AddH not working with metal coordination

[Tristan Croll]

The following edits to add_h/simple.py seem to get things working again:

# line 93:

-  positions = bond_positions(at_pos, geom, bond_with_H_length(atom, geom),
-             bonded_pos, toward=toward, coplanar=planar, away=away, away2=away2)

+  positions = list(bond_positions(at_pos, geom, bond_with_H_length(atom, geom),
+            bonded_pos, toward=toward, coplanar=planar, away=away, away2=away2))

# Since Numpy arrays don't have a remove() method

# line 119:
+  if h is None:
+      continue 

# Since new_hydrogen returns None if the new H would clash with a metal

[pett]

These all seem correct, but is there an example PDB ID I can test against?

[tic20@…]

I was playing with 3io4. Not necessarily the best example (old and 
somewhat crappy structure). Try 5h0u (a high-res matrix 
metalloproteinase).

On 2017-10-13 01:11, ChimeraX wrote:

[pett]

Mostly used your changes; with one addition in the actually-adding-hydrogen that also skips some code if the hydrogen is None