml
rename to src/aria/conbox/templates/aria_project_v2.3.0.xml
index 1a57a04350c795551227cfedb64a5acad78e53ff..3ddd8e50df0e0e4ef009e3648ab62247e6338f05 100644
--- a/aria/conbox/templates/aria_project_v2.3.0.xml
+++ b/src/aria/conbox/templates/aria_project_v2.3.0.xml
@@ -72,7 +72,7 @@
<procheck executable="${procheck_executable}" enabled="${procheck_enabled}"/>
<prosa executable="${prosa_executable}" enabled="${prosa_enabled}"/>
<whatif executable="${whatif_executable}" enabled="${whatif_enabled}"/>
- <clashlist executable="${clashlist_executable}" enabled="${clahlist_enabled}"/>
+ <clashlist executable="${clashlist_executable}" enabled="${clashlist_enabled}"/>
</analysis>
<report>
<ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>
diff --git a/aria/conbox/templates/aria_project_v2.3.2.xml b/src/aria/conbox/templates/aria_project_v2.3.2.xml
similarity index 99%
rename from aria/conbox/templates/aria_project_v2.3.2.xml
rename to src/aria/conbox/templates/aria_project_v2.3.2.xml
index 18f870e03571a41b875613bf2447e0c1b7f22c3a..8e67b297e182eb49b8392f656a65f11d8a85611b 100644
--- a/aria/conbox/templates/aria_project_v2.3.2.xml
+++ b/src/aria/conbox/templates/aria_project_v2.3.2.xml
@@ -74,7 +74,7 @@
<procheck executable="${procheck_executable}" enabled="${procheck_enabled}"/>
<prosa executable="${prosa_executable}" enabled="${prosa_enabled}"/>
<whatif executable="${whatif_executable}" enabled="${whatif_enabled}"/>
- <clashlist executable="${clashlist_executable}" enabled="${clahlist_enabled}"/>
+ <clashlist executable="${clashlist_executable}" enabled="${clashlist_enabled}"/>
</analysis>
<report>
<ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>
diff --git a/aria/conbox/templates/aria_project_v2.3.3.xml b/src/aria/conbox/templates/aria_project_v2.3.3.xml
similarity index 99%
rename from aria/conbox/templates/aria_project_v2.3.3.xml
rename to src/aria/conbox/templates/aria_project_v2.3.3.xml
index 22c5b061e60848472306597af132b4e338afbfdb..8b46ccd287575452e9c08ab05c9754cbc6c6a2a8 100644
--- a/aria/conbox/templates/aria_project_v2.3.3.xml
+++ b/src/aria/conbox/templates/aria_project_v2.3.3.xml
@@ -75,7 +75,7 @@
<procheck executable="${procheck_executable}" enabled="${procheck_enabled}"/>
<prosa executable="${prosa_executable}" enabled="${prosa_enabled}"/>
<whatif executable="${whatif_executable}" enabled="${whatif_enabled}"/>
- <clashlist executable="${clashlist_executable}" enabled="${clahlist_enabled}"/>
+ <clashlist executable="${clashlist_executable}" enabled="${clashlist_enabled}"/>
</analysis>
<report>
<ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>
diff --git a/aria/conbox/templates/aria_project_v2.3.4.xml b/src/aria/conbox/templates/aria_project_v2.3.4.xml
similarity index 99%
rename from aria/conbox/templates/aria_project_v2.3.4.xml
rename to src/aria/conbox/templates/aria_project_v2.3.4.xml
index 5263884c028d293196db2b7fc79be70223395b3f..3ebae29eb0e1fb518650bace3617d097f3a624bc 100644
--- a/aria/conbox/templates/aria_project_v2.3.4.xml
+++ b/src/aria/conbox/templates/aria_project_v2.3.4.xml
@@ -76,7 +76,7 @@
<procheck executable="${procheck_executable}" enabled="${procheck_enabled}"/>
<prosa executable="${prosa_executable}" enabled="${prosa_enabled}"/>
<whatif executable="${whatif_executable}" enabled="${whatif_enabled}"/>
- <clashlist executable="${clashlist_executable}" enabled="${clahlist_enabled}"/>
+ <clashlist executable="${clashlist_executable}" enabled="${clashlist_enabled}"/>
</analysis>
<report>
<ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>
diff --git a/aria/conbox/templates/aria_project_v2.3.5.xml b/src/aria/conbox/templates/aria_project_v2.3.5.xml
similarity index 99%
rename from aria/conbox/templates/aria_project_v2.3.5.xml
rename to src/aria/conbox/templates/aria_project_v2.3.5.xml
index 3d44cedc2292da7096a4da37a6f1913a2f336887..247e2761c7173ed88fe1bec6e81bbc633aece018 100644
--- a/aria/conbox/templates/aria_project_v2.3.5.xml
+++ b/src/aria/conbox/templates/aria_project_v2.3.5.xml
@@ -76,7 +76,7 @@
<procheck executable="${procheck_executable}" enabled="${procheck_enabled}"/>
<prosa executable="${prosa_executable}" enabled="${prosa_enabled}"/>
<whatif executable="${whatif_executable}" enabled="${whatif_enabled}"/>
- <clashlist executable="${clashlist_executable}" enabled="${clahlist_enabled}"/>
+ <clashlist executable="${clashlist_executable}" enabled="${clashlist_enabled}"/>
</analysis>
<report>
<ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>
diff --git a/aria/conbox/templates/aria_project_v2.3.6.xml b/src/aria/conbox/templates/aria_project_v2.3.6.xml
similarity index 99%
rename from aria/conbox/templates/aria_project_v2.3.6.xml
rename to src/aria/conbox/templates/aria_project_v2.3.6.xml
index 5734b97007b5f9eebce27b5abe03dfa845942c39..9eecefa4661d59d43945159330a9845b0c972c31 100644
--- a/aria/conbox/templates/aria_project_v2.3.6.xml
+++ b/src/aria/conbox/templates/aria_project_v2.3.6.xml
@@ -76,7 +76,7 @@
<procheck executable="${procheck_executable}" enabled="${procheck_enabled}"/>
<prosa executable="${prosa_executable}" enabled="${prosa_enabled}"/>
<whatif executable="${whatif_executable}" enabled="${whatif_enabled}"/>
- <clashlist executable="${clashlist_executable}" enabled="${clahlist_enabled}"/>
+ <clashlist executable="${clashlist_executable}" enabled="${clashlist_enabled}"/>
</analysis>
<report>
<ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>
diff --git a/src/aria/conbox/templates/aria_project_v2.3.7.xml b/src/aria/conbox/templates/aria_project_v2.3.7.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3f86fbe79aa7b624aab1e0ea58811d9dac0801c3
--- /dev/null
+++ b/src/aria/conbox/templates/aria_project_v2.3.7.xml
@@ -0,0 +1,87 @@
+<!-- Template with method field in clustering tag -->
+<!DOCTYPE project SYSTEM "project1.0.dtd">
+<project name="${project_name}" version="1.0" author="" date="${date}" description="" comment="" references="" working_directory="${working_directory}" temp_root="${temp_root}" run="${runid}" file_root="${file_root}" cache="yes" cleanup="yes">
+ <data>
+ <ccpn_model filename=""/>
+ <molecule file="${molecule_file}" format="xml" ccpn_id="">
+ <linkage_definition name="automatic" filename=""/>
+ <parameter_definition name="${parameter_definition}" filename=""/>
+ <topology_definition name="automatic" filename=""/>
+ </molecule>
+ % if unambiguous_distance_restraints:
+ % for unambig_id in unambiguous_distance_restraints:
+ <unambiguous_distance_restraints file="${unambiguous_distance_restraints[unambig_id]['file']}" format="${unambiguous_distance_restraints[unambig_id]['format']}" ccpn_id="${unambiguous_distance_restraints[unambig_id]['ccpn_id']}" enabled="${unambiguous_distance_restraints[unambig_id]['enabled']}" add_to_network="${unambiguous_distance_restraints[unambig_id]['add_to_network']}" calibrate="${unambiguous_distance_restraints[unambig_id]['calibrate']}" run_network_anchoring="${unambiguous_distance_restraints[unambig_id]['run_network_anchoring']}" filter_contributions="${unambiguous_distance_restraints[unambig_id]['filter_contributions']}"/>
+ % endfor
+ % endif
+ % if ambiguous_distance_restraints:
+ % for ambig_id in ambiguous_distance_restraints:
+ <ambiguous_distance_restraints file="${ambiguous_distance_restraints[ambig_id]['file']}" format="${ambiguous_distance_restraints[ambig_id]['format']}" ccpn_id="${ambiguous_distance_restraints[ambig_id]['ccpn_id']}" enabled="${ambiguous_distance_restraints[ambig_id]['enabled']}" add_to_network="${ambiguous_distance_restraints[ambig_id]['add_to_network']}" calibrate="${ambiguous_distance_restraints[ambig_id]['calibrate']}" run_network_anchoring="${ambiguous_distance_restraints[ambig_id]['run_network_anchoring']}" filter_contributions="${ambiguous_distance_restraints[ambig_id]['filter_contributions']}" avg_exponent="${ambiguous_distance_restraints[ambig_id]['avg_exponent']}"/>
+ % endfor
+ % endif
+ % if hbond_dist_file:
+ <hbonds file="${hbond_dist_file}" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/>
+ % endif
+ % if dihed_angle_file:
+ <dihedrals file="${dihed_angle_file}" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/>
+ % endif
+ <symmetry enabled="no" method="standard" n_monomers="1" symmetry_type="None" ncs_enabled="no" packing_enabled="no"/>
+ <initial_structure file="" format="iupac" ccpn_id="" enabled="no"/>
+ </data>
+ <structure_generation engine="cns">
+ <cns local_executable="${cns_executable}" keep_output="${cns_keep_output}" keep_restraint_files="yes" create_psf_file="yes" generate_template="yes" nonbonded_parameters="PROLSQ">
+ <annealing_parameters>
+ <unambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="${unambiguous_restraints_k_cool1_initial}" k_cool1_final="${unambiguous_restraints_k_cool1_final}" k_cool2="${unambiguous_restraints_k_cool2}"/>
+ <ambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" k_cool1_final="50.0" k_cool2="50.0"/>
+ <hbond_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="${hbond_restraints_k_cool1_initial}" k_cool1_final="${hbond_restraints_k_cool1_final}" k_cool2="${hbond_restraints_k_cool2}"/>
+ <dihedral_restraints k_hot="5.0" k_cool1="${dihedral_restraints_k_cool1}" k_cool2="${dihedral_restraints_k_cool2}"/>
+ <karplus_restraints parameter_class="1" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
+ <karplus_restraints parameter_class="2" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
+ <karplus_restraints parameter_class="3" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
+ <karplus_restraints parameter_class="4" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
+ <karplus_restraints parameter_class="5" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
+ <rdc_restraints parameter_class="1" method="SANI" first_iteration="0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" center_cool2_final="10.0"/>
+ <rdc_restraints parameter_class="2" method="SANI" first_iteration="0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" center_cool2_final="10.0"/>
+ <rdc_restraints parameter_class="3" method="SANI" first_iteration="0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" center_cool2_final="10.0"/>
+ <rdc_restraints parameter_class="4" method="SANI" first_iteration="0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" center_cool2_final="10.0"/>
+ <rdc_restraints parameter_class="5" method="SANI" first_iteration="0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" center_cool2_final="10.0"/>
+ <flat_bottom_harmonic_wall m_rswitch_hot="0.5" m_rswitch_cool1="0.5" m_rswitch_cool2="0.5" rswitch_hot="0.5" rswitch_cool1="0.5" rswitch_cool2="0.5" m_asymptote_hot="-1.0" m_asymptote_cool1="-1.0" m_asymptote_cool2="-0.1" asymptote_hot="1.0" asymptote_cool1="1.0" asymptote_cool2="0.1"/>
+ <symmetry_restraints k_packing_hot="15.0" k_packing_cool1="10.0" k_packing_cool2="5.0" last_iteration_packing="8" k_ncs="50.0"/>
+ <logharmonic_potential enabled="${logharmonic_potential_enabled}" use_auto_weight="${logharmonic_potential_use_auto_weight}" weight_unambig="${logharmonic_potential_weight_unambig}" weight_ambig="${logharmonic_potential_weight_ambig}" weight_hbond="${logharmonic_potential_weight_hbond}"/>
+ <rama_potential enabled="${rama_potential_enabled}" weight_rama="1.0"/>
+ <hbdb_potential enabled="${hbdb_potential_enabled}"/>
