Dear Guillaume,

I'm not sure what your code should do and what behavior you expect. I see
that you do not change the value of t when you see a single bond. So maybe
you just do not update this value and print and old one? Also, you iterate
over bonds of atom's last neighbor (so for H you loop over bonds of
aromatic C). Is that intended?

Best
Marta SD

2017-09-14 11:32 GMT+02:00 Guillaume GODIN <guillaume.go...@firmenich.com>:

> ​
>
>
> Dear all
>
>
> from rdkit import Chem
> from rdkit.Chem.rdchem import BondType
>
>
> AROMATIC = BondType.AROMATIC
> SINGLE = BondType.SINGLE
> DOUBLE = BondType.DOUBLE
> TRIPLE = BondType.TRIPLE
>
>
> suppl = 
> Chem.SDMolSupplier('/Users/GVALMTGG/Downloads/neemp-sources/examples/set00.sdf',removeHs
>  = False)
> i=0
> for mol in suppl:
>     i+=1
>     v=-1
>     for atom in mol.GetAtoms():
>         v+=1
>         t=1
>         for bond in atom.GetNeighbors()[-1].GetBonds():
>             if bond.GetBondType() == AROMATIC:
>                 t=1.5
>             if bond.GetBondType() == DOUBLE:
>                 t=2
>             if bond.GetBondType() == TRIPLE:
>                 t=3
>         if i<2:
>             print str(v) + " " + atom.GetSymbol() + " " + str(t)
>
>
> Why the code return H with 1.5 type bond ?
>
>
> I used anaconda environment to run the code:
>
>
> /Users/GVALMTGG/anaconda/envs/my-rdkit-env/bin/python /Users/GVALMTGG/
> PycharmProjects/neemp/neemp.py
> 0 N 1
> 1 O 2
> 2 O 2
> 3 C 1
> 4 C 1
> 5 C 1
> 6 C 1
> 7 C 1
> 8 C 1
> 9 C 1
> 10 C 1
> 11 C 1.5
> 12 C 2
> 13 C 1
> 14 C 1
> 15 C 2
> 16 C 2
> 17 C 1
> 18 H 1.5
> 19 H 1.5
> 20 H 1.5
> 21 H 1.5
> 22 H 1.5
> 23 H 1.5
> 24 H 1.5
> 25 H 1.5
> 26 H 1.5
> 27 H 1
> 28 H 1
>
>
> *Dr. Guillaume GODIN*
> Principal Scientist
> Chemoinformatic & Datamining
> Innovation
> CORPORATE R&D DIVISION
> DIRECT LINE +41 (0)22 780 3645 <+41%2022%20780%2036%2045>
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>         Firmenich SA
>         RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
>
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