Dear RDKit experts,
I need your advice on finding a source Smiles library for reference, to build
the template molecule from Smiles for
AssignBondOrdersFromTemplate<https://www.rdkit.org/docs/source/rdkit.Chem.AllChem.html>.
I am using AssignBondOrdersFromTemplate to perceive bonds in a residue-wise
manner from an input PDB, using a reference Smiles library like this:
ref_smi = {
"ALA": "NC(C)C(=O)",
"GLY": "NCC(=O)",
"ILE": "NC(C(C)CC)C(=O)",
}
I wonder if there has been an open reference library for common amino acids and
ligands that present in PDB files. A previous post on rdkit-discuss
(https://rdkit-discuss.narkive.com/JM2IGLQz/pdb-reader-and-bond-perception)
points me to this website:
ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/pdb.tar.gz
and useful links from
http://www.ebi.ac.uk/pdbe-srv/pdbechem/
But I am no longer able to access the contents.
I guess we could always generate Smiles from the standardized SDF files.. Still
I am wondering if there is an existing Smiles library (like a reference
datafile), where we can retrieve the Smiles string using the residue names of
common amino acids and maybe also ligands.
Any comments or suggestions would be greatly appreciated. Thank you for your
time and kind support in advance!
Bests,
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Lab
Ohio State University
he.1...@osu.edu<mailto:he.1...@osu.edu>
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