+ <scoring method="${scoring_method}"/>
+ </annealing_parameters>
+ <md_parameters dynamics="${md_parameters_dynamics}" random_seed="${md_parameters_random_seed}" tad_temp_high="${md_parameters_tad_temp_high}" tad_timestep_factor="${md_parameters_tad_timestep_factor}" cartesian_temp_high="${md_parameters_cartesian_temp_high}" cartesian_first_iteration="${md_parameters_cartesian_first_iteration}" timestep="${md_parameters_timestep}" temp_cool1_final="${md_parameters_temp_cool1_final}" temp_cool2_final="${md_parameters_temp_cool2_final}" steps_high="${md_parameters_steps_high}" steps_refine="${md_parameters_steps_refine}" steps_cool1="${md_parameters_steps_cool1}" steps_cool2="${md_parameters_steps_cool2}"/>
+ </cns>
+ <job_manager default_command="csh -f">
+ <host enabled="yes" command="${host_command}" executable="${host_executable}" n_cpu="${n_cpus}" use_absolute_path="yes"/>
+ </job_manager>
+ </structure_generation>
+ <protocol floating_assignment="yes">
+ % for iter in range(0, int(iterations + 1)):
+ <iteration number="${iter}" n_structures="${iteration_n_structures}" sort_criterion="${iteration_sort_criterion}" n_best_structures="${iteration_n_best_structures}" n_kept_structures="${iteration_n_kept_structures}">
+ <assignment/>
+ <merging method="${merging_method}"/>
+ <calibration relaxation_matrix="${calib_relaxation_matrix}" distance_cutoff="${calib_distance_cutoff}" estimator="${calib_estimator}" error_estimator="${calib_error_estimator}"/>
+ <violation_analysis violation_tolerance="${viol_violation_tolerance[iter]}" violation_threshold="${viol_violation_threshold}" sigma_mode="${viol_sigma_mode}"/>
+ <partial_assignment weight_threshold="${partassign_weight_threshold[iter]}" max_contributions="${partassign_max_contributions}" exponent="${partassign_exponent}"/>
+ <network_anchoring high_residue_threshold="${netanch_high_residue_threshold}" enabled="${netanch_enabled}" min_residue_threshold="${netanch_min_residue_threshold}" min_atom_threshold="${netanch_min_atom_threshold}"/>
+ <clustering enabled="${clustering_enabled}" mask="${clustering_mask}" n_clusters="${clustering_nclusters}" method="${clustering_method}"/>
+ </iteration>
+ % endfor
+ <water_refinement solvent="${water_refinement_solvent}" n_structures="${water_refinement_n_structures}" enabled="${water_refinement_enabled}" write_solvent_molecules="${water_refinement_write_solvent_molecules}"/>
+ </protocol>
+ <analysis>
+ <structures_analysis enabled="${structures_analysis_enabled}"/>
+ <procheck executable="${procheck_executable}" enabled="${procheck_enabled}"/>
+ <prosa executable="${prosa_executable}" enabled="${prosa_enabled}"/>
+ <whatif executable="${whatif_executable}" enabled="${whatif_enabled}"/>
+ <clashlist executable="${clashlist_executable}" enabled="${clashlist_enabled}"/>
+ </analysis>
+ <report>
+ <ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>
+ <molmol enabled="yes"/>
+ <noe_restraint_list pickle_output="${pickle_output}" text_output="yes" xml_output="no"/>
+ <spectra write_assigned="no" write_assigned_force="no" iteration="last" write_unambiguous_only="yes"/>
+ </report>
+</project>
\ No newline at end of file
diff --git a/aria/conbox/test/__init__.py b/src/aria/conbox/test/__init__.py
similarity index 100%
rename from aria/conbox/test/__init__.py
rename to src/aria/conbox/test/__init__.py
diff --git a/aria/conbox/test/test_analysis.py b/src/aria/conbox/test/test_analysis.py
similarity index 100%
rename from aria/conbox/test/test_analysis.py
rename to src/aria/conbox/test/test_analysis.py
diff --git a/aria/conbox/test/test_commands.py b/src/aria/conbox/test/test_commands.py
similarity index 100%
rename from aria/conbox/test/test_commands.py
rename to src/aria/conbox/test/test_commands.py
diff --git a/aria/conbox/test/test_common.py b/src/aria/conbox/test/test_common.py
similarity index 100%
rename from aria/conbox/test/test_common.py
rename to src/aria/conbox/test/test_common.py
diff --git a/aria/conbox/test/test_converter.py b/src/aria/conbox/test/test_converter.py
similarity index 100%
rename from aria/conbox/test/test_converter.py
rename to src/aria/conbox/test/test_converter.py
diff --git a/aria/conbox/test/test_maplot.py b/src/aria/conbox/test/test_maplot.py
similarity index 100%
rename from aria/conbox/test/test_maplot.py
rename to src/aria/conbox/test/test_maplot.py
diff --git a/aria/conbox/test/test_ndconv.py b/src/aria/conbox/test/test_ndconv.py
similarity index 100%
rename from aria/conbox/test/test_ndconv.py
rename to src/aria/conbox/test/test_ndconv.py
diff --git a/aria/conbox/test/test_pdbdist.py b/src/aria/conbox/test/test_pdbdist.py
similarity index 100%
rename from aria/conbox/test/test_pdbdist.py
rename to src/aria/conbox/test/test_pdbdist.py
diff --git a/aria/conbox/test/test_pdbqual.py b/src/aria/conbox/test/test_pdbqual.py
similarity index 100%
rename from aria/conbox/test/test_pdbqual.py
rename to src/aria/conbox/test/test_pdbqual.py
diff --git a/aria/conbox/test/test_pdbstat.py b/src/aria/conbox/test/test_pdbstat.py
similarity index 100%
rename from aria/conbox/test/test_pdbstat.py
rename to src/aria/conbox/test/test_pdbstat.py
diff --git a/aria/conbox/test/test_protein.py b/src/aria/conbox/test/test_protein.py
similarity index 100%
rename from aria/conbox/test/test_protein.py
rename to src/aria/conbox/test/test_protein.py
diff --git a/aria/conbox/test/test_protmap.py b/src/aria/conbox/test/test_protmap.py
similarity index 100%
rename from aria/conbox/test/test_protmap.py
rename to src/aria/conbox/test/test_protmap.py
diff --git a/aria/conbox/test/test_reader.py b/src/aria/conbox/test/test_reader.py
similarity index 100%
rename from aria/conbox/test/test_reader.py
rename to src/aria/conbox/test/test_reader.py
diff --git a/aria/conbox/test/test_settings.py b/src/aria/conbox/test/test_settings.py
similarity index 100%
rename from aria/conbox/test/test_settings.py
rename to src/aria/conbox/test/test_settings.py
diff --git a/aria/conbox/test/test_setup.py b/src/aria/conbox/test/test_setup.py
similarity index 100%
rename from aria/conbox/test/test_setup.py
rename to src/aria/conbox/test/test_setup.py
diff --git a/aria/core/Analyser.py b/src/aria/core/Analyser.py
similarity index 100%
rename from aria/core/Analyser.py
rename to src/aria/core/Analyser.py
diff --git a/aria/core/AriaPeak.py b/src/aria/core/AriaPeak.py
similarity index 99%
rename from aria/core/AriaPeak.py
rename to src/aria/core/AriaPeak.py
index 5056c79b475782991eda8e8d94fc672f28124e98..b3f58c058ee87483224c3f57634528f7209dc73f 100644
--- a/aria/core/AriaPeak.py
+++ b/src/aria/core/AriaPeak.py
@@ -1371,7 +1371,8 @@ class DistanceRestraint(AbstractPeak):
# TODO: call Id -> Number? or is it another thing?
- counter = 0
+ # counter = 0
+ counter = 100000
def __init__(self, id=None):
diff --git a/aria/core/AriaXML.py b/src/aria/core/AriaXML.py
similarity index 100%
rename from aria/core/AriaXML.py
rename to src/aria/core/AriaXML.py
diff --git a/aria/core/Assignment.py b/src/aria/core/Assignment.py
similarity index 100%
rename from aria/core/Assignment.py
rename to src/aria/core/Assignment.py
diff --git a/aria/core/AssignmentFilter.py b/src/aria/core/AssignmentFilter.py
similarity index 100%
rename from aria/core/AssignmentFilter.py
rename to src/aria/core/AssignmentFilter.py
diff --git a/aria/core/Atom.py b/src/aria/core/Atom.py
similarity index 100%
rename from aria/core/Atom.py
rename to src/aria/core/Atom.py
diff --git a/aria/core/Calibrator.py b/src/aria/core/Calibrator.py
similarity index 100%
rename from aria/core/Calibrator.py
rename to src/aria/core/Calibrator.py
diff --git a/aria/core/Chain.py b/src/aria/core/Chain.py
similarity index 100%
rename from aria/core/Chain.py
rename to src/aria/core/Chain.py
diff --git a/aria/core/ChemicalShiftFilter.py b/src/aria/core/ChemicalShiftFilter.py
similarity index 100%
rename from aria/core/ChemicalShiftFilter.py
rename to src/aria/core/ChemicalShiftFilter.py
diff --git a/aria/core/ChemicalShiftList.py b/src/aria/core/ChemicalShiftList.py
similarity index 100%
rename from aria/core/ChemicalShiftList.py
rename to src/aria/core/ChemicalShiftList.py
diff --git a/aria/core/Cluster.py b/src/aria/core/Cluster.py
similarity index 99%
rename from aria/core/Cluster.py
rename to src/aria/core/Cluster.py
index fe548c376aa2cb75d7d813e79f3ac73ed3efd0c7..fa17a2be4201a2e9bac9edbfb3409dad6dafc2b7 100644
--- a/aria/core/Cluster.py
+++ b/src/aria/core/Cluster.py
@@ -110,7 +110,7 @@ class ClusteringXMLPickler(XMLBasePickler):
def load_from_element(self, xml_elt):
"""
- Load clustering settings from XMLElement
+ Instantiate clustering settings from XMLElement
Parameters
----------
diff --git a/aria/core/Contribution.py b/src/aria/core/Contribution.py
similarity index 100%
rename from aria/core/Contribution.py
rename to src/aria/core/Contribution.py
diff --git a/aria/core/ContributionAssigner.py b/src/aria/core/ContributionAssigner.py
similarity index 100%
rename from aria/core/ContributionAssigner.py
rename to src/aria/core/ContributionAssigner.py
diff --git a/aria/core/ConversionTable.py b/src/aria/core/ConversionTable.py
similarity index 100%
rename from aria/core/ConversionTable.py
rename to src/aria/core/ConversionTable.py
diff --git a/aria/core/CovalentDistances.py b/src/aria/core/CovalentDistances.py
similarity index 100%
rename from aria/core/CovalentDistances.py
rename to src/aria/core/CovalentDistances.py
diff --git a/aria/core/CrossPeak.py b/src/aria/core/CrossPeak.py
similarity index 100%
rename from aria/core/CrossPeak.py
rename to src/aria/core/CrossPeak.py
diff --git a/aria/core/CrossPeakFilter.py b/src/aria/core/CrossPeakFilter.py
similarity index 100%
rename from aria/core/CrossPeakFilter.py
rename to src/aria/core/CrossPeakFilter.py
diff --git a/aria/core/DataContainer.py b/src/aria/core/DataContainer.py
similarity index 100%
rename from aria/core/DataContainer.py
rename to src/aria/core/DataContainer.py
diff --git a/aria/core/Datum.py b/src/aria/core/Datum.py
similarity index 100%
rename from aria/core/Datum.py
rename to src/aria/core/Datum.py
diff --git a/aria/core/Experiment.py b/src/aria/core/Experiment.py
similarity index 100%
rename from aria/core/Experiment.py
rename to src/aria/core/Experiment.py
diff --git a/aria/core/Factory.py b/src/aria/core/Factory.py
similarity index 100%
rename from aria/core/Factory.py
rename to src/aria/core/Factory.py
diff --git a/aria/core/FloatFile.py b/src/aria/core/FloatFile.py
similarity index 100%
rename from aria/core/FloatFile.py
rename to src/aria/core/FloatFile.py
diff --git a/aria/core/Infrastructure.py b/src/aria/core/Infrastructure.py
similarity index 100%
rename from aria/core/Infrastructure.py
rename to src/aria/core/Infrastructure.py
diff --git a/aria/core/Iteration.py b/src/aria/core/Iteration.py
similarity index 100%
rename from aria/core/Iteration.py
rename to src/aria/core/Iteration.py
diff --git a/aria/core/JobManager.py b/src/aria/core/JobManager.py
similarity index 95%
rename from aria/core/JobManager.py
rename to src/aria/core/JobManager.py
index 1c04f641c02b947cd91beea23bd6f5ade4450617..7ed8284a2137015091613b841badb7515ab4b25a 100644
--- a/aria/core/JobManager.py
+++ b/src/aria/core/JobManager.py
@@ -25,7 +25,6 @@
.. $Date: 2010/03/23 15:27:24 $ ..
.. .......................................................................... ..
