# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>,
# <NAME>, <NAME>, <NAME>, <NAME>, and <NAME>.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# <NAME>, <NAME>, <NAME>, and <NAME>.
# 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 <NAME>
# 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
   ========== ============== ==================== =====

.. [*] 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,
  [residue, segment, radius, bfactor, resnum, moltype]
* Bonds
* Angels
* 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.

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.

.. 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

"""
from __future__ import absolute_import
__author__ = "<NAME>"
__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")


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'

    def parse(self, **kwargs):
        """Parse a Gromacs TPR file into a MDAnalysis internal topology structure.

        Returns
        -------
        structure : dict
        """
        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:
            msg = "{0}: Invalid tpr file or cannot be recognized".format(self.filename)
            logger.critical(msg)
            raise IOError(msg)

        self._log_header(th)

        V = th.fver                                    # since it's used very often

        # Starting with gromacs 2020 (tpx version 119), the body of the file
        # is encoded differently. We change the unpacker accordingly.
        if V >= 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, V)

        if state_ngtc > 0 and V >= 28:
            if V < 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 V < 26:
            tpr_utils.fileVersion_err(V)

        if th.bTop:
            tpr_top = tpr_utils.do_mtop(data, V)
        else:
            msg = "{0}: No topology found in tpr file".format(self.filename)
            logger.critical(msg)
            raise IOError(msg)

        tpr_top.add_TopologyAttr(Resnums(tpr_top.resids.values.copy()))

        return tpr_top

    # THE FOLLOWING CODE IS WORKING FOR TPX VERSION 58, BUT SINCE THESE INFO IS
    # NOT INTERESTED, SO IT'S NOT COVERED IN ALL VERSIONS. PARSING STOPS HERE.

    # if th.bX:
    #     ndo_rvec(data, th.natoms)

    # if th.bV:
    #     ndo_rvec(data, th.natoms)

    # if th.bF:
    #     ndo_rvec(data, th.natoms)

    # not useful at the moment
    # ePBC = -1;
    # bPeriodicMols = False
    # if th.bIr:
    #     # update
    #     data.unpack_int()                                # ePBC
    #     data.unpack_bool()                               # bPeriodicMols
    #     # 17 < 23. and ir (ir is from the c code, seems not apply here
    #     if th.fgen < setting.tpx_generation:
    #         # a crazily long (670 lines) function in c, slightly better here
    #         # (240 lines), so put it in setting.py
    #         utils.do_inputrec(data)

    def _log_header(self, th):
        logger.info("Gromacs version   : {0}".format(th.ver_str))
        logger.info("tpx version       : {0}".format(th.fver))
        logger.info("tpx generation    : {0}".format(th.fgen))
        logger.info("tpx precision     : {0}".format(th.precision))
        logger.info("tpx file_tag      : {0}".format(th.file_tag))
        logger.info("tpx natoms        : {0}".format(th.natoms))
        logger.info("tpx ngtc          : {0}".format(th.ngtc))
        logger.info("tpx fep_state     : {0}".format(th.fep_state))
        logger.info("tpx lambda        : {0}".format(th.lamb))
        logger.debug("tpx bIr (input record): {0}".format(th.bIr))
        logger.debug("tpx bTop         : {0}".format(th.bTop))
        logger.debug("tpx bX           : {0}".format(th.bX))
        logger.debug("tpx bV           : {0}".format(th.bV))
        logger.debug("tpx bF           : {0}".format(th.bF))
        logger.debug("tpx bBox         : {0}".format(th.bBox))

# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>,
# <NAME>, <NAME>, <NAME>, <NAME>, and <NAME>.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# <NAME>, <NAME>, <NAME>, and <NAME>.
# 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 <NAME>
# 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
   ========== ============== ==================== =====

.. [*] 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,
  [residue, segment, radius, bfactor, resnum, moltype]
* Bonds
* Angels
* 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.

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.

.. 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

"""
from __future__ import absolute_import
__author__ = "<NAME>"
__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")


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'

    def parse(self, **kwargs):
        """Parse a Gromacs TPR file into a MDAnalysis internal topology structure.

