I'm trying to parse ATOM section of a PDB file. I'm using the dsr-pdb
library for this purpose.
I've encountered a problem. This library interprets CD1 atom of ILE residue in the PDB file as AL_CD instead of AL_CD1*. Does it have a particular reason?
It's maybe helpful that within the source code, in Residue_data.cc
, there is a mapping between atom lebels:
Atom_fallback_data atom_fallback_data_[]= {{Residue::AL_CD1, Residue::AL_CD}, {Residue::AL_1HA, Residue::AL_HA}, {Residue::AL_1HB, Residue::AL_HB}, {Residue::AL_1HD, Residue::AL_HD}, {Residue::AL_1HE, Residue::AL_HE}, {Residue::AL_1HZ, Residue::AL_HZ}, //{Residue::AL_1HH, Residue::AL_HH}, {Residue::AL_1HD1, Residue::AL_1HD}, {Residue::AL_2HD1, Residue::AL_2HD}, {Residue::AL_3HD1, Residue::AL_3HD}, {Residue::AL_INVALID, Residue::AL_INVALID}};
It means that AL_CD1 is deliberately converted to AL_CD or for example AL_1HA to AL_HA.
Thanks.
- In general, in dsr-pdb library, AL_X is the atom label of atom X.