Hi Brian, Thank you for your kind reply. That’s a very good point! The order of atoms in the PDB file (which I extracted from RCSB PDB) is not the same as in the SMILES. And I find that the indexing in newmol will follow the reference molecule.
But I was wrong in thinking that the indexing was different from both. I didn’t realize that the indexing is zero-based… Using the codes in the previous message, the newmol will receive the bond order from smilemol and the indexing from pdbmol, which is exactly what I wanted to do! Thank you again for your time and kind help!! Thanks, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University [email protected] From: Bennion, Brian <[email protected]> Date: Sunday, July 17, 2022 at 8:20 PM To: He, Amy <[email protected]>, [email protected] <[email protected]> Subject: Re: [Rdkit-discuss] Atom indexing with AssignBondOrdersFromTemplate I don’t know if this is the issue but Are the order of atoms the same between the pdb file and the smiles string? --- Sent from Workspace ONE Boxer On July 16, 2022 at 8:14:51 PM PDT, He, Amy <[email protected]> wrote: I don’t know if this is the issue but Are the order of atoms the same between the pdb file and the smiles string? --- Sent from Workspace ONE Boxer<https://urldefense.com/v3/__https:/whatisworkspaceone.com/boxer__;!!KGKeukY!ys014tzEXJmNi8IQW56hTW857n_g_PPt2PXLOUBlwv2sRR__E6NIIDJeLXnpF8VrEQlDqMnesvLXIQc-55S-Qekas4gYPes$> On July 16, 2022 at 8:14:51 PM PDT, He, Amy <[email protected]> wrote: 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]> <ATT00001.txt> <ATT00002.txt>
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