Merge pull request #282 from marrink-lab/fix/top-dih

Fix/top dih

polyply/src/top_parser.py

@@ -356,7 +356,7 @@ def _type_params(self, line, lineno=0):
         atoms, params = self._split_atoms_and_parameters(line.split(),
                                                          self.atom_idxs[section_name])
 
-        self.topology.types[inter_type][tuple(atoms)] = (params, self.current_meta)
+        self.topology.types[inter_type][tuple(atoms)].append((params, self.current_meta))
 
 
     @SectionLineParser.section_parser('implicit_genborn_params')

polyply/src/topology.py

@@ -25,6 +25,7 @@
 from vermouth.forcefield import ForceField
 from vermouth.gmx.gro import read_gro
 from vermouth.pdb import read_pdb
+from vermouth.molecule import Interaction
 from .top_parser import read_topology
 from .linalg_functions import center_of_geometry
 
@@ -221,7 +222,7 @@ def __init__(self, force_field, name=None):
         self.defines = {}
         self.description = []
         self.atom_types = {}
-        self.types = defaultdict(dict)
+        self.types = defaultdict(lambda: defaultdict(list))
         self.nonbond_params = {}
         self.mol_idx_by_name = defaultdict(list)
         self.persistences = []
@@ -288,19 +289,38 @@ def gen_pairs(self):
 
     def gen_bonded_interactions(self):
         """
-        Check for each interaction if there is
-        no parameter for an interaction if that
-        parameter is defined in the bonded directive
-        of the topology.
+        Check for each interaction, if the parameter list is empty. If it is
+        check if the parameters are defined in the bonded types directive
+        of the topology. This essentially does part of the step done by
+        grompp.
+
+        Updates
+        -------
+        self.molecules.interactions
+        self.blocks.interactions
+
+        Raises
+        ------
+        OSError
+            no match for an interaction in the bonded types provided
         """
-        for block in self.force_field.blocks.values():
+        # We loop over blocks not molecules, because there is only
+        # one unique block per molecule, whereas there cab be a large number of
+        # duplicate molecules in the topology.molecules list. As the interactions
+        # in those molecules are still references to the blocks updating them here
+        # will propagate into the molecules. This works except for one case where
+        # a single dihedral directive is expanded into multiple ones. Updating the
+        # block dict will not propagate into the molecules.
+        for mol_name, block in self.force_field.blocks.items():
+            additional_interactions = defaultdict(list)
             for inter_type, interactions in block.interactions.items():
+                # these interactions have no types associated
                 if inter_type in ["pairs", "exclusions", "virtual_sitesn",
                                   "virtual_sites2", "virtual_sites3", "virtual_sites4"]:
                     continue
+
                 for interaction in interactions:
                     if len(interaction.parameters) == 1:
-
                         # Some force-fields - in GMX library only OPLS - use bond-type
                         # definitions. Each atomtype matches one bond-type, which
                         # in turn matches an expression in the bondedtypes section
@@ -312,14 +332,17 @@ def gen_bonded_interactions(self):
                         else:
                             atoms = tuple(block.nodes[node]["atype"] for node in interaction.atoms)
 
+                        # now we match the atom or bondtypes to the types defined in the topology
                         if atoms in self.types[inter_type]:
-                            new_params, meta = self.types[inter_type][atoms]
+                            new_params = self.types[inter_type][atoms]
                         elif atoms[::-1] in self.types[inter_type]:
-                            new_params, meta = self.types[inter_type][atoms[::-1]]
+                            new_params  = self.types[inter_type][atoms[::-1]]
+                        # dihedrals are more complicated because they are treated as symmetric and
+                        # can have wild-cards
                         elif inter_type in "dihedrals":
                             match = match_dihedral_interaction_types(atoms, self.types[inter_type])
                             if match:
-                                new_params, meta = self.types[inter_type][match]
+                                new_params = self.types[inter_type][match]
                             else:
                                 msg = ("In section dihedrals interaction of atoms {} has no "
                                        "corresponding bonded type.")
@@ -332,9 +355,29 @@ def gen_bonded_interactions(self):
                             atoms = " ".join(list(map(lambda x: str(x), interaction.atoms)))
                             raise OSError(msg.format(inter_type, atoms))
 