"""
-
from .TypeChecking import *
from threading import Thread
from .ariabase import *
@@ -215,7 +214,8 @@ class Job(Thread, AriaBaseClass):
# 'sge_job_hostname' : qsubhosts} ##### BARDIAUX
f = open(settings['script'])
- s = f.read() % d
+ s = f.read()
+ s = string.Formatter().vformat(s, (), d)
f.close()
# write new csh script
@@ -245,11 +245,12 @@ class Job(Thread, AriaBaseClass):
# Remove the file path (if exists)
try:
- os.unlink(filename)
- os.unlink(checkfile)
- except OSError:
+ [os.unlink(foo) for foo in (filename, checkfile)]
+ except Exception as e:
+ # TODO: same
+ # self.logger.exception(e)
pass
-
+
# start job
d = self.getSettings().as_dict()
@@ -268,22 +269,33 @@ class Job(Thread, AriaBaseClass):
# self.message(msg % job_desc)
self.debug(command)
- process = subprocess.Popen(command, shell=True,
- stdout=subprocess.PIPE,
- stderr=subprocess.PIPE)
- (out, err) = process.communicate()
+ try:
+ process = subprocess.Popen(command, shell=True,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+ (out, err) = process.communicate()
+ except Exception as e:
+ # TODO : make it functionnal
+ # self.logger.exception(e)
+ pass
+
self.message(out.replace("\n", "") + " (%s)" % job_desc)
# Parse output to get jobid and launch another job which depend on it to
# create checkpoint file
jobid = self.get_jobid(out)
- checkscript = '_%s' % jobid if jobid else ''
+ checkscript = '_%s' % str(jobid) if jobid else ''
if jobid:
+ # Update script output with job id
+ script = checkscript.join(os.path.splitext(d['script']))
+ self._up_script(d['script'], {'sge_job_id': jobid},
+ script)
# Create specific checkpoint file
checkscript = checkscript.join(os.path.splitext(d['check_script']))
self._up_script(d['check_script'], {'sge_job_id': jobid},
checkscript)
+ d['script'] = script
d['check_script'] = checkscript
checkcmd = self.checkcmd_template % d
@@ -323,8 +335,8 @@ class Job(Thread, AriaBaseClass):
# Remove if exists updated checkpoint script
try:
os.unlink(checkscript)
- except OSError:
- pass
+ except Exception as e:
+ LOG.exception(e)
if not self.isStopped() and terminated and checkpoint:
self.message('Job %s completed.' % job_desc)
@@ -383,8 +395,8 @@ class JobScheduler(JobManager):
try:
f.close()
- except:
- pass
+ except Exception as e:
+ LOG.exception(e)
return reason
diff --git a/aria/core/JobManager.py.ori b/src/aria/core/JobManager.py.ori
similarity index 100%
rename from aria/core/JobManager.py.ori
rename to src/aria/core/JobManager.py.ori
diff --git a/aria/core/Merger.py b/src/aria/core/Merger.py
similarity index 99%
rename from aria/core/Merger.py
rename to src/aria/core/Merger.py
index 013d72c14ea3f1b6d2f325fbf5a61953a813500d..76f579f043a5c6db115fa5e1ab02f9af760a6be8 100644
--- a/aria/core/Merger.py
+++ b/src/aria/core/Merger.py
@@ -32,6 +32,7 @@ from .Settings import Settings
from .xmlutils import XMLBasePickler as _XMLBasePickler
from past.builtins import cmp, xrange
+# TODO[FALLAIN]: m_no is REALLY number of peak that has been merged ??? (not spectrum id ??)
REPORT_HEADER = \
"""
# List of merged peaks.
diff --git a/aria/core/MolMol.py b/src/aria/core/MolMol.py
similarity index 100%
rename from aria/core/MolMol.py
rename to src/aria/core/MolMol.py
diff --git a/aria/core/Molecule.py b/src/aria/core/Molecule.py
similarity index 100%
rename from aria/core/Molecule.py
rename to src/aria/core/Molecule.py
diff --git a/aria/core/Molprobity.py b/src/aria/core/Molprobity.py
similarity index 100%
rename from aria/core/Molprobity.py
rename to src/aria/core/Molprobity.py
diff --git a/aria/core/NOEModel.py b/src/aria/core/NOEModel.py
similarity index 100%
rename from aria/core/NOEModel.py
rename to src/aria/core/NOEModel.py
diff --git a/aria/core/NOESYSpectrum.py b/src/aria/core/NOESYSpectrum.py
similarity index 100%
rename from aria/core/NOESYSpectrum.py
rename to src/aria/core/NOESYSpectrum.py
diff --git a/aria/core/NOESYSpectrumFilter.py b/src/aria/core/NOESYSpectrumFilter.py
similarity index 100%
rename from aria/core/NOESYSpectrumFilter.py
rename to src/aria/core/NOESYSpectrumFilter.py
diff --git a/aria/core/Network.py b/src/aria/core/Network.py
similarity index 100%
rename from aria/core/Network.py
rename to src/aria/core/Network.py
diff --git a/aria/core/OrderedDict.py b/src/aria/core/OrderedDict.py
similarity index 100%
rename from aria/core/OrderedDict.py
rename to src/aria/core/OrderedDict.py
diff --git a/aria/core/PDBReader.py b/src/aria/core/PDBReader.py
similarity index 100%
rename from aria/core/PDBReader.py
rename to src/aria/core/PDBReader.py
diff --git a/aria/core/PeakAssigner.py b/src/aria/core/PeakAssigner.py
similarity index 99%
rename from aria/core/PeakAssigner.py
rename to src/aria/core/PeakAssigner.py
index 63f8f1ed0f1e207e7b04e482535e2d47eb227cb0..840bd0b3cfe94cb6e7214fcba803432b58f9c23e 100644
--- a/aria/core/PeakAssigner.py
+++ b/src/aria/core/PeakAssigner.py
@@ -41,6 +41,8 @@ def peak_shape(deltas, errors):
class PeakAssignerSettings(Settings):
+ order = ()
+
def create(self):
from .Settings import NonNegativeFloat
from .Settings import YesNoChoice, FourLetterString, String
@@ -710,6 +712,17 @@ class PeakAssignerTextPickler(AriaBaseClass):
class PeakAssignerXMLPickler(XMLBasePickler):
def _xml_state(self, x):
+ """
+ Instantiate Peak assigner xml tag from PeakAssignerSettings object
+
+ Parameters
+ ----------
+ settings : PeakAssignerSettings object
+
+ Returns
+ -------
+
+ """
e = XMLElement()
return e
diff --git a/aria/core/Project.py b/src/aria/core/Project.py
similarity index 99%
rename from aria/core/Project.py
rename to src/aria/core/Project.py
index 493a9797c059cdea8ea45d72ce9536659008818a..bb4d2ef3247fda52062b1f69154a47c38440b253 100644
--- a/aria/core/Project.py
+++ b/src/aria/core/Project.py
@@ -1755,6 +1755,7 @@ class Project(AriaBaseClass):
from time import ctime
+ # Run protocol on iteration
last_iteration = self.getProtocol().go(iteration, self.getMolecule())
# run analysis on last iteration and solvent-refined
diff --git a/aria/core/Protocol.py b/src/aria/core/Protocol.py
similarity index 100%
rename from aria/core/Protocol.py
rename to src/aria/core/Protocol.py
diff --git a/aria/core/Relaxation.py b/src/aria/core/Relaxation.py
similarity index 100%
rename from aria/core/Relaxation.py
rename to src/aria/core/Relaxation.py
diff --git a/aria/core/Report.py b/src/aria/core/Report.py
similarity index 100%
rename from aria/core/Report.py
rename to src/aria/core/Report.py
diff --git a/aria/core/Residue.py b/src/aria/core/Residue.py
similarity index 100%
rename from aria/core/Residue.py
rename to src/aria/core/Residue.py
diff --git a/aria/core/RmsReport.py b/src/aria/core/RmsReport.py
similarity index 100%
rename from aria/core/RmsReport.py
rename to src/aria/core/RmsReport.py
diff --git a/aria/core/Settings.py b/src/aria/core/Settings.py
similarity index 100%
rename from aria/core/Settings.py
rename to src/aria/core/Settings.py
diff --git a/aria/core/ShiftAssignment.py b/src/aria/core/ShiftAssignment.py
similarity index 100%
rename from aria/core/ShiftAssignment.py
rename to src/aria/core/ShiftAssignment.py
diff --git a/aria/core/ShiftAssignmentFilter.py b/src/aria/core/ShiftAssignmentFilter.py
similarity index 100%
rename from aria/core/ShiftAssignmentFilter.py
rename to src/aria/core/ShiftAssignmentFilter.py
diff --git a/aria/core/Singleton.py b/src/aria/core/Singleton.py
similarity index 100%
rename from aria/core/Singleton.py
rename to src/aria/core/Singleton.py
diff --git a/aria/core/SpinPair.py b/src/aria/core/SpinPair.py
similarity index 100%
rename from aria/core/SpinPair.py
rename to src/aria/core/SpinPair.py
diff --git a/aria/core/StructureEnsemble.py b/src/aria/core/StructureEnsemble.py
similarity index 99%
rename from aria/core/StructureEnsemble.py
rename to src/aria/core/StructureEnsemble.py
index e5dc1b3041e1b3cdfceb03d4680e207428b22fd8..c1d03c1e36be98038fa0cdd58a64c3e84da7d696 100644
--- a/aria/core/StructureEnsemble.py
+++ b/src/aria/core/StructureEnsemble.py
@@ -28,8 +28,7 @@
"""
from .ariabase import AriaBaseClass
-from .Settings import NonNegativeInt
-from .Settings import Settings as _Settings
+from .Settings import Settings, NonNegativeInt
from .TypeChecking import *
# from .ConversionTable import CNS_CONVENTION, IUPAC_CONVENTION, \
# DYANA_CONVENTION
@@ -78,7 +77,7 @@ class NumberOfBestStructures(NonNegativeInt):
return NonNegativeInt.is_valid(self, value) or value == "all"
-class StructureEnsembleSettings(_Settings):
+class StructureEnsembleSettings(Settings):
# (DONE (BARDIAUX)) TODO: allow 'restraint_energy' to be sorting criterion
def create(self):
diff --git a/aria/core/SuperImposer.py b/src/aria/core/SuperImposer.py
similarity index 100%
rename from aria/core/SuperImposer.py
rename to src/aria/core/SuperImposer.py
diff --git a/aria/core/Topology.py b/src/aria/core/Topology.py
similarity index 100%
rename from aria/core/Topology.py
rename to src/aria/core/Topology.py
diff --git a/aria/core/TypeChecking.py b/src/aria/core/TypeChecking.py
similarity index 97%
rename from aria/core/TypeChecking.py
rename to src/aria/core/TypeChecking.py
index ab6fa0d09e28f321d655973cab2f4d79adc6a568..5d4cce329e03af73b977348db064bdc3c98b2115 100644
--- a/aria/core/TypeChecking.py
+++ b/src/aria/core/TypeChecking.py
@@ -32,6 +32,7 @@ import sys
import numpy
import logging
from numpy import zeros as _zeros
+from collections import OrderedDict
FLOAT = 'FLOAT'
@@ -40,6 +41,7 @@ INT = 'INT'
STRING = 'STRING'
UNICODE = 'UNICODE'
DICT = 'DICT'
+ORDEREDICT = 'ORDEREDICT'
LIST = 'LIST'
TUPLE = 'TUPLE'
ARRAY = 'ARRAY'
@@ -54,6 +56,7 @@ TYPES = {type(0.): FLOAT,
type(''): STRING,
type(u''): UNICODE if sys.version_info[:2] < (3, 0) else STRING,
type({}): DICT,
+ type(OrderedDict()): ORDEREDICT,
type([]): LIST,
type(()): TUPLE,
type(_zeros(0)): ARRAY,
@@ -167,7 +170,7 @@ check_float = lambda x: check_type(x, FLOAT, FLOAT64)
check_string = lambda x: check_type(x, STRING, UNICODE)
check_list = lambda x: check_type(x, LIST)
check_tuple = lambda x: check_type(x, TUPLE)
-check_dict = lambda x: check_type(x, DICT)
+check_dict = lambda x: check_type(x, DICT, ORDEREDICT)
check_array = lambda x: check_type(x, ARRAY)
check_file = lambda x: check_type(x, 'file')
check_bool = lambda x: check_type(x, INT, BOOL)
diff --git a/aria/core/ViolationAnalyser.py b/src/aria/core/ViolationAnalyser.py
similarity index 99%
rename from aria/core/ViolationAnalyser.py
rename to src/aria/core/ViolationAnalyser.py
index c546c81be781e19393a920f427ae688fb1270033..ede8d1c44f65c07999da9fe4b88dedef083c0e6f 100644
--- a/aria/core/ViolationAnalyser.py
+++ b/src/aria/core/ViolationAnalyser.py
@@ -259,7 +259,7 @@ class ViolationAnalyser(AriaBaseClass):
"""
check_type(ensemble, 'StructureEnsemble')
- check_type(peak, 'AriaPeak')
+ check_type(peak, 'AriaPeak', 'DistanceRestraint')
check_int(store_analysis)
check_type(lower_correction, FLOAT, NONE)
check_type(upper_correction, FLOAT, NONE)
diff --git a/aria/core/WhatifProfile.py b/src/aria/core/WhatifProfile.py
similarity index 99%
rename from aria/core/WhatifProfile.py
rename to src/aria/core/WhatifProfile.py
index c5d50f6d0844affed846aa8f3272b2dbf3e4ed6f..4dfc2d14b4d9b90b63085b41ab811c9d86d30ae8 100644
--- a/aria/core/WhatifProfile.py
+++ b/src/aria/core/WhatifProfile.py
@@ -27,6 +27,7 @@
"""
from __future__ import print_function
+import os
import time
CHECK_LIST = ['QUACHK', 'NQACHK', 'RAMCHK', 'C12CHK',
diff --git a/aria/core/_PDBReader.py b/src/aria/core/_PDBReader.py
similarity index 100%
rename from aria/core/_PDBReader.py
rename to src/aria/core/_PDBReader.py
diff --git a/aria/core/__N.py b/src/aria/core/__N.py
similarity index 100%
rename from aria/core/__N.py
rename to src/aria/core/__N.py
diff --git a/aria/core/__init__.py b/src/aria/core/__init__.py
similarity index 100%
rename from aria/core/__init__.py
rename to src/aria/core/__init__.py
diff --git a/aria/core/ariabase.py b/src/aria/core/ariabase.py
similarity index 83%
rename from aria/core/ariabase.py
rename to src/aria/core/ariabase.py
index 626d34e25701298dfc0819909f6157a45e83e263..0514f8f79860b72deae4a373071c2fd366602cd3 100644
--- a/aria/core/ariabase.py
+++ b/src/aria/core/ariabase.py
@@ -21,21 +21,17 @@
.. Distribution of substantively modified versions of this module is ..
