Merge pull request #57 from open-forcefield-group/searchList

Fixing bug with basetypes vs. used_basetypes
openforcefield · Jul 11, 2016 · 4423c1a · 4423c1a
2 parents cb2f093 + be3dd26
commit 4423c1a
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Showing 2 changed files with 14 additions and 4 deletions.
diff --git a/examples/AlkEtOH2/atomtypes/decorators.smarts b/examples/AlkEtOH2/atomtypes/decorators.smarts
@@ -1,5 +1,5 @@
 % bonded to atoms
-$(*-z) simply-bonded
+$(*-z) singly-bonded
 $(*=z) doubly-bonded
 $(*#z) triply-bonded
 $(*:z) aromatic-bond

diff --git a/smarty/sampler.py b/smarty/sampler.py
@@ -491,7 +491,6 @@ def sample_atomtypes(self):
 
                 # Update proposed parent dictionary
                 proposed_parents[original_basetype].append([proposed_atomtype, proposed_typename])
-                print "proposed_parents: " + str(proposed_parents)
 
             proposed_parents[proposed_atomtype] = []
 
@@ -568,7 +567,6 @@ def sample_atomtypes(self):
             self.atomtypes = proposed_atomtypes
             self.molecules = proposed_molecules
             self.parents = proposed_parents
-            print "------------ self.parents= " + str(self.parents)
             self.atom_type_matches = proposed_atom_type_matches
             self.total_atom_type_matches = proposed_total_atom_type_matches
             return True
@@ -718,7 +716,7 @@ def get_unfinishedAtomList(self, atom_typecounts, molecule_typecounts, atomtype_
                     reference_counts[typename] = count
 
         # If all of a basetype and it's children match found atoms and reference remove from list
-        for [base_smarts, base_typename] in self.basetypes:
+        for [base_smarts, base_typename] in self.used_basetypes:
             includeBase = True
 
             # If the number of atoms matches the references are the same for basetypes and their children
@@ -797,6 +795,18 @@ def run(self, niterations, trajFile=None):
                 self.show_type_statistics(self.atomtypes, atom_typecounts, molecule_typecounts, atomtype_matches=self.atom_type_matches)
                 print('')
 
+                # Print parent tree as it is now.
+                roots = self.parents.keys()
+                # Remove keys from roots if they are children
+                for parent, children in self.parents.items():
+                    child_smarts = [smarts for [smarts, name] in children]
+                    for child in child_smarts:
+                        if child in roots:
+                            roots.remove(child)
+
+                print("Atom type hierarchy:")
+                self.print_parent_tree(roots, '\t')
+
         if trajFile is not None:
             # make "trajectory" file
             if os.path.isfile(trajFile):