Thanks Paolo, this works brilliantly. Let's hope astatine inhibitors won't gain
in popularity 😉
Best,
Jenke
________________________________
From: Paolo Tosco <paolo.tosco.m...@gmail.com>
Sent: 30 October 2019 13:25
To: SCHEEN Jenke <j.sch...@sms.ed.ac.uk>; RDKit Discuss
<rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] fingerprint a molecule with pseudoatoms denoted by
'Du'
Hi Jenke,
I have put together a small gist showing a slightly hacky way to round-trip a
molecule containing dummy atoms through a PDB block (assuming that your
molecules do not contain astatine). If your dummy atoms are called "DU" rather
than " *", you may just change the replace() expression with something that
fits your needs.
HTH, cheers
p.
On 10/30/19 12:06, SCHEEN Jenke wrote:
Hi RDKitters,
I'm trying to use rdkit to generate molecular fingerprints (such as AP or ECFP)
on molecules that have non-interactive pseudoatoms ('dummy atoms', denoted by
Du). I attached a sample PDB file containing the dummy atoms on positions
21-24. Reading this file (Chem.rdmolfiles.MolFromPDBFile("test.pdb",
sanitize=False) throws a post-condition violation because the element 'Du'
isn't recognised, which makes sense. I've been searching online and haven't
been able to find any workarounds, do you have any suggestions?
Some notes:
* I'm hoping that once rdkit is able to read in the pdb file the mol object
can be parsed without the FP constructor (e.g. AllChem.GetMorganFingerprint)
complaining.
* The use of the term dummy atoms here should not be confused with the
dummy atoms depiction in fragmentising molecules in rdkit (where * is the
smiles notation).
* For this project all I aim to do is generate structural fingerprints for
these types of ligands. This means I won't have to worry about defining
chemical properties to Du.
* The context for this issue is that we're aiming to featurise the ligands
for an ML protocol where the dummy atoms are one of the major descriptors of
the problem.
* I thought manually inserting a 119th element in atomic_data.cpp might
resolve the issue but I've been unable to locate the file in my conda
installation.
* The ODDT python API seems to parse the Du element without any issues but
is limited in its FP generator diversity.
Best,
Jenke
The University of Edinburgh is a charitable body, registered in Scotland, with
registration number SC005336.
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