5. 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 Table of 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 Universe.

Topology formats

• 5.1. Topology readers — MDAnalysis.topology
• 5.2. CRD topology parser
• 5.3. DL Poly format Topology Readers — MDAnalysis.topology.DLPolyParser
• 5.4. DESRES Molecular Structure file format topology parser
• 5.5. FHI-AIMS Topology Parser — MDAnalysis.topolgy.FHIAIMSParser
• 5.6. GAMESS Topology Parser
• 5.7. GRO topology parser
• 5.8. GSD topology parser
• 5.9. HOOMD XML topology parser
• 5.10. ITP topology parser
• 5.11. LAMMPSParser
• 5.12. Minimal topology parser
• 5.13. MMTF Topology Parser
• 5.14. MOL2 file format — MDAnalysis.coordinates.MOL2
• 5.15. PDB Topology Parser
• 5.16. Extended PDB topology parser
• 5.17. PDBQT topology parser
• 5.18. PQR topology parser
• 5.19. PSF topology parser
• 5.20. AMBER PRMTOP topology parser
• 5.21. Gromacs portable run input TPR format parser
• 5.22. TXYZ topology parser
• 5.23. XYZ Topology Parser

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.

• 5.24. Base topology reader classes — MDAnalysis.topology.base
• 5.25. Common functions for topology building — MDAnalysis.topology.core
• 5.26. Guessing unknown Topology information — MDAnalysis.topology.guessers
• get_atom_mass()
• guess_angles()
• guess_aromaticities()
• guess_atom_charge()
• guess_atom_element()
• guess_atom_mass()
• guess_atom_type()
• guess_bonds()
• guess_dihedrals()
• guess_gasteiger_charges()
• guess_improper_dihedrals()
• guess_masses()
• guess_types()
• validate_atom_types()
• 5.27. MDAnalysis topology tables
• 5.28. Utility functions for the TPR topology parser