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We want to get each atom fingerprint feature for further analysis. But we found a problem for atom 13.
Please find the code and the results below. from rdkit import Chem from rdkit.Chem import AllChem from rdkit.Chem import Draw import rdkit print(rdkit.__version__) mol = Chem.MolFromSmiles('Cc1c(C)c2c(c(C)c1O)CC[C@@](C)(CCC[C@H](C)CCC[C@H](C)CCCC(C)C)O2') def show_atom_number(mol, label): for atom in mol.GetAtoms(): atom.SetProp(label, str(atom.GetIdx())) return mol show_atom_number(mol, 'atomLabel')
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We want to get each atom fingerprint feature for further analysis. But we found a problem for atom 13.
Please find the code and the results below.
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
import rdkit
print(rdkit.__version__)
mol = Chem.MolFromSmiles('Cc1c(C)c2c(c(C)c1O)CC[C@@](C)(CCC[C@H](C)CCC[C@H](C)CCCC(C)C)O2')
def show_atom_number(mol, label):
for atom in mol.GetAtoms():
atom.SetProp(label, str(atom.GetIdx()))
return mol
show_atom_number(mol, 'atomLabel')
mol = Chem.MolFromSmiles('Cc1c(C)c2c(c(C)c1O)CC[C@@](C)(CCC[C@H](C)CCC[C@H](C)CCCC(C)C)O2')
bi ={}
fp = AllChem.GetMorganFingerprintAsBitVect(mol,nBits=256, radius=2, bitInfo=bi,fromAtoms=[13])
print(bi)
No feature for (13,2) in the final output. I want to know if something is wrong or it is the right result.
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