.. prohibited without the explicit permission of the copyright holders. ..
.. ..
-.. $Author: bardiaux $ ..
-.. $Revision: 1.1.1.1 $ ..
-.. $Date: 2010/03/23 15:27:24 $ ..
.. .......................................................................... ..
"""
from __future__ import absolute_import, division, print_function
from future.builtins import input
from threading import Lock
-from .TypeChecking import *
-
+import inspect
import pkg_resources as pkgr
-
+from .TypeChecking import *
+from ..conbox.common import CustomLogging
# set correct python-path
-
ARIA_ENV = 'ARIA2'
MODULE_NAME = 'aria'
# TODO: sounds like PATH_MODULES global variable is not used anymore
@@ -60,6 +56,11 @@ VL_LOW = 1
# Print lock
PRINT_LOCK = Lock()
+# Logging Config
+# TODO: generate doc string at the package level with up to date version number
+LOG_CONF = CustomLogging(desc=__doc__, decorator=False)
+LOG = logging.getLogger(__name__)
+
def get_path():
"""Ask user to give aria installation path in ARIA2 env variable"""
@@ -175,7 +176,7 @@ def isprimitive(value):
# TODO[FALLAIN]: If we want to convert AriaBaseClass into new style class, we
# have to change Singleton class before (can't raise new style classes)
class AriaBaseClass:
- """Main aria base class which define settings and log messages"""
+ """Main aria base class which defines settings and log messages"""
use_restraint_weights = 0
@@ -188,9 +189,9 @@ class AriaBaseClass:
display_messages = 1
display_deprecated = 1
display_debug = 0
-
+
warnings_as_errors = 0
-
+
wrap_lines = 1
line_length = 80
description_length = 100
@@ -200,6 +201,7 @@ class AriaBaseClass:
# BB extendNmr
log_gui = None
log_stdout = 1
+ logger = LOG
# BB
check_type.active = 0
verbose_level = 0
@@ -218,7 +220,8 @@ class AriaBaseClass:
if new_flag:
data_path = pkgr.resource_filename(MODULE_NAME, 'data')
toppar_path = pkgr.resource_filename(MODULE_NAME, 'cns/toppar')
- protocols_path = pkgr.resource_filename(MODULE_NAME, 'cns/protocols')
+ protocols_path = pkgr.resource_filename(MODULE_NAME,
+ 'cns/protocols')
analysis_path = pkgr.resource_filename(MODULE_NAME,
'cns/protocols/analysis')
@@ -243,7 +246,8 @@ class AriaBaseClass:
be assigned with its own name. it will be used when displaying
warnings, errors, messages etc.
"""
-
+ self.logger = logging.getLogger(self.__module__)
+
if settings is not None:
self.setSettings(settings)
else:
@@ -251,9 +255,30 @@ class AriaBaseClass:
if name is not None:
self._set_name(name)
+
+ if self.__class__.display_debug:
+ logging.getLogger().setLevel(logging.DEBUG)
+
+ def __setstate__(self, d):
+ d['logger'] = logging.getLogger(self.__module__)
+ self.__dict__.update(d)
+
+ if self.__class__.display_debug:
+ logging.getLogger().setLevel(logging.DEBUG)
- def get_version_string(self):
- return self.VERSION_FORMAT % (self.VERSION, self.VERSION_RELEASE)
+ def __getstate__(self):
+ """
+ Remove logger attribute in order to pickle every ariabase object instance
+ """
+ d = dict(self.__dict__)
+ if 'logger' in d:
+ del d['logger']
+ return d
+
+ @staticmethod
+ def get_version_string():
+ return AriaBaseClass.VERSION_FORMAT % (
+ AriaBaseClass.VERSION, AriaBaseClass.VERSION_RELEASE)
def _set_name(self, name):
check_string(name)
@@ -295,7 +320,7 @@ class AriaBaseClass:
if self.__class__.display_debug:
self.message(msg, prefix='DEBUG')
- def error(self, exception=None, error='', msg=None):
+ def error(self, exception=None, error='', msg=""):
"""
Error log
@@ -316,7 +341,7 @@ class AriaBaseClass:
import inspect
- msg = msg if msg else ''
+ msg = str(msg) if msg else ''
if exception is None:
exception = Exception
@@ -338,12 +363,12 @@ class AriaBaseClass:
filename = code.co_filename
lineno = frame.f_lineno
- descr = '\nFile "%s", line %d in %s\n%s'
- msg += descr % (filename, lineno, func_name, error)
+ descr = 'File "%s", line %d in %s\n%s'
+ msg += descr % (filename, lineno, func_name, str(error))
- msg = 'USER ERROR <%s> ' % str(self.__class__) + msg
-
- self.__log(msg)
+ # msg = 'USER ERROR <%s> \n' % str(self.__class__) + msg
+ self.message(msg, 'ERROR')
+ # self.__log(msg)
raise exception(msg)
@@ -351,15 +376,15 @@ class AriaBaseClass:
check_string(tag)
check_string(msg)
-
+
from . import tools as tools
if self.wrap_lines:
- lines = tools.make_block(msg, self.line_length - len(tag))
+ lines = tools.make_block(msg, self.line_length - len(tag) - 8)
else:
lines = [msg]
-
- lines = tools.indent(lines, tag)
+
+ lines = tools.indent(lines, tag, extra=9)
return lines
@@ -368,26 +393,31 @@ class AriaBaseClass:
name = self._name
else:
name = self.__class__.__name__
-
- return '%s [%s]: ' % (prefix, name)
- def __print(self, prefix, msg, verbose_level):
+ return ' '.join(filter(None, (prefix, "[" + name + "]"))) + ': '
+
+ def __print(self, prefix, msg, verbose_level, func=None):
if verbose_level <= self.verbose_level or self.display_debug:
- lines = self.__format(prefix, msg)
+ lvl = logging.getLevelName(prefix)
+ lines = self.__format(self.__compile_name(""), msg)
if self.log_gui:
self.log_gui.write(lines + '\n')
if self.log_stdout:
with PRINT_LOCK:
- print(lines)
- self.__log(lines)
+ kw = {"extra": {
+ "abc_name": func.co_filename,
+ "abc_funcName": func.co_name,
+ "abc_lineno": func.co_firstlineno}}
+ self.logger.log(lvl, lines, **kw)
+ # self.__log(lines)
def __log(self, s):
if self.log_file is not None:
self.log_file.write(s + '\n')
self.log_file.flush()
- def message(self, msg, prefix='MESSAGE', verbose_level=VL_STANDARD):
+ def message(self, msg, prefix="INFO", verbose_level=VL_STANDARD):
"""
Message log
@@ -396,7 +426,7 @@ class AriaBaseClass:
msg :
prefix :
- (Default value = 'MESSAGE')
+ (Default value = 'INFO')
verbose_level :
(Default value = VL_STANDARD)
@@ -405,10 +435,9 @@ class AriaBaseClass:
"""
+ func = inspect.currentframe().f_back.f_code
if self.display_messages:
- prefix = self.__compile_name(prefix)
- msg = str(msg)
- self.__print(prefix, msg, verbose_level)
+ self.__print(prefix, str(msg), verbose_level, func=func)
def warning(self, msg, verbose_level=VL_STANDARD):
"""
@@ -426,16 +455,17 @@ class AriaBaseClass:
"""
-
+ func = inspect.currentframe().f_back.f_code
if self.display_warnings:
msg = str(msg)
-
+
if self.warnings_as_errors:
self.error(msg=msg)
else:
- prefix = self.__compile_name('WARNING')
- self.__print(prefix, msg, verbose_level)
+ # TODO: Find a way to use prefix correctly
+ # prefix = self.__compile_name('WARNING')
+ self.__print('WARNING', str(msg), verbose_level, func=func)
def halt(self):
"""aborts ARIA"""
diff --git a/aria/core/ccpn2top.py b/src/aria/core/ccpn2top.py
similarity index 100%
rename from aria/core/ccpn2top.py
rename to src/aria/core/ccpn2top.py
diff --git a/aria/core/ccpn_conversion.py b/src/aria/core/ccpn_conversion.py
similarity index 100%
rename from aria/core/ccpn_conversion.py
rename to src/aria/core/ccpn_conversion.py
diff --git a/aria/core/cns.py b/src/aria/core/cns.py
similarity index 98%
rename from aria/core/cns.py
rename to src/aria/core/cns.py
index 7b833db8fcfa62bad026665207dc49be29f7dc29..239374ff3897972ab7d8fc69410cd42174ed357e 100644
--- a/aria/core/cns.py
+++ b/src/aria/core/cns.py
@@ -82,40 +82,42 @@ PLAN = 'plan.tbl'
CNS_OUTPUT_PATH_NAME = 'cns'
CSH_SCRIPT_REFINE = '''\
-#! %(sge_job_shell)s
+#! {sge_job_shell}
# SGE/PBS/SLURM/LFS facility
-#$ -N %(sge_job_name)s
-#$ -S %(sge_job_shell)s
-#PBS -N %(sge_job_name)s
-#PBS -S %(sge_job_shell)s
-#BSUB -J %(sge_job_name)s
-#BSUB -L %(sge_job_shell)s
+#$ -N {sge_job_name}
+#$ -S {sge_job_shell}
+#PBS -N {sge_job_name}
+#PBS -S {sge_job_shell}
+#BSUB -J {sge_job_name}
+#BSUB -L {sge_job_shell}
#BSUB -oo refine.lsf.out
#BSUB -eo refine.lsf.err
-#SBATCH -J %(sge_job_name)s
+#SBATCH -o refine.%j.slurm.out
+#SBATCH -e refine.%j.slurm.err
+#SBATCH -J {sge_job_name}
#SBATCH --ignore-pbs
# results will be stored here
-setenv NEWIT %(iteration_path)s
+setenv NEWIT {iteration_path}
# project path
-setenv RUN %(cns_resource_path)s
+setenv RUN {cns_resource_path}
# individual run.cns is stored here
-setenv RUN_CNS %(cns_working_dir)s
+setenv RUN_CNS {cns_working_dir}
# path of ARIA2 cns protocos (for RAMA)
-setenv RAMA_DATA %(rama_data_dir)s
+setenv RAMA_DATA {rama_data_dir}
# CNS working directory
-cd %(cns_working_dir)s
+cd {cns_working_dir}
# solves some NFS sync problems
-cat %(cns_input_file)s > /dev/null
+cat {cns_input_file} > /dev/null
# command line
-%(cns_executable)s < %(cns_input_file)s >! %(cns_output_file)s
+{cns_executable} < {cns_input_file} >! {cns_output_file}
touch done
'''
@@ -135,6 +137,8 @@ CSH_SCRIPT_CHECKPOINT = '''\
#BSUB -eo checkpoint.lsf.err
#SBATCH -J {sge_checkjob_name}
#SBATCH -d afterany:{sge_job_id}
+#SBATCH -o checkpoint.{sge_job_id}.slurm.out
+#SBATCH -e checkpoint.{sge_job_id}.slurm.err
#SBATCH --ignore-pbs
# CSH script which depends on refine.csh
@@ -163,20 +167,20 @@ Requirements = Arch == "X86_64" && OpSys == "LINUX" && Memory > 200
CSH_SCRIPT_REFINE_CONDOR = '''\
# results will be stored here
-setenv NEWIT %(iteration_path)s
+setenv NEWIT {iteration_path}
# project path
-setenv RUN %(cns_resource_path)s
+setenv RUN {cns_resource_path}
# individual run.cns is stored here
-setenv RUN_CNS %(cns_working_dir)s
+setenv RUN_CNS {cns_working_dir}
# CNS working directory
-cd %(cns_working_dir)s
+cd {cns_working_dir}
# solves some NFS sync problems
-cat %(cns_input_file)s > /dev/null
+cat {cns_input_file} > /dev/null
# command line
condor_submit condor.job
@@ -190,19 +194,19 @@ cp /dev/null done
CSH_SCRIPT_ANALYSIS = """\
# results will be stored here
-setenv ANALYSIS %(analysis_output_path)s
+setenv ANALYSIS {analysis_output_path}
# results from last iteration
-setenv NEWIT %(iteration_path)s
+setenv NEWIT {iteration_path}
# project path
-setenv RUN %(cns_resource_path)s
+setenv RUN {cns_resource_path}
# individual run.cns and output-files are stored here
-setenv RUN_CNS %(cns_working_dir)s
+setenv RUN_CNS {cns_working_dir}
