[MMTK] problem reading PDB files with hydrogens
Andrew J. Bordner
bordner at ornl.gov
Thu May 26 16:33:00 CEST 2005
I would like to read PDB files while ignoring hydrogen atom coordinates.
MMTK seems to throw an exception for non-standard hydrogen atom names
even when model = 'no_hydrogens'. It would probably be better for the
PDB file parser to just skip hydrogen atoms rather that checking their
names when model = 'no_hydrogens' or 'none'.
An example is PDB entry 7RSA":
conf = MMTK.PDB.PDBConfiguration('7rsa')
molecules = conf.createPeptideChains('no_hydrogens')
IOError: Atom 1H of PDB residue LYS not found in residue Lys of object .Lys1
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