Rings new

cgsmiles/pysmiles_utils.py

@@ -1,8 +1,5 @@
+import networkx as nx
 import pysmiles
-import math
-
-VALENCES = pysmiles.smiles_helper.VALENCES
-VALENCES.update({"H": (1,)})
 
 def rebuild_h_atoms(mol_graph, keep_bonding=False):
     """
@@ -30,27 +27,23 @@ def rebuild_h_atoms(mol_graph, keep_bonding=False):
         graph describing the full molecule without hydrogen atoms
     """
     for node in mol_graph.nodes:
-        if mol_graph.nodes[node].get('bonding', False):
-            # get the degree
-            ele = mol_graph.nodes[node]['element']
-            # hcount is the valance minus the degree minus
-            # the number of bonding descriptors
-            bonds = math.ceil(sum([mol_graph.edges[(node, neigh)]['order'] for neigh in\
-                               mol_graph.neighbors(node)]))
-            charge = mol_graph.nodes[node].get('charge', 0)
-            hcount = pysmiles.smiles_helper._valence(mol_graph, node, minimum=0) -\
-                     bonds +\
-                     charge
-            # in this case we only rebuild hydrogen atoms that are not
-            # replaced by bonding operators.
-            if keep_bonding:
-                hcount -= len(mol_graph.nodes[node]['bonding'])
-
-            mol_graph.nodes[node]['hcount'] = hcount
-            if ele == "H":
-                mol_graph.nodes[node]['single_h_frag'] = True
+        if mol_graph.nodes[node].get('aromatic', False):
+            mol_graph.nodes[node]['hcount'] = 0
+
+        if mol_graph.nodes[node].get('bonding', False) and  \
+        mol_graph.nodes[node].get('ele,emt', '*') == "H":
+            mol_graph.nodes[node]['single_h_frag'] = True
 
+    for edge in mol_graph.edges:
+        if mol_graph.edges[edge]['order'] == 1.5:
+            mol_graph.edges[edge]['order'] = 1
+
+    pysmiles.smiles_helper.mark_aromatic_atoms(mol_graph, strict=False)
+    pysmiles.smiles_helper.mark_aromatic_edges(mol_graph)
+    nx.set_node_attributes(mol_graph, 0, 'hcount')
+    pysmiles.smiles_helper.fill_valence(mol_graph, respect_hcount=False)
     pysmiles.smiles_helper.add_explicit_hydrogens(mol_graph)
+
     for node in mol_graph.nodes:
         if mol_graph.nodes[node].get("element", "*") == "H" and\
         not mol_graph.nodes[node].get("single_h_frag", False):

cgsmiles/resolve.py

@@ -7,13 +7,6 @@
 from .graph_utils import merge_graphs, sort_nodes_by_attr, annotate_fragments
 from .pysmiles_utils import rebuild_h_atoms
 
-def mark_aromatic_edges(graph):
-    for edge in graph.edges:
-        if graph.nodes[edge[0]].get("aromatic", False) and\
-        graph.nodes[edge[1]].get("aromatic", False):
-            graph.edges[edge]["order"] = 1.5
-    return graph
-
 def compatible(left, right):
     """
     Check bonding descriptor compatibility according
@@ -189,6 +182,10 @@ def edges_from_bonding_descrpt(self):
                 # unless they are specifically annotated
                 order = int(bonding[0][-1])
                 self.molecule.add_edge(edge[0], edge[1], bonding=bonding, order=order)
+                if self.all_atom:
+                    for edge_node in edge:
+                        if self.molecule.nodes[edge_node]['element'] != 'H':
+                            self.molecule.nodes[edge_node]['hcount'] -= 1
 
     def squash_atoms(self):
         """
@@ -232,7 +229,6 @@ def resolve(self):
 
         # rebuild hydrogen in all-atom case
         if self.all_atom:
-            mark_aromatic_edges(self.molecule)
             rebuild_h_atoms(self.molecule)
 
         # sort the atoms