# working directory
-cd %(cns_working_dir)s
+cd {cns_working_dir}
# command line
"""
@@ -1987,13 +1991,13 @@ class CNS(StructureEngine):
cns_input = os.path.join(infra.get_cns_protocols_path(),
'%s.inp' % cns_script)
- # name of local output file
+ # name of local output filesge_job_shell
cns_output = '%s.out' % os.path.basename(cns_script)
if use_default_executable or self.use_condor:
cns_executable = self.getSettings()['local_executable']
else:
- cns_executable = '%(executable)s'
+ cns_executable = '{executable}'
d = {'cns_input_file': cns_input,
'cns_output_file': cns_output,
@@ -2013,7 +2017,8 @@ class CNS(StructureEngine):
condor_queue = "input = %(cns_input_file)s\n" \
"output = %(cns_output_file)s\nqueue\n"
self._write_condor_script(d, condor_append=condor_queue)
- script = CSH_SCRIPT_REFINE_CONDOR % d
+ script = string.Formatter().vformat(
+ CSH_SCRIPT_REFINE_CONDOR, (), SafeFormatDict(d))
checkscript = string.Formatter().vformat(
CSH_SCRIPT_CHECKPOINT, (), SafeFormatDict(d))
@@ -2023,10 +2028,11 @@ class CNS(StructureEngine):
# job_name for queue (not mandatory but usefull)
sge_job_name = os.path.basename(cns_working_dir)
d['sge_job_name'] = sge_job_name
- d['sge_job_shell'] = '/bin/csh'
+ d['sge_job_shell'] = '/bin/csh -f'
# d['sge_job_hostname'] = '%(sge_job_hostname)s'
- script = CSH_SCRIPT_REFINE % d
+ script = string.Formatter().vformat(
+ CSH_SCRIPT_REFINE, (), SafeFormatDict(d))
d['sge_checkjob_name'] = sge_job_name + "_checkpoint"
checkscript = string.Formatter().vformat(
CSH_SCRIPT_CHECKPOINT, (), SafeFormatDict(d))
@@ -2462,7 +2468,8 @@ Could not create working directory for CNS analysis scripts ("%s").""" % (
'cns_working_dir': working_dir,
'cns_executable': cns_executable}
- csh_script = CSH_SCRIPT_ANALYSIS % csh_dict
+ csh_script = string.Formatter().vformat(
+ CSH_SCRIPT_ANALYSIS, (), SafeFormatDict(csh_dict))
condor_append = '\n'
@@ -2660,6 +2667,7 @@ Could not create working directory for CNS analysis scripts ("%s").""" % (
job_settings = JM.JobSettings()
job_settings['script'] = csh_script
job_settings['working_directory'] = cns_wdir
+ job_settings['check_script'] = check_script
job = JM.Job(job_settings)
jobs.append(job)
@@ -2822,8 +2830,8 @@ Could not create working directory for CNS analysis scripts ("%s").""" % (
else:
try:
os.unlink(fn)
- except:
- pass
+ except Exception as e:
+ self.logger.exception(e)
if action_performed:
msg = {1: '(un)ambig.tbl files in %s have been gzipped',
diff --git a/aria/core/cns.py.ori b/src/aria/core/cns.py.ori
similarity index 100%
rename from aria/core/cns.py.ori
rename to src/aria/core/cns.py.ori
diff --git a/aria/core/conversion.py b/src/aria/core/conversion.py
similarity index 99%
rename from aria/core/conversion.py
rename to src/aria/core/conversion.py
index 39cebe733776fa9f6c8b0c8e5bcb8619bec1a171..52256b22a0ab706d52cb6b5bf19cea05ce34ea0e 100644
--- a/aria/core/conversion.py
+++ b/src/aria/core/conversion.py
@@ -769,7 +769,8 @@ class SequenceList(AriaBaseClass):
from .PDBReader import BASE_TYPES
import sys
- from io import StringIO
+ # from io import StringIO
+ from io import BytesIO as StringIO
# import StringIO
s = Reader()
@@ -908,7 +909,8 @@ class PpmList(AriaBaseClass):
from .legacy.PpmList import PpmList as Reader
import sys
- from io import StringIO
+ # from io import StringIO
+ from io import BytesIO as StringIO
r = Reader()
@@ -1746,7 +1748,8 @@ class NoeList(AriaBaseClass):
from .legacy.NoeList import NoeList as Reader
import sys
- from io import StringIO
+ # from io import StringIO
+ from io import BytesIO as StringIO
r = Reader()
a = [file]
diff --git a/aria/core/exportToCcpn.py b/src/aria/core/exportToCcpn.py
similarity index 100%
rename from aria/core/exportToCcpn.py
rename to src/aria/core/exportToCcpn.py
diff --git a/aria/core/gui/AriaViewer.py b/src/aria/core/gui/AriaViewer.py
similarity index 100%
rename from aria/core/gui/AriaViewer.py
rename to src/aria/core/gui/AriaViewer.py
diff --git a/aria/core/gui/__init__.py b/src/aria/core/gui/__init__.py
similarity index 100%
rename from aria/core/gui/__init__.py
rename to src/aria/core/gui/__init__.py
diff --git a/aria/core/gui/ccpnGui.py b/src/aria/core/gui/ccpnGui.py
similarity index 100%
rename from aria/core/gui/ccpnGui.py
rename to src/aria/core/gui/ccpnGui.py
diff --git a/aria/core/gui/decorators.py b/src/aria/core/gui/decorators.py
similarity index 100%
rename from aria/core/gui/decorators.py
rename to src/aria/core/gui/decorators.py
diff --git a/aria/core/gui/gui.py b/src/aria/core/gui/gui.py
similarity index 100%
rename from aria/core/gui/gui.py
rename to src/aria/core/gui/gui.py
diff --git a/aria/core/gui/logo.gif b/src/aria/core/gui/logo.gif
similarity index 100%
rename from aria/core/gui/logo.gif
rename to src/aria/core/gui/logo.gif
diff --git a/aria/core/gui/panels.py b/src/aria/core/gui/panels.py
similarity index 100%
rename from aria/core/gui/panels.py
rename to src/aria/core/gui/panels.py
diff --git a/aria/core/gui/shaded_folder.xpm b/src/aria/core/gui/shaded_folder.xpm
similarity index 100%
rename from aria/core/gui/shaded_folder.xpm
rename to src/aria/core/gui/shaded_folder.xpm
diff --git a/aria/core/gui/warning.xpm b/src/aria/core/gui/warning.xpm
similarity index 100%
rename from aria/core/gui/warning.xpm
rename to src/aria/core/gui/warning.xpm
diff --git a/aria/core/gui/widgets.py b/src/aria/core/gui/widgets.py
similarity index 100%
rename from aria/core/gui/widgets.py
rename to src/aria/core/gui/widgets.py
diff --git a/aria/core/importFromCcpn.py b/src/aria/core/importFromCcpn.py
similarity index 100%
rename from aria/core/importFromCcpn.py
rename to src/aria/core/importFromCcpn.py
diff --git a/aria/core/legacy/AminoAcid.py b/src/aria/core/legacy/AminoAcid.py
similarity index 100%
rename from aria/core/legacy/AminoAcid.py
rename to src/aria/core/legacy/AminoAcid.py
diff --git a/aria/core/legacy/Comparisons.py b/src/aria/core/legacy/Comparisons.py
similarity index 100%
rename from aria/core/legacy/Comparisons.py
rename to src/aria/core/legacy/Comparisons.py
diff --git a/aria/core/legacy/DeleteCnsComments.py b/src/aria/core/legacy/DeleteCnsComments.py
similarity index 100%
rename from aria/core/legacy/DeleteCnsComments.py
rename to src/aria/core/legacy/DeleteCnsComments.py
diff --git a/aria/core/legacy/DeleteComments.py b/src/aria/core/legacy/DeleteComments.py
similarity index 95%
rename from aria/core/legacy/DeleteComments.py
rename to src/aria/core/legacy/DeleteComments.py
index ca8b978decac5f4cbdc68a748f80df023c7258b2..702b2ccf5ff36246ae6b1a4b7dbd0cdb36f9ba78 100644
--- a/aria/core/legacy/DeleteComments.py
+++ b/src/aria/core/legacy/DeleteComments.py
@@ -72,7 +72,7 @@ def GetFile(input, output):
"""
getback = GetString(input)
- print(u'writing the output to %s' % str(output))
+ print('writing the output to %s' % str(output))
outhandle = open(output, 'w')
outhandle.write(getback)
outhandle.close()
@@ -97,7 +97,7 @@ def GetString(input):
"""
# message:
- print(u'reading %s' % str(input))
+ print('reading %s' % str(input))
# ARIA2 print 'deleting comments'
# opening the filehandles, get one big string:
@@ -142,8 +142,8 @@ def GetString(input):
# write warning, if there are still braces left:
if openbr.search(stuff) is not None:
- print(u'WARNING: there are more { than }')
+ print('WARNING: there are more { than }')
if closebr.search(stuff) is not None:
- print(u'WARNING: there are more } than {')
+ print('WARNING: there are more } than {')
inhandle.close()
return stuff
diff --git a/aria/core/legacy/DictWithDefault.py b/src/aria/core/legacy/DictWithDefault.py
similarity index 95%
rename from aria/core/legacy/DictWithDefault.py
rename to src/aria/core/legacy/DictWithDefault.py
index 3c87ac58b72c967d1856198f7c1e5c64becfdee3..485d5d8ab2a2fe63fcce56ecd31e4ddd4a048fae 100644
--- a/aria/core/legacy/DictWithDefault.py
+++ b/src/aria/core/legacy/DictWithDefault.py
@@ -10,7 +10,7 @@ import copy
class DictWithDefault(UserDict):
def __init__(self, default, **kwargs):
- super(UserDict, self).__init__(**kwargs)
+ UserDict.__init__(self, **kwargs)
self.data = {}
self.default = default
diff --git a/aria/core/legacy/FortranFormat.py b/src/aria/core/legacy/FortranFormat.py
similarity index 100%
rename from aria/core/legacy/FortranFormat.py
rename to src/aria/core/legacy/FortranFormat.py
diff --git a/aria/core/legacy/HeteronucleusPlusProton.py b/src/aria/core/legacy/HeteronucleusPlusProton.py
similarity index 100%
rename from aria/core/legacy/HeteronucleusPlusProton.py
rename to src/aria/core/legacy/HeteronucleusPlusProton.py
diff --git a/aria/core/legacy/NoeList.py b/src/aria/core/legacy/NoeList.py
similarity index 100%
rename from aria/core/legacy/NoeList.py
rename to src/aria/core/legacy/NoeList.py
diff --git a/aria/core/legacy/Nomenclature.py b/src/aria/core/legacy/Nomenclature.py
similarity index 100%
rename from aria/core/legacy/Nomenclature.py
rename to src/aria/core/legacy/Nomenclature.py
diff --git a/aria/core/legacy/PpmList.py b/src/aria/core/legacy/PpmList.py
similarity index 100%
rename from aria/core/legacy/PpmList.py
rename to src/aria/core/legacy/PpmList.py
diff --git a/aria/core/legacy/PseudoAtom.py b/src/aria/core/legacy/PseudoAtom.py
similarity index 100%
rename from aria/core/legacy/PseudoAtom.py
rename to src/aria/core/legacy/PseudoAtom.py
diff --git a/aria/core/legacy/QualityChecks/DelTrailingSlash.py b/src/aria/core/legacy/QualityChecks/DelTrailingSlash.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/DelTrailingSlash.py
rename to src/aria/core/legacy/QualityChecks/DelTrailingSlash.py
diff --git a/aria/core/legacy/QualityChecks/Descriptive.py b/src/aria/core/legacy/QualityChecks/Descriptive.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/Descriptive.py
rename to src/aria/core/legacy/QualityChecks/Descriptive.py
diff --git a/aria/core/legacy/QualityChecks/QualityChecks.py b/src/aria/core/legacy/QualityChecks/QualityChecks.py
