.. Contains the formatted docstrings from the topology modules located in 'mdanalysis/MDAnalysis/topology'
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Topology modules
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The topology module contains the functions to read topology
files. MDAnalysis uses topology files to identify atoms and bonds
between the atoms. It can use topology files from MD packages such as
CHARMM's and NAMD's PSF format or Amber's PRMTOP files. In addition,
it can also glean atom information from single frame coordinate files
such the PDB, CRD, or PQR formats (see the :ref:`Supported topology
formats`).
Typically, MDAnalysis recognizes formats by the file extension and
hence most users probably do not need to concern themselves with
classes and functions described here. However, if MDAnalysis does not
properly recognize a file format then a user can explicitly set the
topology file format in the *topology_format* keyword argument to
:class:`~MDAnalysis.core.universe.Universe`.
.. rubric:: Topology formats
.. toctree::
:maxdepth: 1
topology/init
topology/CRDParser
topology/DLPolyParser
topology/DMSParser
topology/FHIAIMSParser
topology/GMSParser
topology/GROParser
topology/GSDParser
topology/HoomdXMLParser
topology/ITPParser
topology/LAMMPSParser
topology/MinimalParser
topology/MMTFParser
topology/MOL2Parser
topology/PDBParser
topology/ExtendedPDBParser
topology/PDBQTParser
topology/PQRParser
topology/PSFParser
topology/TOPParser
topology/TPRParser
topology/TXYZParser
topology/XYZParser
.. rubric:: Topology core modules
The remaining pages are primarily of interest to developers as they
contain functions and classes that are used in the implementation of
the topology readers.
.. toctree::
:maxdepth: 1
topology/base
topology/core
topology/guessers
topology/tables
topology/tpr_util