?
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
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Firmenich SA
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set00.sdf
Description: set00.sdf
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