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bis-aria
ariaec
Commits
737dd533
Commit
737dd533
authored
Mar 08, 2019
by
Fabrice Allain
Browse files
fix: solve import issue with pdbqual command
parent
8416e6fe
Changes
7
Hide whitespace changes
Inline
Side-by-side
.gitignore
View file @
737dd533
...
...
@@ -474,5 +474,5 @@ pip-selfcheck.json
# TODO: remove line below if we want to keep eclipse metadata
.settings/
.vscode
aria/conbox/pdbqual.py
View file @
737dd533
...
...
@@ -9,7 +9,7 @@ import logging
import
os
import
shutil
from
..core.legacy
import
Quality
Checks
from
..core.legacy
.QualityChecks.QualityChecks
import
run
Checks
from
.common
import
CommandProtocol
LOG
=
logging
.
getLogger
(
__name__
)
...
...
@@ -29,7 +29,7 @@ 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
,
...
...
aria/core/Merger.py
View file @
737dd533
...
...
@@ -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.
...
...
aria/core/Project.py
View file @
737dd533
...
...
@@ -1756,6 +1756,7 @@ 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
...
...
aria/core/StructureEnsemble.py
View file @
737dd533
...
...
@@ -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
):
...
...
aria/core/ariabase.py
View file @
737dd533
...
...
@@ -145,7 +145,7 @@ def get_aria_root():
# 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 define
s
settings and log messages"""
use_restraint_weights
=
0
...
...
aria/core/cns.py
View file @
737dd533
...
...
@@ -92,8 +92,8 @@ CSH_SCRIPT_REFINE = '''\
#BSUB -L %(sge_job_shell)s
#BSUB -oo refine.lsf.out
#BSUB -eo refine.lsf.err
#SBATCH -o refine.
{
sge_job_id
}
.slurm.out
#SBATCH -e refine.
{
sge_job_id
}
.slurm.err
#SBATCH -o refine.
%(
sge_job_id
)s
.slurm.out
#SBATCH -e refine.
%(
sge_job_id
)s
.slurm.err
#SBATCH -J %(sge_job_name)s
#SBATCH --ignore-pbs
...
...
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