correct atomlist selection in apply_modifications.py

polyply/src/apply_modifications.py

@@ -98,8 +98,7 @@ def apply_mod(meta_molecule, modifications):
         for i in mod_interactions:
             for j in molecule.force_field.modifications[desired_mod].interactions[i]:
                 molecule.add_interaction(i,
-                                         (anum_dict[j.atoms[0]]-1,
-                                          anum_dict[j.atoms[1]]-1),
+                                         [anum_dict[k]-1 for k in j.atoms],
                                          j.parameters,
                                          meta=j.meta)
 
@@ -114,8 +113,13 @@ class ApplyModifications(Processor):
     """
     def __init__(self, meta_molecule, modifications=[]):
         self.target_mods = _patch_protein_termini(meta_molecule)
+        default_resspecs = [i[0] for i in self.target_mods]
         for resspec, val in modifications:
-            self.target_mods.append((parse_residue_spec(resspec), val))
+            parsed_resspec = parse_residue_spec(resspec)
+            # if the residue being targeted in the additional resspec is already there, remove the first instance
+            if parsed_resspec in default_resspecs:
+                del self.target_mods[default_resspecs==parsed_resspec]
+            self.target_mods.append((parsed_resspec, val))
 
     def run_molecule(self, meta_molecule):
         apply_mod(meta_molecule, self.target_mods)

polyply/src/generate_templates.py

@@ -109,7 +109,7 @@ def find_interaction_involving(block, current_node, prev_node):
              linking atom {} and atom {}.'''
     raise IOError(msg.format(block.nodes[0]["resname"], prev_node, current_node))
 
-def _expand_inital_coords(block, max_count=50000):
+def _expand_inital_coords(block, max_count=1000):
     """
     Given a `graph` generate initial coordinates in three dimensions
     using the Kamada-Kawai algorithm.
@@ -343,6 +343,7 @@ class variable.
                                       self.topology.defines)
 
                 opt_counter = 0
+                resname = block.nodes[list(block.nodes)[0]]['resname']
                 while True:
 
                     coords = _expand_inital_coords(block)
@@ -363,7 +364,6 @@ class variable.
                         break
                     else:
                         opt_counter += 1
-                resname = block.nodes[list(block.nodes)[0]]['resname']
                 if resname in self.volumes:
                     self.volumes[graph_hash] = self.volumes[resname]
                 else: