fix: solve import issue with pdbqual command

.gitignore

@@ -474,5 +474,5 @@ pip-selfcheck.json
 
 # TODO: remove line below if we want to keep eclipse metadata
 .settings/
-
+.vscode
 

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
 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

@@ -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

@@ -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

@@ -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

@@ -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
 

aria/core/cns.py

@@ -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