Thank you very much Andrew! Indeed, I did not spot the pattern - how silly of me! ________________________________________ From: Andrew Dalke [da...@dalkescientific.com] Sent: 01 February 2017 16:49 To: Susan Leung Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Rdkit atom indexing vs indexing in written pdb file
Dear Susan, If I understand what's going on correctly, you have run across the difference between 0-based and 1-based indexing. See https://en.wikipedia.org/wiki/Zero-based_numbering . RDKit, like most programming libraries and languages, index based on an offset from the beginning, so 0 means the beginning, 1 means one after the beginning, etc. This is somewhat like how some buildings use "1" as the first floor above the ground, while others regard "1" as the ground floor, which is confusing if you are not used to it. (My apartment number says its on the second floor, while the elevator button says I live on floor 3.) On Feb 1, 2017, at 5:15 PM, Susan Leung <susan.le...@st-hildas.ox.ac.uk> wrote: > I am producing rdkit conformers and writing them to pdb files but am finding > the atom indexing in rdkit is different from the written pdb. ... > Here is my code and output (the C=O looks like it's atoms 3,4 in rdkit but > 4,5 in the pdb file): ... > In [3]: mol = Chem.MolFromSmiles("CC1=C(C(=O)C)C=CC=C1") ... > In [4]: mol.GetSubstructMatch(Chem.MolFromSmiles('C(=O)')) > Out[4]: (3, 4) ... > record_name atom_number blank_1 atom_name alt_loc residue_name blank_2 \ > 0 HETATM 1 C1 UNL > 1 HETATM 2 C2 UNL > 2 HETATM 3 C3 UNL > 3 HETATM 4 C4 UNL > 4 HETATM 5 O1 UNL > 5 HETATM 6 C5 UNL > 6 HETATM 7 C6 UNL > 7 HETATM 8 C7 UNL > 8 HETATM 9 C8 UNL > 9 HETATM 10 C9 UNL If I understand you correctly, then the "(3, 4)" as RDKit atom indices is (3+1, 4+1) = (4,5) as PDB atom number, that is, the RDKit indices correspond to the left-most column of your table, rather than the atom_number column. Cheers, Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss