Hi All,
I'm a bit confused about counting hydrogen atoms. It's a perennial problem
with cheminformatics toolkits in my experience, but this seems particularly
perverse. If I run the code:
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles( 'CCO' )
mol = Chem.AddHs( mol )
cids = AllChem.EmbedMultipleConfs(mol , useExpTorsionAnglePrefs=True ,
useBasicKnowledge=True , numConfs=1 )
AllChem.MMFFOptimizeMoleculeConfs( mol , mmffVariant='MMFF94s' )
for a in mol.GetAtoms() :
num_heavy = a.GetTotalDegree() - a.GetTotalNumHs()
print '%d : %d num_heavy = %d num_H = %d %d %d' % ( a.GetIdx() ,
a.GetAtomicNum() , num_heavy , a.GetTotalNumHs() , a.GetNumImplicitHs() ,
a.GetNumExplicitHs() )
for nb in a.GetNeighbors() :
print ' %d : %d' % ( nb.GetIdx() , nb.GetAtomicNum() )
I get the output
0 : 6 num_heavy = 4 num_H = 0 0 0
1 : 6
3 : 1
4 : 1
5 : 1
1 : 6 num_heavy = 4 num_H = 0 0 0
0 : 6
2 : 8
6 : 1
7 : 1
2 : 8 num_heavy = 2 num_H = 0 0 0
1 : 6
8 : 1
3 : 1 num_heavy = 1 num_H = 0 0 0
0 : 6
4 : 1 num_heavy = 1 num_H = 0 0 0
0 : 6
5 : 1 num_heavy = 1 num_H = 0 0 0
0 : 6
6 : 1 num_heavy = 1 num_H = 0 0 0
1 : 6
7 : 1 num_heavy = 1 num_H = 0 0 0
1 : 6
8 : 1 num_heavy = 1 num_H = 0 0 0
2 : 8
It seems that in a 3D mol, after embedding and minimisation, an H atom is
just like any other atom, and is ignored in the various H atom counting
functions. Is that expected behaviour? Depending on the answer, either
the documentation or the behaviour is incorrect.
Cheers,
Dave
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