pdb parser issue in IMP.atom.read_pdb
You probably know it, but some atom names would simply result in read_pdb to fail. This behavior seems a bit drastic too me. Maybe it would be possible to build a hierarchy containing atoms that could be recognized, and provide some warnings, or give access to the number of encountered errors or ignored atoms when building the hierarchy; leaving the final choice to the user to play with its structure or to reject it.
As an example : pdb code 1E1Q
mh = IMP.atom.read_pdb(pdbFilePath,m) _IMP.ValueException: Illegal character in atom name, only A-Z, 0-9, " "allowed. Got "HET: O5'"
I'll relax the check to allow ' characters in atom names.
On Jul 20, 2010, at 6:58 AM, Benjamin SCHWARZ wrote:
> You probably know it, but some atom names would simply result in read_pdb to fail. This behavior seems a bit drastic too me. Maybe it would be possible to build a hierarchy containing atoms that could be recognized, and provide some warnings, or give access to the number of encountered errors or ignored atoms when building the hierarchy; leaving the final choice to the user to play with its structure or to reject it. > > As an example : pdb code 1E1Q > > mh = IMP.atom.read_pdb(pdbFilePath,m) > _IMP.ValueException: Illegal character in atom name, only A-Z, 0-9, " "allowed. Got "HET: O5'" > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
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Daniel Russel