[OpenBabel-scripting] Fwd: pybel: Addition of hydrogens

[Noel O'B. <bao...@gm...>]

---------- Forwarded message ----------
From: Florian Nigsch <fn...@ca...>
Date: 2008/4/29
Subject: pybel: Addition of hydrogens
To: Noel O'Boyle <bao...@gm...>


Hi Noel,

 And here we go with the next question:

 1) I read in a molecule (sildenafil), remove the hydrogens, get a
canonical smiles
(CCOc1ccc(cc1c1nc(=O)c2n(C)nc(CCC)c2[nH]1)S(=O)(=O)N1CCN(C)CC1) which
I keep to create the same molecule again later.
 2) I read the molecule back in from the smiles with pybel.readstring()
 3) I delete the hydrogens with OBMol.DeleteHydrogens()
 4) I match with pybel.Smarts("[R]~[!R]") - i.e., get anything
non-ring that is connected to a ring
 5) print [m.atoms[x-1].OBAtom.GetType() for (y,x) in SmartsMatch] and get

 ['O3', 'So2', 'O2', 'C3', 'C3', 'So2', 'C3'] - which is fine.

 If I leave out step 3, then I find

 ['O3', 'So2', 'O2', 'C3', 'C3', 'H', 'So2', 'C3']

 and there is suddenly a hydrogen in there. Where does it come from?
Does OpenBabel add hydrogens internally when reading in from a smiles?
Why does it only match one out of all possible ring-hydrogens (there
are about 8 I think)?

 Thanks a lot,

 Flo