similarity index 99%
rename from aria/core/legacy/QualityChecks/QualityChecks.py
rename to src/aria/core/legacy/QualityChecks/QualityChecks.py
index 6fe0259b78eee0ad6117c84ec10058c19f9d1dab..16d1f0a736019b6ba6af7d8fdffbbe3050cb79b4 100644
--- a/aria/core/legacy/QualityChecks/QualityChecks.py
+++ b/src/aria/core/legacy/QualityChecks/QualityChecks.py
@@ -145,12 +145,12 @@ def runChecks(workingDirectory='/tmp/test_pdb',
return_procheck_results=0,
fileList=None,
skipPrefix=None):
- from . import RunProcheck
- from . import RunProsa
+ from .RunProcheck import RunProcheck
+ from .RunProsa import RunProsa
from .RunWhatif import RunWhatif
- from . import Descriptive
+ from .Descriptive import Descriptive
# from . import readCheckDB
- from . import ReadCheckDB as readCheckDB
+ from .ReadCheckDB import readCheckDB
from ...Molprobity import MolprobityClashlist
diff --git a/aria/core/legacy/QualityChecks/ReadCheckDB.py b/src/aria/core/legacy/QualityChecks/ReadCheckDB.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/ReadCheckDB.py
rename to src/aria/core/legacy/QualityChecks/ReadCheckDB.py
diff --git a/aria/core/legacy/QualityChecks/RunProcheck.py b/src/aria/core/legacy/QualityChecks/RunProcheck.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/RunProcheck.py
rename to src/aria/core/legacy/QualityChecks/RunProcheck.py
diff --git a/aria/core/legacy/QualityChecks/RunProsa.py b/src/aria/core/legacy/QualityChecks/RunProsa.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/RunProsa.py
rename to src/aria/core/legacy/QualityChecks/RunProsa.py
diff --git a/aria/core/legacy/QualityChecks/RunWhatif.py b/src/aria/core/legacy/QualityChecks/RunWhatif.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/RunWhatif.py
rename to src/aria/core/legacy/QualityChecks/RunWhatif.py
diff --git a/aria/core/legacy/QualityChecks/__init__.py b/src/aria/core/legacy/QualityChecks/__init__.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/__init__.py
rename to src/aria/core/legacy/QualityChecks/__init__.py
diff --git a/aria/core/legacy/QualityChecks/test/__init__.py b/src/aria/core/legacy/QualityChecks/test/__init__.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/test/__init__.py
rename to src/aria/core/legacy/QualityChecks/test/__init__.py
diff --git a/aria/core/legacy/QualityChecks/test/test_DelTrailingSlash.py b/src/aria/core/legacy/QualityChecks/test/test_DelTrailingSlash.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/test/test_DelTrailingSlash.py
rename to src/aria/core/legacy/QualityChecks/test/test_DelTrailingSlash.py
diff --git a/aria/core/legacy/QualityChecks/test/test_Descriptive.py b/src/aria/core/legacy/QualityChecks/test/test_Descriptive.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/test/test_Descriptive.py
rename to src/aria/core/legacy/QualityChecks/test/test_Descriptive.py
diff --git a/aria/core/legacy/QualityChecks/test/test_QualityChecks.py b/src/aria/core/legacy/QualityChecks/test/test_QualityChecks.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/test/test_QualityChecks.py
rename to src/aria/core/legacy/QualityChecks/test/test_QualityChecks.py
diff --git a/aria/core/legacy/QualityChecks/test/test_ReadCheckDB.py b/src/aria/core/legacy/QualityChecks/test/test_ReadCheckDB.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/test/test_ReadCheckDB.py
rename to src/aria/core/legacy/QualityChecks/test/test_ReadCheckDB.py
diff --git a/aria/core/legacy/QualityChecks/test/test_RunProcheck.py b/src/aria/core/legacy/QualityChecks/test/test_RunProcheck.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/test/test_RunProcheck.py
rename to src/aria/core/legacy/QualityChecks/test/test_RunProcheck.py
diff --git a/aria/core/legacy/QualityChecks/test/test_RunProsa.py b/src/aria/core/legacy/QualityChecks/test/test_RunProsa.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/test/test_RunProsa.py
rename to src/aria/core/legacy/QualityChecks/test/test_RunProsa.py
diff --git a/aria/core/legacy/QualityChecks/test/test_RunWhatif.py b/src/aria/core/legacy/QualityChecks/test/test_RunWhatif.py
similarity index 100%
rename from aria/core/legacy/QualityChecks/test/test_RunWhatif.py
rename to src/aria/core/legacy/QualityChecks/test/test_RunWhatif.py
diff --git a/aria/core/legacy/ReadXeasy.py b/src/aria/core/legacy/ReadXeasy.py
similarity index 100%
rename from aria/core/legacy/ReadXeasy.py
rename to src/aria/core/legacy/ReadXeasy.py
diff --git a/aria/core/legacy/SequenceList.py b/src/aria/core/legacy/SequenceList.py
similarity index 91%
rename from aria/core/legacy/SequenceList.py
rename to src/aria/core/legacy/SequenceList.py
index 5a656723fee1c701936a7489b9ea7bc9f3cfa995..6c4a2c0e0372375ecafee185ad23a5f66075890d 100644
--- a/aria/core/legacy/SequenceList.py
+++ b/src/aria/core/legacy/SequenceList.py
@@ -11,6 +11,7 @@ from . import TextFile as TextFile
import os
import re
import string
+#from builtins import str
from . import AminoAcid as AminoAcid
@@ -275,7 +276,7 @@ class SequenceList:
"""
if os.path.exists(fileName):
- print(u'reading sequence %s' % str(fileName))
+ print('reading sequence %s' % str(fileName))
self.fileName = fileName
else:
print(u'the file %s does not exist. Abort ReadSeq method.' %
@@ -298,7 +299,7 @@ class SequenceList:
# catch all the numbers and non-standard amino acids:
if string.strip(aaoutlist[2]) == '':
print(u'could not understand: %s' % str(element[0:3]))
- print(u'=> this is not included in the sequence!')
+ print('=> this is not included in the sequence!')
continue
# append in to the list attribute:
self.aalist.append(aaoutlist[1])
@@ -308,9 +309,9 @@ class SequenceList:
def Stdout(self):
"""writes the list of aminoacids to stdout"""
- print(u'the file %s contains the sequence:' % str(self.fileName))
+ print('the file %s contains the sequence:' % str(self.fileName))
for eachaa in self.aalist:
- print(u'%s' % str(eachaa))
+ print('%s' % str(eachaa))
###############################################################################
@@ -326,12 +327,12 @@ class SequenceList:
-------
"""
- print(u'the file %s contains the sequence:' % str(self.fileName))
+ print('the file %s contains the sequence:' % str(self.fileName))
outS = ''
for eachaa in self.aalist:
outS = outS + AminoAcid.AminoAcid(eachaa)[0]
- print(u'%s' % str(outS))
- print(u'the sequence includes %s residues.' % str(len(self.aalist)))
+ print('%s' % str(outS))
+ print('the sequence includes %s residues.' % str(len(self.aalist)))
###############################################################################
def WriteFasta(self, outfile):
@@ -351,10 +352,10 @@ class SequenceList:
try:
outhandle = TextFile.TextFile(outfile, 'w')
except IOError:
- print(u'could not open the file %s' % str(outfile))
- print(u'Abort WriteFasta method.')
+ print('could not open the file %s' % str(outfile))
+ print('Abort WriteFasta method.')
return
- print(u'writing to the file: %s' % str(outfile))
+ print('writing to the file: %s' % str(outfile))
# for the comment use the fileName
# (if it's empty use 'SEQUENCELIST_OUTPUT'):
@@ -392,10 +393,10 @@ class SequenceList:
try:
outhandle = TextFile.TextFile(outfile, 'w')
except IOError:
- print(u'could not open the file %s' % str(outfile))
- print(u'Abort WriteSeq method.')
+ print('could not open the file %s' % str(outfile))
+ print('Abort WriteSeq method.')
return
- print(u'writing to the file: %s' % str(outfile))
+ print('writing to the file: %s' % str(outfile))
for eachaa in self.aalist:
outhandle.write(eachaa + '\n')
outhandle.close()
@@ -418,10 +419,10 @@ class SequenceList:
try:
outhandle = TextFile.TextFile(outfile, 'w')
except IOError:
- print(u'could not open the file %s' % str(outfile))
- print(u'Abort WriteSeq method.')
+ print('could not open the file %s' % str(outfile))
+ print('Abort WriteSeq method.')
return
- print(u'writing to the file: %s' % str(outfile))
+ print('writing to the file: %s' % str(outfile))
for eachaa in self.aalist:
outhandle.write(string.lower(eachaa) + '\n')
outhandle.close()
@@ -444,10 +445,10 @@ class SequenceList:
try:
outhandle = TextFile.TextFile(outfile, 'w')
except IOError:
- print(u'could not open the file %s' % str(outfile))
- print(u'Abort WriteSeq1 method.')
+ print('could not open the file %s' % str(outfile))
+ print('Abort WriteSeq1 method.')
return
- print(u'writing to the file: %s' % str(outfile))
+ print('writing to the file: %s' % str(outfile))
for eachaa in self.aalist:
outhandle.write(AminoAcid.AminoAcid(eachaa)[0])
outhandle.write('\n')
@@ -530,10 +531,10 @@ class SequenceList:
try:
outhandle = TextFile.TextFile(fileName, 'w')
except IOError:
- print(u'could not open the file %s' % str(fileName))
- print(u'Abort WriteXML2File method.')
+ print('could not open the file %s' % str(fileName))
+ print('Abort WriteXML2File method.')
return
- print(u'writing to the file: %s' % str(fileName))
+ print('writing to the file: %s' % str(fileName))
outhandle.write(outString)
outhandle.close()
@@ -541,7 +542,7 @@ class SequenceList:
###############################################################################
def _DoesFileExist(fileName):
if os.path.exists(fileName) == 0:
- print(u'WARNING: %s does not exist.' % str(fileName))
+ print('WARNING: %s does not exist.' % str(fileName))
return 0
return 1
@@ -549,13 +550,13 @@ def _DoesFileExist(fileName):
###############################################################################
# test code:
if __name__ == "__main__":
- print(u'testing module:')
+ print('testing module:')
SL = SequenceList()
SL.aalist = ['ARG', 'GLY', 'HIS', 'PRO', 'GLU', 'TYR', 'ASP', 'GLN']
- print(u'1. The test sequence is:')
+ print('1. The test sequence is:')
print(SL.aalist)
- print(u'\n2. The Stdout() method prints:')
+ print('\n2. The Stdout() method prints:')
SL.Stdout()
- print(u'\n3. The XML output is:')
+ print('\n3. The XML output is:')
print(SL.WriteXML2String())
- print(u'\ntest done. bye.')
+ print('\ntest done. bye.')
