I just wanted to quickly update the List on how I've got on with this,
in case it is of use / interest to others. I followed Greg's advice and
did the following:
1. Exported molfile from PyMOL
2. Read into RDKit
3. Read in an SDF of already-constructed molecules based on the core
(could have built the products in RDKit, but the SDF was already
available!)
4. Iterated over the objects in the supplier to do the
AllChem.ConstrainedEmbed as discussed, then load the results into PyMOL
NOTE - Because the molecules weren't built in RDKit, I couldn't rely on
the atom numbering when read into PyMOL (maybe this can't be relied on
anyway?). So I ran mol.GetSubstructMatch(core) for each molecule to get
the aligned product atom IDs that matched the core. I then flagged
these in PyMOL with flag 3 [Fixed Atoms (no movement allowed)] (flag 2 -
harmonically constrained may be better..?) so that I could subsequently
run the mengine 'clean' command in PyMOL to tidy-up the UFF output
without allowing the template to move:
from rdkit import Chem
core = Chem.MolFromMolFile(mol_filepath)
supplier = Chem.SDMolSupplier(sdf_filepath)
for n,mol in enumerate(supplier):
mol = Chem.AddHs(mol)
newMol = AllChem.ConstrainedEmbed(mol, core, True)
name = "mol"+str(n)
fix = ','.join([str(n) for n in mol.GetSubstructMatch(core)])
v.ShowMol(newMol, name=name, showOnly=False)
selection = '('+name+' and (id '+fix+'))'
v.server.do('flag 3, '+selection+', set')
Kind regards
James
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