hydrogen processing fixed.

cimm-kzn · Feb 22, 2019 · c006de2 · c006de2
1 parent 98d4606
commit c006de2
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/CGRtools/containers/molecule.py b/CGRtools/containers/molecule.py
@@ -74,9 +74,9 @@ def implicify_hydrogens(self):
         c = 0
         for n, atom in self.atoms():
             if atom.element == 'H':
-                m = next(self.neighbors(n))
-                if self._node[m].element != 'H':
-                    explicit[m].append(n)
+                for m in self.neighbors(n):
+                    if self._node[m].element != 'H':
+                        explicit[m].append(n)
 
         for n, h in explicit.items():
             atom = self._node[n]

diff --git a/CGRtools/periodictable/data.py b/CGRtools/periodictable/data.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2017, 2018 Ramil Nugmanov <stsouko@live.ru>
+#  Copyright 2017-2019 Ramil Nugmanov <stsouko@live.ru>
 #  This file is part of CGRtools.
 #
 #  CGRtools is free software; you can redistribute it and/or modify
@@ -22,6 +22,7 @@
 # http://onlinelibrarystatic.wiley.com/marvin/help/sci/ValenceCalculator.html
 # elements, charge, radical, bonds, [implicitH]
 _valence_rules = (
+    ('H', -1, 0, 0, 0),
     # elemental Me
     (('Li', 'Na', 'K', 'Rb', 'Cs', 'Fr'), 0, 0, 0, 0),
     # 1 bond is accepted