.. Contains the formatted docstrings from the topology modules located in 'mdanalysis/MDAnalysis/topology' ************************** Topology modules ************************** 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