6.18. Gromacs portable run input TPR format parser¶
6.18.2. Development notes¶
The TPR reader is a pure-python implementation of a basic TPR parser. Currently the following sections of the topology are parsed:
- Atoms: number, name, type, resname, resid, segid, mass, charge, [residue, segment, radius, bfactor, resnum, moltype]
- Bonds
- Angels
- Dihedrals
- Impropers
This tpr parser is written according to the following files
gromacs_dir/src/kernel/gmxdump.c
gromacs_dir/src/gmxlib/tpxio.c
(the most important one)gromacs_dir/src/gmxlib/gmxfio_rw.c
gromacs_dir/src/gmxlib/gmxfio_xdr.c
gromacs_dir/include/gmxfiofio.h
or their equivalent in more recent versions of Gromacs.
The function read_tpxheader()
is based on the
TPRReaderDevelopment notes. Functions with names starting with
read_
or do_
are trying to be similar to those in
gmxdump.c
or tpxio.c
, those with extract_
are new.
Wherever fver_err(fver)
is used, it means the tpx version problem
has not been solved. Versions prior to Gromacs 4.0.x are not supported.