Hi James,
Okay, now it's clear. I somehow (wrongly) thought the PDB reader would give
you the protein and the ligand as two molecules and then it wouldn't have
been a problem... I will discuss with Greg on how to best do this and get
back to you.
Best,
Sereina
2013/10/25 James Davidson <j.david...@vernalis.com>
> Hi Sereina,
>
> Sereina wrote:
> > Regarding the AssignBondOrdersFromTemplate() method:
> > As far as I understood, the PDB reader assigns bond orders to the amino
> acids in a protein, but if a ligand is present it puts all bonds of it to
> SINGLE bonds as auto bond-type perception is not trivial (see Roger's
> comments).
> > However, usually one knows which ligand was crystallized (i.e. the
> SMILES is available), so the AssignBondOrdersFromTemplate() method can be
> used to set the bond orders based on the known ligand structure.
> > This is the idea of the method. Now, to your real-world application. I'm
> sorry but I don't think I understand it completely. Do you want to set only
> the bond orders of a specific substructure?
> > Or would you like to give the function a set of ligands and a set of
> templates and it figures out which template belongs to which ligand and
> sets the bonds orders accordingly?
>
> This is very likely to be me being stupid - so please bear with me!
> If I read in a complex (pdb), and already have my reference ligand (lig),
> then AllChem.AssignBondOrdersFromTemplate(lig, pdb) fails because the
> reference ligand has not been matched to the ligand in the pdb 'complex'
> (dot-separated list of molecules).
> The doc-string states that the method works on two molecules - but I want
> to work on a reference molecule (lig) and a *substructure* of the
> macromolecule (pdb). How should I be getting the bound ligand out as a
> molecule object to then use the AssignBondOrdersFromTemplate() method? Am
> I missing some new PDB-related methods, or have I forgotten some
> fundamental RDKit methods for dealing with multi-component molecules?
>
> I guess a sensible process would be:
> 1. Identify any HETATM residues
> 2. For each residue (or at least those that have bonds!) extract or copy
> the mol (unless it can be addressed 'in place'?)
> 3. Use AssignBondOrdersFromTemplate() - relying on lookup be eg residue
> name, etc
> 4. Insert the molecule back into the complex (or update the info if it has
> been modified 'in place')
>
> Is this how the method is intended to be used with complexes (and if so,
> do you have an example for steps 2 and 4?
>
> Thanks
>
> James
>
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