Dear Nimal,
You are using atoms to enumerate bonds and a bond has 2 atoms so the number of
bonds are not the real ones.
Use this instead :
for bond in molecule.GetBonds()
bond.GetBondType() == …
best regards,
Guillaume
De : nCloud <nimalnaser.cl...@gmail.com>
Date : mardi, 28 avril 2020 à 05:06
À : "rdkit-discuss@lists.sourceforge.net" <rdkit-discuss@lists.sourceforge.net>
Objet : [*External*] [Rdkit-discuss] Uniqueness of bonds
Hi RDKiters,
I recently started using this wonderful package and I have been getting
familiarized with many of its capabilities.
The problem I am working on now is to determine the number of individual bonds
in any given molecule. I am able to classify the groups in to single, double or
triple and aromatic; however, it seems in some cases some bonds are recounted.
As an example based on my minimum working example (MWE) given below; ethane
should provide only 1 single bond (output also given); propane should give 2
single bonds, but every time an additional bond is counted. Another example
would be of 1,3-hexadien-5-yne, which has 2 double and 1 triple bond, but the
output has 3 double bonds.
The problem, I believe, is due to the function I created does not consider the
uniqueness of the bonds; how can the uniqueness of the bond be considered with
RDKit?
MWE
from rdkit import Chem
def n_bonds(molecule):
molecule = Chem.MolFromSmiles(molecule)
fuel_bonds = {'single': 0, 'double': 0, 'triple': 0, 'aromatic': 0}
for atom in molecule.GetAtoms():
if str(atom.GetBonds()[0].GetBondType()) == 'SINGLE':
fuel_bonds['single'] += 1
elif str(atom.GetBonds()[0].GetBondType()) == 'DOUBLE':
fuel_bonds['double'] += 1
elif str(atom.GetBonds()[0].GetBondType()) == 'TRIPLE':
fuel_bonds['triple'] += 1
elif str(atom.GetBonds()[0].GetBondType()) == 'AROMATIC':
fuel_bonds['aromatic'] += 1
return fuel_bonds
smiles_test = [ 'CC', # 1. ethane
'CCC', # 2. propane
'C1CC1', # 3. cyclopropane
'C1CCC1', # 4. cyclobutane
'CC(C)(C)C', # 5. neopentane
'CCCCC1=CC=CC=C1', # 6. butylbenzene
'CCC(CC)CCC(C)C', # 7. 5-ethyl-3-methylheptane
'CCCCCC=CC=CC=C', # 8. 1,3,5-undecatriene
'C=CC=CC#C', # 9. 1,3-Hexadien-5-yne
'CC#CC#CC#CC=CC=CCCCC=C'] # 10.
Hexadeca-1,6,8-triene-10,12,14-triyne
for i in range(len(smiles_test)):
f = n_bonds(smiles_test[i])
print i+1, '-', f
Output
1 - {'double': 0, 'single': 2, 'aromatic': 0, 'triple': 0}
2 - {'double': 0, 'single': 3, 'aromatic': 0, 'triple': 0}
3 - {'double': 0, 'single': 3, 'aromatic': 0, 'triple': 0}
4 - {'double': 0, 'single': 4, 'aromatic': 0, 'triple': 0}
5 - {'double': 0, 'single': 5, 'aromatic': 0, 'triple': 0}
6 - {'double': 0, 'single': 5, 'aromatic': 5, 'triple': 0}
7 - {'double': 0, 'single': 10, 'aromatic': 0, 'triple': 0}
8 - {'double': 3, 'single': 8, 'aromatic': 0, 'triple': 0}
9 - {'double': 3, 'single': 2, 'aromatic': 0, 'triple': 1}
10 - {'double': 3, 'single': 10, 'aromatic': 0, 'triple': 3}
Regards,
Nimal
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