Dear All,
I am trying to work out the best way to accomplish some tasks involving
RDKit, using PyMOL as an interface, and would appreciate some help. I
would like to be able to start from a PDB file of a ligand-bound crystal
structure loaded in PyMOL and be able to 'virtually' build some
analogues - initially just simple substitutions - and visually inspect
the results.
(1) So my first question is - having started PyMOL with the -R option,
is there an easy or recommended way of transferring molecules from PyMOL
to RDKit? I can accomplish this by writing molfiles to a temporary
file, but wondered if I am creating work, if eg RDKit could
automatically create Mol objects from non-biopolymer atoms in PyMol(?).
ie it would be nice if:
from rdkit import Chem
from rdkit.Chem import PyMol
v = PyMol.MolViewer()
# Invented function to create an RDKit mol object
mol = v.GetAtomsAsMol(selection)
(2) Once the ligand is converted to an RDKit mol object (by whatever
means) I want to enumrate some libraries of virtual products - eg
choosing an atom in PyMol as the attachment point, then running a set of
reactions to get products with a set of substituents added. In
principle I think this is quite straightforward; however, what I am
struggling with is a mechanism to 'freeze' the 3D coordintes of the
original ligand atoms, but still be able to use RDKit to generate
sensible 3D positions for the newly added atoms so that the products can
be passed back to PyMOL and minimised in situ (if required) using
'mengine.exe'. Am I looking at this the wrong way, and should I
actually try aligning the virtual products back on the starting ligand
conformation?
(3) Apologies that this last point is maybe a bit off-topic, but I
wondered if anyone has an opinion as to whether MMTK is the way to go
for 'simple' minimisations of modified ligands bound to proteins? (I
don't have any real experience with MMTK...
Kind regards
James
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