5.21. Gromacs portable run input TPR format parser¶
The TPRParser
module allows reading of a
Gromacs portable run input file (a TPR file). 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 |
100 | 26 | 5.0, 5.0.1, 5.0.2, 5.0.3,5.0.4, 5.0.5 | yes |
103 | 26 | 5.1 | yes |
110 | 26 | 2016 | yes |
112 | 26 | 2018 | yes |
116 | 26 | 2019 | yes |
119 | 27 | 2020[*]_ | yes |
122 | 28 | 2021 | yes |
[*] | Files generated by the beta versions of Gromacs 2020 are NOT supported. See Issue 2428 for more details. |
For further discussion and notes see Issue 2. Please open a new issue in the Issue Tracker when a new or different TPR file format version should be supported.
Bonded interactions available in Gromacs are described in table 5.5 of the Gromacs manual. The following ones are used to build the topology (see Issue 463):
- bonds: regular bonds (type 1), G96 bonds (type 2), Morse (type 3), cubic bonds (type 4), connections (type 5), harmonic potentials (type 6), FENE bonds (type 7), restraint potentials (type 10), tabulated potential with exclusion/connection (type 8), tabulated potential without exclusion/connection (type 9), constraints with exclusion/connection (type 1), constraints without exclusion/connection (type 2), SETTLE constraints
- angles: regular angles (type 1), G96 angles (type 2), cross bond-bond (type3), cross-bond-angle (type 4), Urey-Bradley (type 5), quartic angles (type 6), restricted bending potential (type 10), tabulated angles (type 8)
- dihedrals: proper dihedrals (type 1 and type 9), Ryckaert-Bellemans dihedrals (type 3), Fourier dihedrals (type 5), restricted dihedrals (type 10), combined bending-torsion potentials (type 11), tabulated dihedral (type 8)
- impropers: improper dihedrals (type 2), periodic improper dihedrals (type 4)
5.21.1. Classes¶
-
class
MDAnalysis.topology.TPRParser.
TPRParser
(filename)[source]¶ Read topology information from a Gromacs TPR file.
-
close
()¶ Close the trajectory file.
-
convert_forces_from_native
(force, inplace=True)¶ Conversion of forces array force from native to base units
Parameters: - force (array_like) – Forces to transform
- inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
New in version 0.7.7.
-
convert_forces_to_native
(force, inplace=True)¶ Conversion of force array force from base to native units.
Parameters: - force (array_like) – Forces to transform
- inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
New in version 0.7.7.
-
convert_pos_from_native
(x, inplace=True)¶ Conversion of coordinate array x from native units to base units.
Parameters: - x (array_like) – Positions to transform
- inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
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.
Parameters: - x (array_like) – Positions to transform
- inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
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.
Parameters: - t (array_like) – Time values to transform
- inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
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.) In-place operations improve performance because allocating new arrays is avoided.
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.
Parameters: - t (array_like) – Time values to transform
- inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data
Note
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)¶ Conversion of velocities array v from native to base units
Parameters: - v (array_like) – Velocities to transform
- inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
New in version 0.7.5.
-
convert_velocities_to_native
(v, inplace=True)¶ Conversion of coordinate array v from base to native units
Parameters: - v (array_like) – Velocities to transform
- inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
New in version 0.7.5.
-
parse
(tpr_resid_from_one=True, **kwargs)[source]¶ Parse a Gromacs TPR file into a MDAnalysis internal topology structure.
Parameters: tpr_resid_from_one (bool (optional)) – Toggle whether to index resids from 1 or 0 from TPR files. TPR files index resids from 0 by default, even though GRO and ITP files index from 1. Returns: structure Return type: dict Changed in version 1.1.0: Added the
tpr_resid_from_one
keyword to control if resids are indexed from 0 or 1. DefaultFalse
.Changed in version 2.0.0: Changed to
tpr_resid_from_one=True
by default.
-
See also
5.21.2. 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, element [residue, segment, radius, bfactor, resnum, moltype]
- Bonds
- Angles
- 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.
Versions prior to Gromacs 4.0.x are not supported.
Changed in version 2.0.0: The elements topology attribute is now exposed if at least one atom has a valid element symbol. In that case, atoms for which the element is not recognized have their element attribute set to an empty string. If none of the elements are recognized, then the elements attribute is not set in the topology.