drawMolecule() can now cope with either implicit or explicit Hydrogens.

It doesn't need to change. It deletes the hydrogens that it's not going to draw
from the lists and dicts that it has copied, leaving the originals alone, and
it keeps track independently of how many times it has done this for each heavy
atom.

Author: rwest

rmgpy/molecule_draw.py

@@ -1134,9 +1134,12 @@ def drawMolecule(molecule, path=None, surface=''):
         print 'Cairo not found; molecule will not be drawn.'
         return
 
-    # This algorithm requires that the hydrogen atoms be implicit
-    implicitH = molecule.implicitHydrogens
-    molecule.makeHydrogensImplicit()
+    # This algorithm now works with explicit hydrogen atoms on the molecule.
+    # Please ensure all the subroutines do also.
+    # We will delete them from the *copied* list of atoms, and store them here:
+    implicitHydrogensToDraw = {}
+    for atom in molecule.atoms:
+        implicitHydrogensToDraw[atom] = atom.implicitHydrogens
 
     atoms = molecule.atoms[:]
     # bonds = molecule.bonds.copy() is too shallow for a dict-of-dicts,
@@ -1149,15 +1152,17 @@ def drawMolecule(molecule, path=None, surface=''):
 
     # Special cases: H, H2, anything with one heavy atom
 
-    # Remove all unlabeled hydrogen atoms from the molecule, as they are not drawn
+    # Remove all unlabeled hydrogen atoms from the copied atoms and bonds, as they are not drawn
     # However, if this would remove all atoms, then don't remove any
     atomsToRemove = []
     for atom in atoms:
         if atom.isHydrogen() and atom.label == '': atomsToRemove.append(atom)
     if len(atomsToRemove) < len(atoms):
         for atom in atomsToRemove:
             atoms.remove(atom)
-            for atom2 in bonds[atom]: del bonds[atom2][atom]
+            for atom2 in bonds[atom]:
+                del bonds[atom2][atom]
+                implicitHydrogensToDraw[atom2] = implicitHydrogensToDraw[atom2] + 1
             del bonds[atom]
 
     # Generate the coordinates to use to draw the molecule
@@ -1191,8 +1196,8 @@ def drawMolecule(molecule, path=None, surface=''):
     # Add implicit hydrogens
     for i in range(len(symbols)):
         if symbols[i] != '':
-            if atoms[i].implicitHydrogens == 1: symbols[i] = symbols[i] + 'H'
-            elif atoms[i].implicitHydrogens > 1: symbols[i] = symbols[i] + 'H{0:d}'.format(atoms[i].implicitHydrogens)
+            if implicitHydrogensToDraw.get(atoms[i],0) == 1: symbols[i] = symbols[i] + 'H'
+            elif implicitHydrogensToDraw.get(atoms[i],0) > 1: symbols[i] = symbols[i] + 'H{0:d}'.format(implicitHydrogensToDraw[atoms[i]])
 
     # Special case: H2 (render as H2 and not H-H)
     if symbols == ['H','H']:
@@ -1228,8 +1233,6 @@ def drawMolecule(molecule, path=None, surface=''):
             else:
                 surface.finish()
 
-    if not implicitH: molecule.makeHydrogensExplicit()
-
     return surface, cr, (0, 0, width, height)
 
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