diff --git a/aria/core/legacy/Talos2Aria.py b/src/aria/core/legacy/Talos2Aria.py
similarity index 100%
rename from aria/core/legacy/Talos2Aria.py
rename to src/aria/core/legacy/Talos2Aria.py
diff --git a/aria/core/legacy/TextFile.py b/src/aria/core/legacy/TextFile.py
similarity index 100%
rename from aria/core/legacy/TextFile.py
rename to src/aria/core/legacy/TextFile.py
diff --git a/aria/core/legacy/__init__.py b/src/aria/core/legacy/__init__.py
similarity index 100%
rename from aria/core/legacy/__init__.py
rename to src/aria/core/legacy/__init__.py
diff --git a/aria/core/legacy/test/__init__.py b/src/aria/core/legacy/test/__init__.py
similarity index 100%
rename from aria/core/legacy/test/__init__.py
rename to src/aria/core/legacy/test/__init__.py
diff --git a/aria/core/legacy/test/test_AminoAcid.py b/src/aria/core/legacy/test/test_AminoAcid.py
similarity index 100%
rename from aria/core/legacy/test/test_AminoAcid.py
rename to src/aria/core/legacy/test/test_AminoAcid.py
diff --git a/aria/core/legacy/test/test_Comparisons.py b/src/aria/core/legacy/test/test_Comparisons.py
similarity index 100%
rename from aria/core/legacy/test/test_Comparisons.py
rename to src/aria/core/legacy/test/test_Comparisons.py
diff --git a/aria/core/legacy/test/test_DeleteCnsComments.py b/src/aria/core/legacy/test/test_DeleteCnsComments.py
similarity index 100%
rename from aria/core/legacy/test/test_DeleteCnsComments.py
rename to src/aria/core/legacy/test/test_DeleteCnsComments.py
diff --git a/aria/core/legacy/test/test_DeleteComments.py b/src/aria/core/legacy/test/test_DeleteComments.py
similarity index 100%
rename from aria/core/legacy/test/test_DeleteComments.py
rename to src/aria/core/legacy/test/test_DeleteComments.py
diff --git a/aria/core/legacy/test/test_DictWithDefault.py b/src/aria/core/legacy/test/test_DictWithDefault.py
similarity index 100%
rename from aria/core/legacy/test/test_DictWithDefault.py
rename to src/aria/core/legacy/test/test_DictWithDefault.py
diff --git a/aria/core/legacy/test/test_FortranFormat.py b/src/aria/core/legacy/test/test_FortranFormat.py
similarity index 100%
rename from aria/core/legacy/test/test_FortranFormat.py
rename to src/aria/core/legacy/test/test_FortranFormat.py
diff --git a/aria/core/legacy/test/test_HeteronucleusPlusProton.py b/src/aria/core/legacy/test/test_HeteronucleusPlusProton.py
similarity index 100%
rename from aria/core/legacy/test/test_HeteronucleusPlusProton.py
rename to src/aria/core/legacy/test/test_HeteronucleusPlusProton.py
diff --git a/aria/core/legacy/test/test_NoeList.py b/src/aria/core/legacy/test/test_NoeList.py
similarity index 100%
rename from aria/core/legacy/test/test_NoeList.py
rename to src/aria/core/legacy/test/test_NoeList.py
diff --git a/aria/core/legacy/test/test_Nomenclature.py b/src/aria/core/legacy/test/test_Nomenclature.py
similarity index 100%
rename from aria/core/legacy/test/test_Nomenclature.py
rename to src/aria/core/legacy/test/test_Nomenclature.py
diff --git a/aria/core/legacy/test/test_PpmList.py b/src/aria/core/legacy/test/test_PpmList.py
similarity index 100%
rename from aria/core/legacy/test/test_PpmList.py
rename to src/aria/core/legacy/test/test_PpmList.py
diff --git a/aria/core/legacy/test/test_PseudoAtom.py b/src/aria/core/legacy/test/test_PseudoAtom.py
similarity index 100%
rename from aria/core/legacy/test/test_PseudoAtom.py
rename to src/aria/core/legacy/test/test_PseudoAtom.py
diff --git a/aria/core/legacy/test/test_ReadXeasy.py b/src/aria/core/legacy/test/test_ReadXeasy.py
similarity index 100%
rename from aria/core/legacy/test/test_ReadXeasy.py
rename to src/aria/core/legacy/test/test_ReadXeasy.py
diff --git a/aria/core/legacy/test/test_SequenceList.py b/src/aria/core/legacy/test/test_SequenceList.py
similarity index 100%
rename from aria/core/legacy/test/test_SequenceList.py
rename to src/aria/core/legacy/test/test_SequenceList.py
diff --git a/aria/core/legacy/test/test_Talos2Aria.py b/src/aria/core/legacy/test/test_Talos2Aria.py
similarity index 100%
rename from aria/core/legacy/test/test_Talos2Aria.py
rename to src/aria/core/legacy/test/test_Talos2Aria.py
diff --git a/aria/core/legacy/test/test_TextFile.py b/src/aria/core/legacy/test/test_TextFile.py
similarity index 100%
rename from aria/core/legacy/test/test_TextFile.py
rename to src/aria/core/legacy/test/test_TextFile.py
diff --git a/aria/core/mathutils.py b/src/aria/core/mathutils.py
similarity index 100%
rename from aria/core/mathutils.py
rename to src/aria/core/mathutils.py
diff --git a/aria/core/scientific/FortranFormat.py b/src/aria/core/scientific/FortranFormat.py
similarity index 100%
rename from aria/core/scientific/FortranFormat.py
rename to src/aria/core/scientific/FortranFormat.py
diff --git a/aria/core/scientific/PDB.py b/src/aria/core/scientific/PDB.py
similarity index 100%
rename from aria/core/scientific/PDB.py
rename to src/aria/core/scientific/PDB.py
diff --git a/aria/core/scientific/TextFile.py b/src/aria/core/scientific/TextFile.py
similarity index 100%
rename from aria/core/scientific/TextFile.py
rename to src/aria/core/scientific/TextFile.py
diff --git a/aria/core/scientific/__init__.py b/src/aria/core/scientific/__init__.py
similarity index 100%
rename from aria/core/scientific/__init__.py
rename to src/aria/core/scientific/__init__.py
diff --git a/aria/core/scientific/test/__init__.py b/src/aria/core/scientific/test/__init__.py
similarity index 100%
rename from aria/core/scientific/test/__init__.py
rename to src/aria/core/scientific/test/__init__.py
diff --git a/aria/core/test/__init__.py b/src/aria/core/test/__init__.py
similarity index 100%
rename from aria/core/test/__init__.py
rename to src/aria/core/test/__init__.py
diff --git a/aria/core/test/test_Analyser.py b/src/aria/core/test/test_Analyser.py
similarity index 100%
rename from aria/core/test/test_Analyser.py
rename to src/aria/core/test/test_Analyser.py
diff --git a/aria/core/test/test_AriaPeak.py b/src/aria/core/test/test_AriaPeak.py
similarity index 100%
rename from aria/core/test/test_AriaPeak.py
rename to src/aria/core/test/test_AriaPeak.py
diff --git a/aria/core/test/test_Assignment.py b/src/aria/core/test/test_AriaXML.py
similarity index 100%
rename from aria/core/test/test_Assignment.py
rename to src/aria/core/test/test_AriaXML.py
diff --git a/aria/core/test/test_AssignmentFilter.py b/src/aria/core/test/test_Assignment.py
similarity index 100%
rename from aria/core/test/test_AssignmentFilter.py
rename to src/aria/core/test/test_Assignment.py
diff --git a/aria/core/test/test_Atom.py b/src/aria/core/test/test_AssignmentFilter.py
similarity index 100%
rename from aria/core/test/test_Atom.py
rename to src/aria/core/test/test_AssignmentFilter.py
diff --git a/aria/core/test/test_Calibrator.py b/src/aria/core/test/test_Atom.py
similarity index 100%
rename from aria/core/test/test_Calibrator.py
rename to src/aria/core/test/test_Atom.py
diff --git a/aria/core/test/test_Chain.py b/src/aria/core/test/test_Calibrator.py
similarity index 100%
rename from aria/core/test/test_Chain.py
rename to src/aria/core/test/test_Calibrator.py
diff --git a/aria/core/test/test_ChemicalShiftFilter.py b/src/aria/core/test/test_Chain.py
similarity index 100%
rename from aria/core/test/test_ChemicalShiftFilter.py
rename to src/aria/core/test/test_Chain.py
diff --git a/aria/core/test/test_ChemicalShiftList.py b/src/aria/core/test/test_ChemicalShiftFilter.py
similarity index 100%
rename from aria/core/test/test_ChemicalShiftList.py
rename to src/aria/core/test/test_ChemicalShiftFilter.py
diff --git a/aria/core/test/test_Cluster.py b/src/aria/core/test/test_ChemicalShiftList.py
similarity index 100%
rename from aria/core/test/test_Cluster.py
rename to src/aria/core/test/test_ChemicalShiftList.py
diff --git a/aria/core/test/test_Contribution.py b/src/aria/core/test/test_Cluster.py
similarity index 100%
rename from aria/core/test/test_Contribution.py
rename to src/aria/core/test/test_Cluster.py
diff --git a/aria/core/test/test_ContributionAssigner.py b/src/aria/core/test/test_Contribution.py
similarity index 100%
rename from aria/core/test/test_ContributionAssigner.py
rename to src/aria/core/test/test_Contribution.py
diff --git a/aria/core/test/test_ConversionTable.py b/src/aria/core/test/test_ContributionAssigner.py
similarity index 100%
rename from aria/core/test/test_ConversionTable.py
rename to src/aria/core/test/test_ContributionAssigner.py
diff --git a/aria/core/test/test_CovalentDistances.py b/src/aria/core/test/test_ConversionTable.py
similarity index 100%
rename from aria/core/test/test_CovalentDistances.py
rename to src/aria/core/test/test_ConversionTable.py
diff --git a/aria/core/test/test_CrossPeak.py b/src/aria/core/test/test_CovalentDistances.py
similarity index 100%
rename from aria/core/test/test_CrossPeak.py
rename to src/aria/core/test/test_CovalentDistances.py
diff --git a/aria/core/test/test_CrossPeakFilter.py b/src/aria/core/test/test_CrossPeak.py
similarity index 100%
rename from aria/core/test/test_CrossPeakFilter.py
rename to src/aria/core/test/test_CrossPeak.py
diff --git a/aria/core/test/test_DataContainer.py b/src/aria/core/test/test_CrossPeakFilter.py
similarity index 100%
rename from aria/core/test/test_DataContainer.py
rename to src/aria/core/test/test_CrossPeakFilter.py
diff --git a/aria/core/test/test_Datum.py b/src/aria/core/test/test_DataContainer.py
similarity index 100%
rename from aria/core/test/test_Datum.py
rename to src/aria/core/test/test_DataContainer.py
diff --git a/aria/core/test/test_Experiment.py b/src/aria/core/test/test_Datum.py
similarity index 100%
rename from aria/core/test/test_Experiment.py
rename to src/aria/core/test/test_Datum.py
diff --git a/aria/core/test/test_Factory.py b/src/aria/core/test/test_Experiment.py
similarity index 100%
rename from aria/core/test/test_Factory.py
rename to src/aria/core/test/test_Experiment.py
diff --git a/aria/core/test/test_FloatFile.py b/src/aria/core/test/test_Factory.py
similarity index 100%
rename from aria/core/test/test_FloatFile.py
rename to src/aria/core/test/test_Factory.py
diff --git a/aria/core/test/test_Infrastructure.py b/src/aria/core/test/test_FloatFile.py
similarity index 100%
rename from aria/core/test/test_Infrastructure.py
rename to src/aria/core/test/test_FloatFile.py
diff --git a/aria/core/test/test_Iteration.py b/src/aria/core/test/test_Infrastructure.py
similarity index 100%
rename from aria/core/test/test_Iteration.py
rename to src/aria/core/test/test_Infrastructure.py
diff --git a/aria/core/test/test_JobManager.py b/src/aria/core/test/test_Iteration.py
similarity index 100%
rename from aria/core/test/test_JobManager.py
rename to src/aria/core/test/test_Iteration.py
diff --git a/aria/core/test/test_Merger.py b/src/aria/core/test/test_JobManager.py
similarity index 100%
rename from aria/core/test/test_Merger.py
rename to src/aria/core/test/test_JobManager.py
diff --git a/aria/core/test/test_MolMol.py b/src/aria/core/test/test_Merger.py
similarity index 100%
rename from aria/core/test/test_MolMol.py
rename to src/aria/core/test/test_Merger.py
diff --git a/aria/core/test/test_Molecule.py b/src/aria/core/test/test_MolMol.py
similarity index 100%
rename from aria/core/test/test_Molecule.py
rename to src/aria/core/test/test_MolMol.py
diff --git a/aria/core/test/test_Molprobity.py b/src/aria/core/test/test_Molecule.py
similarity index 100%
rename from aria/core/test/test_Molprobity.py
rename to src/aria/core/test/test_Molecule.py
diff --git a/aria/core/test/test_NOEModel.py b/src/aria/core/test/test_Molprobity.py
similarity index 100%
rename from aria/core/test/test_NOEModel.py
rename to src/aria/core/test/test_Molprobity.py
diff --git a/aria/core/test/test_NOESYSpectrum.py b/src/aria/core/test/test_NOEModel.py
similarity index 100%
rename from aria/core/test/test_NOESYSpectrum.py
rename to src/aria/core/test/test_NOEModel.py
diff --git a/aria/core/test/test_NOESYSpectrumFilter.py b/src/aria/core/test/test_NOESYSpectrum.py
similarity index 100%
rename from aria/core/test/test_NOESYSpectrumFilter.py
rename to src/aria/core/test/test_NOESYSpectrum.py
diff --git a/aria/core/test/test_Network.py b/src/aria/core/test/test_NOESYSpectrumFilter.py
similarity index 100%
rename from aria/core/test/test_Network.py
rename to src/aria/core/test/test_NOESYSpectrumFilter.py
diff --git a/aria/core/test/test_OrderedDict.py b/src/aria/core/test/test_Network.py
