That solves the problem.
Thank you.
--Nimal
On Mon, Apr 27, 2020 at 11:32 PM Guillaume GODIN <
guillaume.go...@firmenich.com> wrote:
> 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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