Source code for MDAnalysis.topology.TPRParser
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# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
# TPR parser and tpr support module
# Copyright (c) 2011 Zhuyi Xue
# Released under the GNU Public Licence, v2
"""Gromacs portable run input TPR format parser
============================================
The :mod:`~MDAnalysis.topology.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
:ref:`TPR format versions <TPR-format-table>`.
.. _`TPR-format-table`:
.. table:: TPR format versions and generations read by :func:`MDAnalysis.topology.TPRParser.parse`.
========== ============== ==================== =====
TPX format TPX generation Gromacs release read
========== ============== ==================== =====
?? ?? 3.3, 3.3.1 no
58 17 4.0, 4.0.2, 4.0.3, yes
4.0.4, 4.0.5, 4.0.6,
4.0.7
73 23 4.5.0, 4.5.1, 4.5.2, yes
4.5.3, 4.5.4, 4.5.5
83 24 4.6, 4.6.1 yes
100 26 5.0, 5.0.1, 5.0.2, yes
5.0.3,5.0.4, 5.0.5
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
127 28 2022 yes
129 28 2023 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)
Classes
-------
.. autoclass:: TPRParser
:members:
:inherited-members:
See Also
--------
:mod:`MDAnalysis.topology.tpr`
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
- :file:`{gromacs_dir}/src/kernel/gmxdump.c`
- :file:`{gromacs_dir}/src/gmxlib/tpxio.c` (the most important one)
- :file:`{gromacs_dir}/src/gmxlib/gmxfio_rw.c`
- :file:`{gromacs_dir}/src/gmxlib/gmxfio_xdr.c`
- :file:`{gromacs_dir}/include/gmxfiofio.h`
or their equivalent in more recent versions of Gromacs.
The function :func:`read_tpxheader` is based on the
`TPRReaderDevelopment`_ notes. Functions with names starting with
``read_`` or ``do_`` are trying to be similar to those in
:file:`gmxdump.c` or :file:`tpxio.c`, those with ``extract_`` are new.
Versions prior to Gromacs 4.0.x are not supported.
.. Links
.. _Gromacs: http://www.gromacs.org
.. _`Gromacs manual`: http://manual.gromacs.org/documentation/5.1/manual-5.1.pdf
.. _TPR file: http://manual.gromacs.org/current/online/tpr.html
.. _`Issue Tracker`: https://github.com/MDAnalysis/mdanalysis/issues
.. _`Issue 2`: https://github.com/MDAnalysis/mdanalysis/issues/2
.. _`Issue 463`: https://github.com/MDAnalysis/mdanalysis/pull/463
.. _TPRReaderDevelopment: https://github.com/MDAnalysis/mdanalysis/wiki/TPRReaderDevelopment
.. _`Issue 2428`: https://github.com/MDAnalysis/mdanalysis/issues/2428
.. versionchanged:: 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.
"""
__author__ = "Zhuyi Xue"
__copyright__ = "GNU Public Licence, v2"
import xdrlib
from . import guessers
from ..lib.util import openany
from .tpr import utils as tpr_utils
from .tpr import setting as S
from .base import TopologyReaderBase
from ..core.topologyattrs import Resnums
import logging
logger = logging.getLogger("MDAnalysis.topology.TPRparser")
[docs]class TPRParser(TopologyReaderBase):
"""Read topology information from a Gromacs_ `TPR file`_.
.. _Gromacs: http://www.gromacs.org
.. _TPR file: http://manual.gromacs.org/current/online/tpr.html
"""
format = 'TPR'
[docs] def parse(self, tpr_resid_from_one=True, **kwargs):
"""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 : dict
.. versionchanged:: 1.1.0
Added the ``tpr_resid_from_one`` keyword to control if
resids are indexed from 0 or 1. Default ``False``.
.. versionchanged:: 2.0.0
Changed to ``tpr_resid_from_one=True`` by default.
"""
with openany(self.filename, mode='rb') as infile:
tprf = infile.read()
data = tpr_utils.TPXUnpacker(tprf)
try:
th = tpr_utils.read_tpxheader(data) # tpxheader
except (EOFError, ValueError):
msg = f"{self.filename}: Invalid tpr file or cannot be recognized"
logger.critical(msg)
raise IOError(msg)
self._log_header(th)
# Starting with gromacs 2020 (tpx version 119), the body of the file
# is encoded differently. We change the unpacker accordingly.
if th.fver >= S.tpxv_AddSizeField and th.fgen >= 27:
actual_body_size = len(data.get_buffer()) - data.get_position()
if actual_body_size == 4 * th.sizeOfTprBody:
# See issue #2428.
msg = (
"TPR files produced with beta versions of gromacs 2020 "
"are not supported."
)
logger.critical(msg)
raise IOError(msg)
data = tpr_utils.TPXUnpacker2020.from_unpacker(data)
state_ngtc = th.ngtc # done init_state() in src/gmxlib/tpxio.c
if th.bBox:
tpr_utils.extract_box_info(data, th.fver)
if state_ngtc > 0:
if th.fver < 69: # redundancy due to different versions
tpr_utils.ndo_real(data, state_ngtc)
tpr_utils.ndo_real(data, state_ngtc) # relevant to Berendsen tcoupl_lambda
if th.bTop:
tpr_top = tpr_utils.do_mtop(data, th.fver,
tpr_resid_from_one=tpr_resid_from_one)
else:
msg = f"{self.filename}: No topology found in tpr file"
logger.critical(msg)
raise IOError(msg)
tpr_top.add_TopologyAttr(Resnums(tpr_top.resids.values.copy()))
return tpr_top
def _log_header(self, th):
logger.info(f"Gromacs version : {th.ver_str}")
logger.info(f"tpx version : {th.fver}")
logger.info(f"tpx generation : {th.fgen}")
logger.info(f"tpx precision : {th.precision}")
logger.info(f"tpx file_tag : {th.file_tag}")
logger.info(f"tpx natoms : {th.natoms}")
logger.info(f"tpx ngtc : {th.ngtc}")
logger.info(f"tpx fep_state : {th.fep_state}")
logger.info(f"tpx lambda : {th.lamb}")
logger.debug(f"tpx bIr (input record): {th.bIr}")
logger.debug(f"tpx bTop : {th.bTop}")
logger.debug(f"tpx bX : {th.bX}")
logger.debug(f"tpx bV : {th.bV}")
logger.debug(f"tpx bF : {th.bF}")
logger.debug(f"tpx bBox : {th.bBox}")