Dear RDKit experts,
I am new to RDKit and I have a simple question about atom indexing with RDKit.
I am using RDKit in Python to process a collection of small molecule, for each
I have the SMILES and a pdb file without explicit hydrogens. To draw the 2D
images of the molecules, I used AssignBondOrdersFromTemplate to assign the bond
order.
pdbmol = rdmolfiles.MolFromPDBFile(<the pdb file>)
smilemol = Chem.MolFromSmiles(<the smiles string>)
newmol = AllChem.AssignBondOrdersFromTemplate(smilemol, pdbmol)
rdDepictor.Compute2DCoords(newmol)
for atom in newmol.GetAtoms():
atom.SetAtomMapNum(atom.GetIdx())
Using the above lines, I was able to draw the ligand in 2D with Idx of atoms.
However, I noticed that the Idx of atoms have changed in the newmol… Is there a
way to keep the original indexing from the PDB file in the newmol (perhaps by
an alternative way to set bond order)? I wanted to label a couple of atoms in
the 2D picture, but I only know their Idx in the PDB file, so I really wish to
keep the original indexing.
Any comments/suggestions would be greatly appreciated. Thank you for your time
and kind advice in advance!!
Many Thanks,
Amy
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
[email protected]<mailto:[email protected]>
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