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 ______________________________________________________________________ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 0000 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. ______________________________________________________________________ ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
