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bis-aria
ariaec
Commits
f3526129
Commit
f3526129
authored
Apr 13, 2018
by
Fabrice ALLAIN
Browse files
Corrected AriaPeak format
parent
ad95b080
Changes
2
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Inline
Side-by-side
README.rst
View file @
f3526129
...
...
@@ -43,6 +43,7 @@ Then the easiest solution is to call the ``pip`` command below :
pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec
Another possibility is to download the ZIP_ or TAR_ version from Gitlab_,
extract the files and run ``pip install .`` inside the new directory
...
...
aria/core/AriaPeak.py
View file @
f3526129
...
...
@@ -48,8 +48,7 @@ HEADER_PROJECT = """\
# Date: %(date)s
# Project: %(project)s
# Run: %(run)s
# Path: %(working_directory)s
"""
[
1
:
-
1
]
# Path: %(working_directory)s"""
HEADER_ASSIGNMENT_TYPE
=
"""
\
# a_type: Assignment type. Valid types are:
...
...
@@ -60,8 +59,7 @@ cross-peak assignment.
# completed the assignment.
# A (automatic): Reference cross-peak has not been assigned.
\
ARIA has generated
# a list of probable assignments.
"""
[
1
:
-
1
]
# a list of probable assignments."""
HEADER_SEQUENCE_SEPARATION
=
"""
\
# sep: sequence separation s: I: s == 0 (intra-residual)
...
...
@@ -69,28 +67,24 @@ HEADER_SEQUENCE_SEPARATION = """\
# S: 2 <= s <= 3 (short)
# M: 4 <= s <= 5 (medium)
# L: s > 5 (long)
# i: inter-monomer
"""
[
1
:
-
1
]
# i: inter-monomer"""
HEADER_RESTRAINT_DEFINITION
=
"""
\
# ref_spec: Spectrum name
# ref_no: Reference peak number (as in spectrum)
# id: Internal ARIA restraint-id (unique over all spectra)
"""
[
1
:
-
1
]
# id: Internal ARIA restraint-id (unique over all spectra)"""
HEADER_RESTRAINT_BOUNDS
=
"""
\
# d: Restaint distance [A], after calibration.
# upper: Upper bound [A]
# lower: Lower bound [A]
"""
[
1
:
-
1
]
# lower: Lower bound [A]"""
HEADER_RESTRAINT_ACTIVE
=
"""
\
# active: yes(no): restraint has (not) been used in the calculation. A
\
restraint is inactive
# either if it was violated in the last iteration or if it has been
\
merged with
# another restraint.
"""
[
1
:
-
1
]
# another restraint."""
HEADER_DICT
=
{
'project'
:
HEADER_PROJECT
,
'assignment_type'
:
HEADER_ASSIGNMENT_TYPE
,
...
...
@@ -120,8 +114,7 @@ structures of
# will not be used in the subsequent iteration.
#
%(assignment_type)s
#
"""
%
HEADER_DICT
)[
1
:
-
1
]
#"""
%
HEADER_DICT
)
HEADER_AMBIG
=
"""
\
#
...
...
@@ -143,7 +136,7 @@ of structures
# (e.g. n lowest energy structures etc.) See <iteration> section in project-xml
\
file.
#
"""
[
1
:]
"""
HEADER_UNAMBIG
=
"""
\
#
...
...
@@ -164,7 +157,7 @@ ensemble of structures
# (e.g. n-lowest energy structures etc). See also <iteration> section in
\
project-xml file.
#
"""
[
1
:]
"""
ABBREVIATIONS_CONTRIBUTIONS
=
"""
\
#
...
...
@@ -207,21 +200,21 @@ only 1 distance),
# <partial_assignment> in the project's xml file.
#
"""
[
1
:]
"""
CONTRIBUTION_SINGLE
=
"""
\
%(spin_pair)s d: %(d_avg)s +/- %(d_sd)s, weight: %(weight)s
"""
[
1
:]
"""
CONTRIBUTION_SPINPAIR
=
"""
\
%(spin_pair)s
"""
[
1
:]
"""
CONTRIBUTIONS_HEADER
=
"""
\
ref_spec: %(spec_name)s, ref_peak: %(peak_no)s, id: %(id)s, d: %(d_avg)s, u:
\
%(d_upper)s, u_viol: %(u_viol)s, %%_viol: %(p_viol)s, viol: %(violated)s,
\
reliable: %(reliable)s, a_type: %(assignment_type)s
"""
[
1
:]
"""
HEADER_VIOLATIONS
=
"""
\
#
...
...
@@ -266,7 +259,7 @@ ensemble of structures
# (e.g. n-lowest energy structures etc). See also <iteration> section in
\
project-xml file.
#
"""
[
1
:]
"""
class
TextPickler
(
AriaBaseClass
):
...
...
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