Merge pull request #134 from marrink-lab/update-m3

Update m3

bin/martinize2

@@ -325,6 +325,9 @@ def entry():
     prot_group.add_argument('-nt', dest='neutral_termini',
                             action='store_true', default=False,
                             help='Set neutral termini (charged is default)')
+    prot_group.add_argument('-scfix', dest='scfix',
+                            action='store_true', default=False,
+                            help='Apply side chain corrections.')
     prot_group.add_argument('-cys', dest='cystein_bridge',
                             type=_cys_argument,
                             default='none', help='Cystein bonds')
@@ -409,21 +412,26 @@ def entry():
         AnnotateMartiniSecondaryStructures().run_system(system)
     elif args.collagen:
         if not target_ff.has_feature('collagen'):
-            logging.warning('The force field "{}" does not have specific '
-                            'parameters for collagen (-collagen).'
-                            .format(target_ff.name))
+            LOGGER.warning('The force field "{}" does not have specific '
+                           'parameters for collagen (-collagen).',
+                           target_ff.name, type='missing-feature')
         AnnotateResidues(attribute='cgsecstruct', sequence='F',
                          molecule_selector=selectors.is_protein).run_system(system)
     if args.extdih and not target_ff.has_feature('extdih'):
-        logging.warning('The force field "{}" does not define dihedral '
-                        'angles for extended regions of proteins (-extdih).'
-                        .format(target_ff.name))
+        LOGGER.warning('The force field "{}" does not define dihedral '
+                       'angles for extended regions of proteins (-extdih).',
+                       target_ff.name, type='missing-feature')
     vermouth.SetMoleculeMeta(extdih=args.extdih).run_system(system)
     if args.neutral_termini and not target_ff.has_feature('neutral_termini'):
-        logging.warning('The force field "{}" does not have specific '
-                        'parameters for neutral termini (-nt).'
-                        .format(target_ff.name))
+        LOGGER.warning('The force field "{}" does not have specific '
+                       'parameters for neutral termini (-nt).',
+                       target_ff.name, type='missing-feature')
     vermouth.SetMoleculeMeta(neutral_termini=args.neutral_termini).run_system(system)
+    if args.scfix and not target_ff.has_feature('scfix'):
+        LOGGER.warning('The force field "{}" does not define angle and '
+                       'torsion for the side chain corrections (-scfix).',
+                       target_ff.name, type='missing-feature')
+    vermouth.SetMoleculeMeta(scfix=args.scfix).run_system(system)
 
     ss_sequence = list(itertools.chain(*(
         dssp.sequence_from_residues(molecule, 'secstruct')