similarity index 100%
rename from aria/core/test/test_OrderedDict.py
rename to src/aria/core/test/test_Network.py
diff --git a/aria/core/test/test_PDBReader.py b/src/aria/core/test/test_OrderedDict.py
similarity index 100%
rename from aria/core/test/test_PDBReader.py
rename to src/aria/core/test/test_OrderedDict.py
diff --git a/aria/core/test/test_PeakAssigner.py b/src/aria/core/test/test_PDBReader.py
similarity index 100%
rename from aria/core/test/test_PeakAssigner.py
rename to src/aria/core/test/test_PDBReader.py
diff --git a/aria/core/test/test_Project.py b/src/aria/core/test/test_PeakAssigner.py
similarity index 100%
rename from aria/core/test/test_Project.py
rename to src/aria/core/test/test_PeakAssigner.py
diff --git a/aria/core/test/test_Protocol.py b/src/aria/core/test/test_Project.py
similarity index 100%
rename from aria/core/test/test_Protocol.py
rename to src/aria/core/test/test_Project.py
diff --git a/aria/core/test/test_Relaxation.py b/src/aria/core/test/test_Protocol.py
similarity index 100%
rename from aria/core/test/test_Relaxation.py
rename to src/aria/core/test/test_Protocol.py
diff --git a/aria/core/test/test_Report.py b/src/aria/core/test/test_Relaxation.py
similarity index 100%
rename from aria/core/test/test_Report.py
rename to src/aria/core/test/test_Relaxation.py
diff --git a/aria/core/test/test_Residue.py b/src/aria/core/test/test_Report.py
similarity index 100%
rename from aria/core/test/test_Residue.py
rename to src/aria/core/test/test_Report.py
diff --git a/aria/core/test/test_RmsReport.py b/src/aria/core/test/test_Residue.py
similarity index 100%
rename from aria/core/test/test_RmsReport.py
rename to src/aria/core/test/test_Residue.py
diff --git a/aria/core/test/test_Settings.py b/src/aria/core/test/test_RmsReport.py
similarity index 100%
rename from aria/core/test/test_Settings.py
rename to src/aria/core/test/test_RmsReport.py
diff --git a/aria/core/test/test_ShiftAssignment.py b/src/aria/core/test/test_Settings.py
similarity index 100%
rename from aria/core/test/test_ShiftAssignment.py
rename to src/aria/core/test/test_Settings.py
diff --git a/aria/core/test/test_ShiftAssignmentFilter.py b/src/aria/core/test/test_ShiftAssignment.py
similarity index 100%
rename from aria/core/test/test_ShiftAssignmentFilter.py
rename to src/aria/core/test/test_ShiftAssignment.py
diff --git a/aria/core/test/test_Singleton.py b/src/aria/core/test/test_ShiftAssignmentFilter.py
similarity index 100%
rename from aria/core/test/test_Singleton.py
rename to src/aria/core/test/test_ShiftAssignmentFilter.py
diff --git a/aria/core/test/test_SpinPair.py b/src/aria/core/test/test_Singleton.py
similarity index 100%
rename from aria/core/test/test_SpinPair.py
rename to src/aria/core/test/test_Singleton.py
diff --git a/aria/core/test/test_StructureEnsemble.py b/src/aria/core/test/test_SpinPair.py
similarity index 100%
rename from aria/core/test/test_StructureEnsemble.py
rename to src/aria/core/test/test_SpinPair.py
diff --git a/aria/core/test/test_SuperImposer.py b/src/aria/core/test/test_StructureEnsemble.py
similarity index 100%
rename from aria/core/test/test_SuperImposer.py
rename to src/aria/core/test/test_StructureEnsemble.py
diff --git a/aria/core/test/test_Topology.py b/src/aria/core/test/test_SuperImposer.py
similarity index 100%
rename from aria/core/test/test_Topology.py
rename to src/aria/core/test/test_SuperImposer.py
diff --git a/aria/core/test/test_TypeChecking.py b/src/aria/core/test/test_Topology.py
similarity index 100%
rename from aria/core/test/test_TypeChecking.py
rename to src/aria/core/test/test_Topology.py
diff --git a/aria/core/test/test_ViolationAnalyser.py b/src/aria/core/test/test_TypeChecking.py
similarity index 100%
rename from aria/core/test/test_ViolationAnalyser.py
rename to src/aria/core/test/test_TypeChecking.py
diff --git a/aria/core/test/test_WhatifProfile.py b/src/aria/core/test/test_ViolationAnalyser.py
similarity index 100%
rename from aria/core/test/test_WhatifProfile.py
rename to src/aria/core/test/test_ViolationAnalyser.py
diff --git a/aria/core/test/test__PDBReader.py b/src/aria/core/test/test_WhatifProfile.py
similarity index 100%
rename from aria/core/test/test__PDBReader.py
rename to src/aria/core/test/test_WhatifProfile.py
diff --git a/aria/core/test/test___N.py b/src/aria/core/test/test__PDBReader.py
similarity index 100%
rename from aria/core/test/test___N.py
rename to src/aria/core/test/test__PDBReader.py
diff --git a/aria/core/test/test_ariabase.py b/src/aria/core/test/test___N.py
similarity index 100%
rename from aria/core/test/test_ariabase.py
rename to src/aria/core/test/test___N.py
diff --git a/aria/core/test/test_ccpn2top.py b/src/aria/core/test/test_ariabase.py
similarity index 100%
rename from aria/core/test/test_ccpn2top.py
rename to src/aria/core/test/test_ariabase.py
diff --git a/aria/core/test/test_ccpn_conversion.py b/src/aria/core/test/test_ccpn2top.py
similarity index 100%
rename from aria/core/test/test_ccpn_conversion.py
rename to src/aria/core/test/test_ccpn2top.py
diff --git a/aria/core/test/test_cns.py b/src/aria/core/test/test_ccpn_conversion.py
similarity index 100%
rename from aria/core/test/test_cns.py
rename to src/aria/core/test/test_ccpn_conversion.py
diff --git a/aria/core/test/test_conversion.py b/src/aria/core/test/test_cns.py
similarity index 100%
rename from aria/core/test/test_conversion.py
rename to src/aria/core/test/test_cns.py
diff --git a/aria/core/test/test_exportToCcpn.py b/src/aria/core/test/test_conversion.py
similarity index 100%
rename from aria/core/test/test_exportToCcpn.py
rename to src/aria/core/test/test_conversion.py
diff --git a/aria/core/test/test_importFromCcpn.py b/src/aria/core/test/test_exportToCcpn.py
similarity index 100%
rename from aria/core/test/test_importFromCcpn.py
rename to src/aria/core/test/test_exportToCcpn.py
diff --git a/aria/core/test/test_mathutils.py b/src/aria/core/test/test_importFromCcpn.py
similarity index 100%
rename from aria/core/test/test_mathutils.py
rename to src/aria/core/test/test_importFromCcpn.py
diff --git a/aria/core/test/test_tools.py b/src/aria/core/test/test_mathutils.py
similarity index 100%
rename from aria/core/test/test_tools.py
rename to src/aria/core/test/test_mathutils.py
diff --git a/aria/core/test/test_xmlparser.py b/src/aria/core/test/test_tools.py
similarity index 100%
rename from aria/core/test/test_xmlparser.py
rename to src/aria/core/test/test_tools.py
diff --git a/aria/core/test/test_xmlutils.py b/src/aria/core/test/test_xmlparser.py
similarity index 100%
rename from aria/core/test/test_xmlutils.py
rename to src/aria/core/test/test_xmlparser.py
diff --git a/src/aria/core/test/test_xmlutils.py b/src/aria/core/test/test_xmlutils.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/aria/core/tools.py b/src/aria/core/tools.py
similarity index 92%
rename from aria/core/tools.py
rename to src/aria/core/tools.py
index 9c4bf188af8d804d9d9dfdd4df01107f5f24e43b..2c8f8eacd7e350bdc28c0835c9a052b4cf3b37b7 100644
--- a/aria/core/tools.py
+++ b/src/aria/core/tools.py
@@ -26,6 +26,10 @@
.. $Date: 2010/03/23 15:27:24 $ ..
.. .......................................................................... ..
"""
+import logging
+
+
+LOG = logging.getLogger(__name__)
def Dump(this, filename, mode='w', as_string=0, gzip=0):
@@ -70,15 +74,32 @@ def Dump(this, filename, mode='w', as_string=0, gzip=0):
if not mode in ['w', 'a']:
raise Exception("mode has to be 'w' (write) or 'a' (append)")
+ mode += 'b'
if gzip:
open_func = gzip_open
else:
open_func = open
- f = open_func(filename, mode)
+ # Issues if we try to dump the logger since it contains the log file instance
+ # TODO: do better testing
+ def remove_logger(this):
+ if hasattr(elt, "items"):
+ for foo in elt.items():
+ if hasattr(foo, "logger"):
+ delattr(foo, "logger")
+
+ if type(this) == list:
+ for elt in this:
+ remove_logger(elt)
+ else:
+ remove_logger(this)
- cPickle.dump(this, f, 1)
+ f = open_func(filename, mode)
+ try:
+ cPickle.dump(this, f, 1)
+ except Exception as e:
+ LOG.exception(e)
f.close()
@@ -171,8 +192,8 @@ def wrap_string(s, length=80, tol=10):
return '\n'.join(block)
-def indent(lines, prefix):
- tag = ' ' * len(str(prefix))
+def indent(lines, prefix, extra=0):
+ tag = ' ' * (len(str(prefix)) + extra)
lines[0] = u'%s%s' % (prefix, lines[0])
lines = [lines[0]] + map(lambda s, t=tag: t + s, lines[1:])
diff --git a/aria/core/xmlparser.py b/src/aria/core/xmlparser.py
similarity index 100%
rename from aria/core/xmlparser.py
rename to src/aria/core/xmlparser.py
diff --git a/aria/core/xmlutils.py b/src/aria/core/xmlutils.py
similarity index 97%
rename from aria/core/xmlutils.py
rename to src/aria/core/xmlutils.py
index fd9e4aa738255f7e3c2e58361d594e1d19394020..2a23256fa27015eeff163dfe9e9c5439b4852a6b 100644
--- a/aria/core/xmlutils.py
+++ b/src/aria/core/xmlutils.py
@@ -104,15 +104,14 @@ class XMLElement:
def get_cdata(self):
return self.__cdata
- # TODO: why this method was commented
- def get_name(self):
- # raise
- attr = '_%s__name' % self.__class__.__name__
-
- if attr in self.__dict__:
- return self.__dict__[attr]
- else:
- return None
+ # TODO: why this method is commented ?
+ # def get_name(self):
+ # raise
+ # attr = '_%s__name' % self.__class__.__name__
+ # if attr in self.__dict__:
+ # return self.__dict__[attr]
+ # else:
+ # return None
def set_tag_order(self, o):
self.__tag_order = o
@@ -137,6 +136,12 @@ class XMLElement:
return 'XMLElement(name=%s, tag_order=%s)' % \
(self.get_name(), str(self.get_tag_order()))
+ def __repr__(self):
+ print('XMLElement(name=%s, tag_order=%s)' % \
+ (str(self.get_name()), str(self.get_tag_order())))
+ return 'XMLElement(name=%s, tag_order=%s)' % \
+ (str(self.get_name()), str(self.get_tag_order()))
+
class ContentConverter:
"""
diff --git a/aria/data/atomnames.xml b/src/aria/data/atomnames.xml
similarity index 100%
rename from aria/data/atomnames.xml
rename to src/aria/data/atomnames.xml
diff --git a/aria/data/covalent_distances.xml b/src/aria/data/covalent_distances.xml
similarity index 100%
rename from aria/data/covalent_distances.xml
rename to src/aria/data/covalent_distances.xml
diff --git a/aria/data/iupac.xml b/src/aria/data/iupac.xml
similarity index 100%
rename from aria/data/iupac.xml
rename to src/aria/data/iupac.xml
diff --git a/aria/data/project_template.xml b/src/aria/data/project_template.xml
similarity index 100%
rename from aria/data/project_template.xml
rename to src/aria/data/project_template.xml
diff --git a/aria/data/run.cns b/src/aria/data/run.cns
similarity index 100%
rename from aria/data/run.cns
rename to src/aria/data/run.cns
diff --git a/aria/templates/csh/check_host.csh b/src/aria/templates/csh/check_host.csh
similarity index 100%
rename from aria/templates/csh/check_host.csh
rename to src/aria/templates/csh/check_host.csh
diff --git a/aria/templates/xml/chemical_shift_list1.0.dtd b/src/aria/templates/xml/chemical_shift_list1.0.dtd
similarity index 100%
rename from aria/templates/xml/chemical_shift_list1.0.dtd
rename to src/aria/templates/xml/chemical_shift_list1.0.dtd
diff --git a/aria/templates/xml/distance_restraint1.0.dtd b/src/aria/templates/xml/distance_restraint1.0.dtd
similarity index 100%
rename from aria/templates/xml/distance_restraint1.0.dtd
rename to src/aria/templates/xml/distance_restraint1.0.dtd
diff --git a/aria/templates/xml/molecule1.0.dtd b/src/aria/templates/xml/molecule1.0.dtd
similarity index 100%
rename from aria/templates/xml/molecule1.0.dtd
rename to src/aria/templates/xml/molecule1.0.dtd
diff --git a/aria/templates/xml/noe_restraint1.0.dtd b/src/aria/templates/xml/noe_restraint1.0.dtd
similarity index 100%
rename from aria/templates/xml/noe_restraint1.0.dtd
rename to src/aria/templates/xml/noe_restraint1.0.dtd
diff --git a/aria/templates/xml/noesy_spectrum1.0.dtd b/src/aria/templates/xml/noesy_spectrum1.0.dtd
similarity index 100%
rename from aria/templates/xml/noesy_spectrum1.0.dtd
rename to src/aria/templates/xml/noesy_spectrum1.0.dtd
diff --git a/aria/templates/xml/project1.0.dtd b/src/aria/templates/xml/project1.0.dtd
similarity index 100%
rename from aria/templates/xml/project1.0.dtd
rename to src/aria/templates/xml/project1.0.dtd
diff --git a/aria/templates/xml/topology1.0.dtd b/src/aria/templates/xml/topology1.0.dtd
similarity index 100%
rename from aria/templates/xml/topology1.0.dtd
rename to src/aria/templates/xml/topology1.0.dtd