4.13. Gromacs portable run input TPR format parser¶
The TPRParser
module allows reading of a
Gromacs portable run input file (a TPR file). At the moment, only
atom information is read and used to build a minimal topology. Because
the file format of the TPR file is changing rapidly, not all versions
are currently supported. The known working versions and the
approximate Gromacs release numbers are listed in the table
TPR format versions.
TPX format | TPX generation | Gromacs release | read |
---|---|---|---|
?? | ?? | 3.3, 3.3.1 | no |
58 | 17 | 4.0, 4.0.2, 4.0.3, 4.0.4, 4.0.5, 4.0.6, 4.0.7 | yes |
73 | 23 | 4.5.0, 4.5.1, 4.5.2, 4.5.3, 4.5.4, 4.5.5 | yes |
83 | 24 | 4.6, 4.6.1 | yes |
For further discussion and notes see Issue 2. Also add a comment to Issue 2 if a new or different TPR file format version should be supported.
4.13.1. Classes¶
-
class
MDAnalysis.topology.TPRParser.
TPRParser
(filename, universe=None, **kwargs)[source]¶ Read topology information from a Gromacs TPR_ file.
See also
MDAnalysis.topology.TPR
Standard arguments for a TopologyReader:
Arguments: - filename
name of the topology file
Keywords: - universe
Supply a Universe to the Parser. This then passes it to the atom instances that are created within parsers.
- kwargs
Other keyword arguments that can vary with the specific format. These are stored as self.kwargs
-
close
()¶ Close the trajectory file.
-
convert_forces_from_native
(force, inplace=True)¶ In-place conversion of forces array force from native units to base units.
By default, the input force is modified in place and also returned.
New in version 0.7.7.
-
convert_forces_to_native
(force, inplace=True)¶ In-place conversion of force array force from base units to native units.
By default, the input force is modified in place and also returned.
New in version 0.7.7.
-
convert_pos_from_native
(x, inplace=True)¶ In-place conversion of coordinate array x from native units to base units.
By default, the input x is modified in place and also returned.
Changed in version 0.7.5: Keyword inplace can be set to
False
so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
-
convert_pos_to_native
(x, inplace=True)¶ Conversion of coordinate array x from base units to native units.
By default, the input x is modified in place and also returned.
Changed in version 0.7.5: Keyword inplace can be set to
False
so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
-
convert_time_from_native
(t, inplace=True)¶ Convert time t from native units to base units.
By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)
Changed in version 0.7.5: Keyword inplace can be set to
False
so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
-
convert_time_to_native
(t, inplace=True)¶ Convert time t from base units to native units.
By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)
Changed in version 0.7.5: Keyword inplace can be set to
False
so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
-
convert_velocities_from_native
(v, inplace=True)¶ In-place conversion of velocities array v from native units to base units.
By default, the input v is modified in place and also returned.
New in version 0.7.5.
-
convert_velocities_to_native
(v, inplace=True)¶ In-place conversion of coordinate array v from base units to native units.
By default, the input v is modified in place and also returned.
New in version 0.7.5.
See also
4.13.2. 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]
- Bonds:
- Angels:
- Dihedrals:
- Impropers:
Potential Bug: in the result of gmxdump, the “Proper Dih.:” section is actually a list of Improper Dih.
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
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
haven’t be resolved for those other than 58 and 73 (or gromacs version
before 4.x)