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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