fixed modifcation parsing

- -mods flag now only read once for all modifications
- patch all molecule termini as proteins, so any modification in addition to these ones are also applied.
- add more modifications from vermouth to martini3 forcefield
- change logging level and fix tests as per #385

bin/polyply

@@ -74,12 +74,12 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
                            help='A linear sequence of residue names.')
     seq_group.add_argument('-seqf', dest='seq_file', type=Path,
                            help='A graph input file (JSON|TXT|FASTA|IG)')
-    dna_group = parser_gen_itp.add_argument_group('DNA specifc options')
+    dna_group = parser_gen_itp.add_argument_group('DNA specific options')
     dna_group.add_argument('-dsdna', dest='dsdna', action='store_true',
                            help='complement single sequence to dsDNA sequence')
     modifications_group = parser_gen_itp.add_argument_group('Modifications group')
-    modifications_group.add_argument('-mods', dest='mods', action='append',
-                                     default=[], type=lambda s: s.split(":"),
+    modifications_group.add_argument('-mods', dest='mods', nargs='+',
+                                     default=[], type=lambda s: [i.split(':') for i in s.split(" ")][0],
                                      help=('Add a modification to a residue. The format is '
                                            '<resname><resid>:modification_name, '
                                            'e.g. ASP1:N-ter')

polyply/data/martini3/modifications.ff

@@ -35,3 +35,72 @@ BB {"replace": {"atype": "P1", "charge": 0.0}}
 NCAP-ter
 [ atoms ]
 BB {"replace": {"atype": "P2", "charge": 0.0}}
+
+[ modification ]
+GLU-HE1
+[ atoms ]
+SC1 {"replace": {"atype": "P2", "charge": 0}}
+
+[ modification ]
+GLU-HE2
+[ atoms ]
+SC1 {"replace": {"atype": "P2", "charge": 0}}
+
+[ modification ]
+ASP-HD1
+[ atoms ]
+SC1 {"replace": {"atype": "P2", "charge": 0}}
+
+[ modification ]
+ASP-HD2
+[ atoms ]
+SC1 {"replace": {"atype": "P2", "charge": 0}}
+
+[ modification ]
+LYS-LSN
+[ atoms ]
+SC2 {"resname": "LYS", "replace": {"atype": "SN6d", "charge": 0}}
+
+[ modification ]
+LYS-HZ3
+[ atoms ]
+SC2 {"replace": {"resname": "LYS"}}
+
+[ modification ]
+HIS-HP
+[ atoms ]
+BB  {"resname": "HIS", "replace": {"resname": "HIS"}}
+SC1 {"resname": "HIS", "replace": {"resname": "HIS"}}
+SC2 {"resname": "HIS", "replace": {"atype": "TP1dq", "charge": "0.5", "resname": "HIS"}}
+SC3 {"resname": "HIS", "replace": {"atype": "TP1dq", "charge": "0.5", "resname": "HIS"}}
+;[ edges ]
+;BB SC1
+;SC1 SC2
+;SC1 SC3
+;SC2 SC3
+
+[ modification ]
+HIS-HE
+[ atoms ]
+BB  {"resname": "HIS", "replace": {"resname": "HIS"}}
+SC1 {"resname": "HIS", "replace": {"resname": "HIS"}}
+SC2 {"resname": "HIS", "replace": {"resname": "HIS"}}
+SC3 {"resname": "HIS", "replace": {"resname": "HIS"}}
+;[ edges ]
+;BB SC1
+;SC1 SC2
+;SC1 SC3
+;SC2 SC3
+
+[ modification ]
+HIS-HD
+[ atoms ]
+BB  {"resname": "HIS", "replace": {"resname": "HIS"}}
+SC1 {"resname": "HIS", "replace": {"resname": "HIS"}}
+SC2 {"resname": "HIS", "replace": {"resname": "HIS", "atype": "TN5a"}}
+SC3 {"resname": "HIS", "replace": {"resname": "HIS", "atype": "TN6a"}}
+;[ edges ]
+;BB SC1
+;SC1 SC2
+;SC1 SC3
+;SC2 SC3

polyply/src/apply_modifications.py

@@ -32,10 +32,10 @@ def _patch_protein_termini(meta_molecule, ter_mods=['N-ter', 'C-ter']):
         protein_termini.append(last_mod)
     else:
         # if only one mod in ter_mods, apply the mod to both start and end residue
-        LOGGER.info("Only one terminal modification specified. "
+        LOGGER.warning("Only one terminal modification specified. "
                     f"Will apply {ter_mods[0]} to both {meta_molecule.nodes[0]['resname']}1 and {last_resname}{max_resid}")
         protein_termini.append(({'resid': max_resid, 'resname': last_resname}, ter_mods[0]))
-
+    print(protein_termini)
     return protein_termini
 
