Dear James,
Thanks for sending along the information about how you did the pymol
steps; I'm sure it will be useful to others. Tighter RDKit-PyMol
integration is definitely a good thing.
Best Regards,
-greg
On Fri, Jul 2, 2010 at 8:09 PM, James Davidson <j.david...@vernalis.com> wrote:
> 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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