-                        interaction.parameters[:] = new_params[:]
-                        if meta:
-                            interaction.meta.update(meta)
+                        for idx, (new_param, meta) in enumerate(new_params):
+                            if not meta:
+                                meta = {}
+                            # there is always at least one interaction in molecule, which
+                            # needs to get the typed parameters
+                            if idx == 0:
+                                interaction.parameters[:] = new_param[:]
+                                interaction.meta.update(meta)
+                            # however, sometimes a single interaction term needs to be
+                            # expanded (i.e. a single statment spwans multiple interactions)
+                            # In that case we update the parameters of the first term and
+                            # need to add the other interactions additionally
+                            else:
+                                new_interaction = Interaction(atoms=tuple(interaction.atoms),
+                                                              parameters=new_param,
+                                                              meta=meta)
+                                additional_interactions[inter_type].append(new_interaction)
+
+
+            # here we add the expanded interactions into the molecules
+            for mol_idx in self.mol_idx_by_name[mol_name]:
+                for inter_type, new_inters in additional_interactions.items():
+                    self.molecules[mol_idx].molecule.interactions[inter_type] += new_inters
 
     def convert_nonbond_to_sig_eps(self):
         """

polyply/tests/test_top_parser.py

@@ -106,8 +106,20 @@ class TestTopParsing:
         OM      O         1    1.9670816e-03  8.5679450e-07
         """,
         "types",
-        {"bonds": {("OM", "O"): (["1", "1.9670816e-03", "8.5679450e-07"], None)}}
+        {"bonds": {("OM", "O"): [(["1", "1.9670816e-03", "8.5679450e-07"], None)]}}
          ),
+        ("""
+        [ dihedraltypes ]
+        CEL1    CEL1    CTL2    CTL2     9  1.800000e+02  3.807440e+00      1
+        CEL1    CEL1    CTL2    CTL2     9  1.800000e+02  7.531200e-01      2
+        CEL1    CEL1    CTL2    CTL2     9  1.800000e+02  7.112800e-01      3
+        """,
+        "types",
+        {"dihedrals": {("CEL1", "CEL1", "CTL2", "CTL2"): [(["9", "1.800000e+02", "3.807440e+00", "1"], None),
+                                                          (["9", "1.800000e+02", "7.531200e-01", "2"], None),
+                                                          (["9", "1.800000e+02", "7.112800e-01", "3"], None)]}}
+        ),
+
         ("""
         [ system ]
         some multiline

polyply/tests/test_topology.py

@@ -617,6 +617,49 @@ def test_convert_nonbond_to_sig_eps():
          "virtual_sites2": [Interaction(atoms=(3, 0, 8), parameters=["1", "0.5000"], meta={})],
          "virtual_sites3": [Interaction(atoms=(4, 3, 7, 0), parameters=["1", "0.200", "0.200"], meta={}),
                             Interaction(atoms=(5, 3, 8, 1), parameters=["1", "0.200", "0.200"], meta={})]}
+        ),
+        # test multiple dihedrals are assigned
+        (
+        """
+        [ defaults ]
+        1.0   1.0   yes  2.0     1.0
+        [ atomtypes ]
+        CTL2     6    12.0110     -0.100     A    3.58141284692e-01    2.343040e-01
+        CEL1     6    12.0110     -0.150     A    3.72395664183e-01    2.845120e-01
+        [ bondtypes ]
+        CEL1    CEL1     1  1.340000e-01  3.681920e+05
+        CEL1    CTL2     1  1.502000e-01  3.054320e+05
+        CTL2    CTL2     1  1.538000e-01  1.861880e+05
+        [ dihedraltypes ]
+        CEL1    CEL1    CTL2    CTL2     9  1.800000e+02  3.807440e+00      1
+        CEL1    CEL1    CTL2    CTL2     9  1.800000e+02  7.531200e-01      2
+        CEL1    CEL1    CTL2    CTL2     9  1.800000e+02  7.112800e-01      3
+
+        [ moleculetype ]
+        test 3
+        [ atoms ]
+        ; CEL1    CEL1    CTL2    CTL2
+        1       CEL1      1     POPC    C12      2     0.000000    12.0110   ; qtot -0.700
+        2       CEL1      1     POPC    C12      2     0.000000    12.0110   ; qtot -0.700
+        3       CTL2      1     POPC    C12      2     0.000000    12.0110   ; qtot -0.700
+        4       CTL2      1     POPC    C12      2     0.000000    12.0110   ; qtot -0.700
+        [ bonds ]
+        1   2 1
+        2   3 1
+        3   4 1
+        [ dihedrals ]
+        1 2 3 4  9
+        [ system ]
+        some title
+        [ molecules ]
+        test 1
+        """,
+        {"bonds": [Interaction(atoms=(0, 1), parameters=["1", "1.340000e-01", "3.681920e+05"], meta={}),
+                   Interaction(atoms=(1, 2), parameters=["1", "1.502000e-01", "3.054320e+05"], meta={}),
+                   Interaction(atoms=(2, 3), parameters=["1", "1.538000e-01", "1.861880e+05"], meta={}),],
+        "dihedrals": [Interaction(atoms=(0, 1, 2, 3), parameters=["9", "1.800000e+02", "3.807440e+00", "1"], meta={}),
+                      Interaction(atoms=(0, 1, 2, 3), parameters=["9", "1.800000e+02", "7.531200e-01", "2"], meta={}),
+                      Interaction(atoms=(0, 1, 2, 3), parameters=["9", "1.800000e+02", "7.112800e-01", "3"], meta={}),]}
         )
 	))
     def test_replace_types(lines, outcome):