Merge pull request #2734 to Draw Hydrogen bonds (again)

Pull request  #1961  introduced the ability to draw hydrogen bonds.

To do so, Hydrogen atoms that have H bonds shouldn't be removed from the drawings.
This check was  removed without explanation in ec95153
which was designed to make drawing work for fragments.
That broke drawing of hydrogen bonds. This pull request fixes it, and also removes some code duplication.

Author: rwest

rmgpy/molecule/draw.py

@@ -184,7 +184,8 @@ def draw(self, molecule, file_format, target=None):
         surface_sites = []
         for atom in self.molecule.atoms:
             if isinstance(atom, Atom) and atom.is_hydrogen() and atom.label == '':
-                atoms_to_remove.append(atom)
+                if not any(bond.is_hydrogen_bond() for bond in atom.bonds.values()):
+                    atoms_to_remove.append(atom)
             elif atom.is_surface_site():
                 surface_sites.append(atom)
         if len(atoms_to_remove) < len(self.molecule.atoms) - len(surface_sites):
@@ -417,17 +418,6 @@ def _generate_coordinates(self, fix_surface_sites=True):
                     coordinates[i1, 1] -= 0.2
                     coordinates[i2, 1] += 0.2
 
-            # If two atoms lie on top of each other, push them apart a bit
-            # This is ugly, but at least the mess you end up with isn't as misleading
-            # as leaving everything piled on top of each other at the origin
-            for atom1, atom2 in itertools.combinations(backbone, 2):
-                i1, i2 = atoms.index(atom1), atoms.index(atom2)
-                if np.linalg.norm(coordinates[i1, :] - coordinates[i2, :]) < 0.5:
-                    coordinates[i1, 0] -= 0.3
-                    coordinates[i2, 0] += 0.3
-                    coordinates[i1, 1] -= 0.2
-                    coordinates[i2, 1] += 0.2
-
             # Center backbone at origin
             xmin = np.min(coordinates[:, 0])
             xmax = np.max(coordinates[:, 0])