On 05/09/2018 10:27 AM, carlo del moro wrote: > Dear All, > > we would like to know if it is possible to map the atom's ID of a SMILES > represented substructure to the atom sequence of a ligand contained in a > pdb file. This in order to get the spatial coordinates related to such > substructure.
http://alatis.nmrfam.wisc.edu/ will generate unique stable IDs from a 3D structure, and output the old->new ID map. It'll take a PDB, you'll have to convert your SMILES into a 3D .mol. ALATIS atom IDs should be the same in the two maps, *provided both inputs describe the exact same ligand*. (It's the *substructure* bit that I'm not entirely sure about.) -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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