New method Molecule.deleteHydrogens()

This is a bit like makeHydrogensImplicit, except that it doesn't increment the
implicitHydrogens counter on the neighboring atoms, so there is no getting them back!
This is useful for some situations where you have a shallow copy of a molecule and you want
to consider it without the hydrogens, but do not want to edit attributes of the atoms
that are shared with the original molecule.

Author: rwest

rmgpy/molecule.pxd

@@ -104,6 +104,8 @@ cdef class Molecule(Graph):
 
     cpdef Graph copy(self, bint deep=?)
 
+    cpdef deleteHydrogens(self)
+
     cpdef makeHydrogensImplicit(self)
 
     cpdef makeHydrogensExplicit(self)

rmgpy/molecule.py

@@ -594,6 +594,32 @@ def split(self):
             molecules.append(molecule)
         return molecules
 
+    def deleteHydrogens(self):
+        """
+        Irreversibly delete all non-labeled hydrogens, without incrementing
+        the "implicitHydrogens" count of the neighbouring atom, or updating
+        Connectivity Values or the implicitHydrogens flag. If there's nothing
+        but Hydrogens, it does nothing.
+        It destroys information; be careful with it.
+        """
+        cython.declare(atom=Atom, neighbor=Atom, hydrogens=list)
+        # Check that the structure contains at least one heavy atom
+        for atom in self.vertices:
+            if not atom.isHydrogen():
+                break
+        else:
+            # No heavy atoms, so leave explicit
+            return
+        hydrogens = []
+        for atom in self.vertices:
+            if atom.isHydrogen() and atom.label == '':
+                neighbor = self.edges[atom].keys()[0]
+                hydrogens.append(atom)
+        # Remove the hydrogen atoms from the structure
+        for atom in hydrogens:
+            self.removeAtom(atom)
+
+
     def makeHydrogensImplicit(self):
         """
         Convert all explicitly stored hydrogen atoms to be stored implicitly,