 
@@ -60,7 +60,7 @@ def apply_mod(meta_molecule, modifications):
     molecule = meta_molecule.molecule
 
     if not molecule.force_field.modifications:
-        LOGGER.warning('No modifications present in forcefield, none will be applied')
+        LOGGER.info('No modifications present in forcefield, none will be applied')
         return meta_molecule
 
     for target, desired_mod in modifications:
@@ -77,12 +77,12 @@ def apply_mod(meta_molecule, modifications):
         target_residue = meta_molecule.nodes[target_resid - 1]
         # takes care to skip all residues that come from an itp file
         if not target_residue.get('from_itp', 'False'):
-            LOGGER.warning("meta_molecule has come from itp. Will not attempt to modify.")
+            LOGGER.info("meta_molecule has come from itp. Will not attempt to modify.")
             continue
         # checks that the resname is a protein resname as defined above
         if not vermouth.molecule.attributes_match(target_residue,
                                               {'resname': vermouth.molecule.Choice(protein_resnames.split("|"))}):
-            LOGGER.warning("The resname of your target residue is not recognised a protein resname. "
+            LOGGER.info("The resname of your target residue is not recognised as a protein resname. "
                            "Will not attempt to modify.")
             continue
 
@@ -114,13 +114,10 @@ class ApplyModifications(Processor):
 
     """
     def __init__(self, meta_molecule, modifications=[]):
-        self.target_mods = []
+        self.target_mods = _patch_protein_termini(meta_molecule)
         for resspec, val in modifications:
             self.target_mods.append((parse_residue_spec(resspec), val))
-        if len(self.target_mods) == 0:
-            self.target_mods = _patch_protein_termini(meta_molecule)
 
     def run_molecule(self, meta_molecule):
-
         apply_mod(meta_molecule, self.target_mods)
         return meta_molecule

polyply/tests/test_apply_modifications.py

@@ -37,8 +37,6 @@
         [({'resid': 1, 'resname': 'A'}, 'Zwitter'),
          ({'resid': 3, 'resname': 'A'}, 'Zwitter')]
         )
-
-
 ))
 def test_annotate_protein(example_meta_molecule, input_mods, expected):
     """"
@@ -75,20 +73,25 @@ def test_mods_in_ff(caplog, ff_files, expected):
     with expected:
         assert len(ff.modifications) > 0
 
-@pytest.mark.parametrize('input_itp, molname, expected',
+@pytest.mark.parametrize('input_itp, molname, expected, text',
                          (
     (
     'ALA5.itp',
     'pALA',
-    False),
+    False,
+    None),
     ('PEO.itp',
      'PEO',
-    True)
-                         ))
-def test_apply_mod(input_itp, molname, expected, caplog):
+    True,
+     ("The resname of your target residue"
+      " is not recognised as a protein resname."
+      " Will not attempt to modify."))
+))
+def test_apply_mod(input_itp, molname, expected, caplog, text):
     """
     test that modifications get applied correctly
     """
+    caplog.set_level(logging.INFO)
     #make the meta molecule from the itp and ff files
     file_name = TEST_DATA / "itp" / input_itp
 
@@ -107,7 +110,12 @@ def test_apply_mod(input_itp, molname, expected, caplog):
     apply_mod(meta_mol, termini)
 
     if expected:
-        assert any(rec.levelname == 'WARNING' for rec in caplog.records)
+        for record in caplog.records:
+            if record.message == text:
+                assert True
+                break
+        else:
+            assert False
 
     else:
         #for each mod applied, check that the mod atom and interactions have been changed correctly
@@ -134,25 +142,27 @@ def test_apply_mod(input_itp, molname, expected, caplog):
                                                        meta=interaction.meta)
                             assert _interaction in meta_mol.molecule.interactions[interaction_type]
 
-@pytest.mark.parametrize('modifications, expected',
+@pytest.mark.parametrize('modifications, expected, text',
      (
-             (
-                 [['A1', 'N-ter']],
-                 True
-             ),
-
              (
                  [],
-                 True
+                 True,
+                 "No modifications present in forcefield, none will be applied"
              ),
 
      ))
-def test_ApplyModifications(example_meta_molecule, caplog, modifications, expected):
+def test_ApplyModifications(example_meta_molecule, caplog, modifications, expected, text):
 
+    caplog.set_level(logging.INFO)
 
     ApplyModifications(modifications=modifications,
                        meta_molecule=example_meta_molecule).run_molecule(example_meta_molecule)
 
     if expected:
-        assert any(rec.levelname == 'WARNING' for rec in caplog.records)
-
+        for record in caplog.records:
+            if record.message == text:
+                assert True
+                break
+        else:
+            assert False
+        assert any(rec.levelname == 'INFO' for rec in caplog.records)