        Returns
        -------
        structure : dict
        """
        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:
            msg = "{0}: Invalid tpr file or cannot be recognized".format(self.filename)
            logger.critical(msg)
            raise IOError(msg)

        self._log_header(th)

        V = th.fver                                    # since it's used very often

        # Starting with gromacs 2020 (tpx version 119), the body of the file
        # is encoded differently. We change the unpacker accordingly.
        if V >= 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, V)

        if state_ngtc > 0 and V >= 28:
            if V < 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 V < 26:
            tpr_utils.fileVersion_err(V)

        if th.bTop:
            tpr_top = tpr_utils.do_mtop(data, V)
        else:
            msg = "{0}: No topology found in tpr file".format(self.filename)
            logger.critical(msg)
            raise IOError(msg)

        tpr_top.add_TopologyAttr(Resnums(tpr_top.resids.values.copy()))

        return tpr_top

    # THE FOLLOWING CODE IS WORKING FOR TPX VERSION 58, BUT SINCE THESE INFO IS
    # NOT INTERESTED, SO IT'S NOT COVERED IN ALL VERSIONS. PARSING STOPS HERE.

    # if th.bX:
    #     ndo_rvec(data, th.natoms)

    # if th.bV:
    #     ndo_rvec(data, th.natoms)

    # if th.bF:
    #     ndo_rvec(data, th.natoms)

    # not useful at the moment
    # ePBC = -1;
    # bPeriodicMols = False
    # if th.bIr:
    #     # update
    #     data.unpack_int()                                # ePBC
    #     data.unpack_bool()                               # bPeriodicMols
    #     # 17 < 23. and ir (ir is from the c code, seems not apply here
    #     if th.fgen < setting.tpx_generation:
    #         # a crazily long (670 lines) function in c, slightly better here
    #         # (240 lines), so put it in setting.py
    #         utils.do_inputrec(data)

    def _log_header(self, th):
        logger.info("Gromacs version   : {0}".format(th.ver_str))
        logger.info("tpx version       : {0}".format(th.fver))
        logger.info("tpx generation    : {0}".format(th.fgen))
        logger.info("tpx precision     : {0}".format(th.precision))
        logger.info("tpx file_tag      : {0}".format(th.file_tag))
        logger.info("tpx natoms        : {0}".format(th.natoms))
        logger.info("tpx ngtc          : {0}".format(th.ngtc))
        logger.info("tpx fep_state     : {0}".format(th.fep_state))
        logger.info("tpx lambda        : {0}".format(th.lamb))
        logger.debug("tpx bIr (input record): {0}".format(th.bIr))
        logger.debug("tpx bTop         : {0}".format(th.bTop))
        logger.debug("tpx bX           : {0}".format(th.bX))
        logger.debug("tpx bV           : {0}".format(th.bV))
        logger.debug("tpx bF           : {0}".format(th.bF))
        logger.debug("tpx bBox         : {0}".format(th.bBox))

# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- https://www.mdanalysis.org # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # # <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, # <NAME>, <NAME>, <NAME>, <NAME>, and <NAME>. # MDAnalysis: A Python package for the rapid analysis of molecular dynamics # simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th # Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. # doi: 10.25080/majora-629e541a-00e # # <NAME>, <NAME>, <NAME>, and <NAME>. # 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 <NAME> # 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    ========== ============== ==================== =====  .. [*] 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,   [residue, segment, radius, bfactor, resnum, moltype] * Bonds * Angels * 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.  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.  .. 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 Read topology information from a Gromacs_ `TPR file`_.      .. _Gromacs: http://www.gromacs.org     .. _TPR file: http://manual.gromacs.org/current/online/tpr.html Parse a Gromacs TPR file into a MDAnalysis internal topology structure.          Returns         -------         structure : dict # tpxheader # since it's used very often # Starting with gromacs 2020 (tpx version 119), the body of the file # is encoded differently. We change the unpacker accordingly. # See issue #2428. # done init_state() in src/gmxlib/tpxio.c # redundancy due to  different versions # relevant to Berendsen tcoupl_lambda # THE FOLLOWING CODE IS WORKING FOR TPX VERSION 58, BUT SINCE THESE INFO IS # NOT INTERESTED, SO IT'S NOT COVERED IN ALL VERSIONS. PARSING STOPS HERE. # if th.bX: #     ndo_rvec(data, th.natoms) # if th.bV: #     ndo_rvec(data, th.natoms) # if th.bF: #     ndo_rvec(data, th.natoms) # not useful at the moment # ePBC = -1; # bPeriodicMols = False # if th.bIr: #     # update #     data.unpack_int()                                # ePBC #     data.unpack_bool()                               # bPeriodicMols #     # 17 < 23. and ir (ir is from the c code, seems not apply here #     if th.fgen < setting.tpx_generation: #         # a crazily long (670 lines) function in c, slightly better here #         # (240 lines), so put it in setting.py #         utils.do_inputrec(data)