Dear Marta,
this function works now:
from rdkit import Chem
from rdkit.Chem.rdchem import BondType
AROMATIC = BondType.AROMATIC
SINGLE = BondType.SINGLE
DOUBLE = BondType.DOUBLE
TRIPLE = BondType.TRIPLE
def atomtype(mol,atom):
t=1
for linkatoms in atom.GetNeighbors():
bond = mol.GetBondBetweenAtoms(atom.GetIdx(),linkatoms.GetIdx())
if bond.GetBondType() == AROMATIC:
t=2
if bond.GetBondType() == DOUBLE:
t=2
if bond.GetBondType() == TRIPLE:
t=3
return t
suppl = Chem.SDMolSupplier('examples/set00.sdf',removeHs = False)
i=0
for mol in suppl:
i+=1
v=-1
for atom in mol.GetAtoms():
v+=1
t=atomtype(mol,atom)
if i<2:
print str(v) + " " + atom.GetSymbol() + " " + str(t)
but not with the previous call to that part
atom.GetNeighbors()[-1].GetBonds()
My desire output is:
0 N 1
1 O 2
2 O 2
3 C 2
4 C 2
5 C 2
6 C 2
7 C 2
8 C 2
9 C 2
10 C 2
11 C 2
12 C 2
13 C 2
14 C 2
15 C 2
16 C 2
17 C 1
18 H 1
19 H 1
20 H 1
21 H 1
22 H 1
23 H 1
24 H 1
25 H 1
26 H 1
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
MOBILE +41 (0)79 536 1039
Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
________________________________
De : Marta Stępniewska-Dziubińska <[email protected]>
Envoyé : jeudi 14 septembre 2017 11:56
A : Guillaume GODIN
Cc : [email protected]
Objet : Re: [Rdkit-discuss] is there an issue with my code or with GetNeighbors
function ?
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
<[email protected]<mailto:[email protected]>>:
?
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<tel:+41%2022%20780%2036%2045>
MOBILE +41 (0)79 536 1039<tel:+41%2079%20536%2010%2039>
Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
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