Commit 737dd533 authored by Fabrice Allain's avatar Fabrice Allain
Browse files

fix: solve import issue with pdbqual command

parent 8416e6fe
......@@ -474,5 +474,5 @@ pip-selfcheck.json
# TODO: remove line below if we want to keep eclipse metadata
.settings/
.vscode
......@@ -9,7 +9,7 @@ import logging
import os
import shutil
from ..core.legacy import QualityChecks
from ..core.legacy.QualityChecks.QualityChecks import runChecks
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,
......
......@@ -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.
......
......@@ -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
......
......@@ -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):
......
......@@ -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 defines settings and log messages"""
use_restraint_weights = 0
......
......@@ -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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