read provided ff file and use these blocks instead of making new ones

bin/polyply

@@ -241,6 +241,8 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
     parser_itp_ff.add_argument('-s', dest="smile_str", required=True)
     parser_itp_ff.add_argument('-o', dest="outpath", type=Path)
     parser_itp_ff.add_argument('-c', dest="res_charges",  nargs='+', type=lambda s: s.split(':'),)
+    parser_itp_ff.add_argument('-f', dest='inpath', type=Path, required=False, default=[],
+                                     help='Input file (ITP|FF)', nargs='*')
 
     parser_itp_ff.set_defaults(func=itp_to_ff)
 

polyply/src/big_smile_mol_processor.py

@@ -74,8 +74,8 @@ class DefBigSmileParser:
     which describes a polymer molecule.
     """
 
-    def __init__(self):
-        self.force_field = None
+    def __init__(self, force_field):
+        self.force_field = force_field
         self.meta_molecule = None
         self.molecule = None
 

polyply/src/big_smile_parsing.py

@@ -250,7 +250,7 @@ def fragment_iter(fragment_str):
         nx.set_node_attributes(mol_graph, resname, 'resname')
         yield resname, mol_graph
 
-def force_field_from_fragments(fragment_str):
+def force_field_from_fragments(fragment_str, force_field=None):
     """
     Collects the fragments defined in a BigSmile string
     as :class:`vermouth.molecule.Blocks` in a force-field
@@ -266,9 +266,11 @@ def force_field_from_fragments(fragment_str):
     -------
     :class:`vermouth.forcefield.ForceField`
     """
-    force_field = ForceField("big_smile_ff")
+    if force_field is None:
+        force_field = ForceField("big_smile_ff")
     frag_iter = fragment_iter(fragment_str)
     for resname, mol_graph in frag_iter:
-        mol_block = Block(mol_graph)
-        force_field.blocks[resname] = mol_block
+        if resname not in force_field.blocks:
+            mol_block = Block(mol_graph)
+            force_field.blocks[resname] = mol_block
     return force_field

polyply/src/itp_to_ff.py

@@ -20,6 +20,7 @@
 from polyply.src.ffoutput import ForceFieldDirectiveWriter
 from polyply.src.charges import balance_charges, set_charges
 from polyply.src.big_smile_mol_processor import DefBigSmileParser
+from .load_library import load_ff_library
 
 def _read_itp_file(itppath):
     """
@@ -34,10 +35,17 @@ def _read_itp_file(itppath):
     mol.make_edges_from_interaction_type(type_="bonds")
     return mol
 
-def itp_to_ff(itppath, smile_str, outpath, res_charges=None):
+def itp_to_ff(itppath, smile_str, outpath, inpath=[], res_charges=None):
     """
     Main executable for itp to ff tool.
     """
+    # load FF files if given
+    if inpath:
+        force_field = load_ff_library("new", None, inpath)
+    # if none are given we create an empty ff
+    else:
+        force_field = ForceField("new")
+
     # what charges belong to which resname
     if res_charges:
         crg_dict = dict(res_charges)
@@ -52,14 +60,16 @@ def itp_to_ff(itppath, smile_str, outpath, res_charges=None):
         target_mol = _read_itp_file(itppath)
 
     # read the big-smile representation
-    meta_mol = DefBigSmileParser().parse(smile_str)
+    meta_mol = DefBigSmileParser(force_field).parse(smile_str)
 
     # identify and extract all unique fragments
     unique_fragments, res_graph = FragmentFinder(target_mol).extract_unique_fragments(meta_mol.molecule)
 
     # extract the blocks with parameters
-    force_field = ForceField("new")
     for name, fragment in unique_fragments.items():
+        # don't overwrite existing blocks
+        if name in force_field.blocks:
+            continue
         new_block = extract_block(target_mol, list(fragment.nodes), defines={})
         nx.set_node_attributes(new_block, 1, "resid")
         new_block.nrexcl = target_mol.nrexcl
@@ -70,7 +80,7 @@ def itp_to_ff(itppath, smile_str, outpath, res_charges=None):
                         charge=float(crg_dict[name]))
 
     # extract the regular links
-    force_field.links = extract_links(target_mol)
+    force_field.links.append(extract_links(target_mol))
     # extract links that span the terminii
     find_termini_mods(res_graph, target_mol, force_field)