Commit f3526129 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

Corrected AriaPeak format

parent ad95b080
......@@ -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
......
......@@ -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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