6. Coordinates modules

The coordinates module contains the classes to read and write trajectories. Typically, MDAnalysis recognizes Table of supported coordinate 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 fails to recognize a coordinate file then the user can provide the format in the keyword argument format to Universe to force the format.

Coordinate formats

• 6.1. Trajectory Readers and Writers — MDAnalysis.coordinates
• 6.2. CRD structure files in MDAnalysis — MDAnalysis.coordinates.CRD
• CRDReader
• CRDWriter
• 6.3. DCD trajectory I/O — MDAnalysis.coordinates.DCD
• 6.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly
• ConfigReader
• HistoryReader
• 6.5. DESRES file format — MDAnalysis.coordinates.DMS
• DMSReader
• 6.6. GAMESS trajectory reader — MDAnalysis.coordinates.GMS
• 6.7. GSD trajectory reader — MDAnalysis.coordinates.GSD
• 6.8. GRO file format — MDAnalysis.coordinates.GRO
• 6.9. H5MD trajectories — MDAnalysis.coordinates.H5MD
• 6.10. INPCRD structure files in MDAnalysis — MDAnalysis.coordinates.INPCRD
• 6.11. LAMMPS DCD trajectory and DATA I/O — MDAnalysis.coordinates.LAMMPS
• 6.12. MMTF trajectory reader — MDAnalysis.coordinates.MMTF
• 6.13. MOL2 file format — MDAnalysis.coordinates.MOL2
• 6.14. NAMDBIN files format — MDAnalysis.coordinates.NAMDBIN
• 6.15. PDB structure files in MDAnalysis — MDAnalysis.coordinates.PDB
• 6.16. PDBQT structure files in MDAnalysis — MDAnalysis.coordinates.PDBQT
• PDBQTReader
• PDBQTWriter
• 6.17. PQR file format — MDAnalysis.coordinates.PQR
• PQRReader
• PQRWriter
• 6.18. TNG trajectory files — MDAnalysis.coordinates.TNG
• TNGReader
• 6.19. AMBER trajectories — MDAnalysis.coordinates.TRJ
• 6.20. TRR trajectory files — MDAnalysis.coordinates.TRR
• TRRReader
• TRRWriter
• 6.21. TRZ trajectory I/O — MDAnalysis.coordinates.TRZ
• 6.22. TXYZ file format — MDAnalysis.coordinates.TXYZ
• 6.23. XTC trajectory files — MDAnalysis.coordinates.XTC
• XTCReader
• XTCWriter
• 6.24. XYZ trajectory reader — MDAnalysis.coordinates.XYZ
• XYZReader
• XYZWriter
• 6.25. FHI-AIMS file format — MDAnalysis.coordinates.FHIAIMS
• 6.26. Reading trajectories from memory — MDAnalysis.coordinates.memory
• 6.27. Reading trajectories with chemfiles — MDAnalysis.coordinates.chemfiles
• 6.28. Null output — MDAnalysis.coordinates.null

Coordinate core modules

The remaining pages are primarily of interest to developers. Programmers and anyone trying to implement new functionality should first read the Trajectory API.

• 6.29. Timestep Class — MDAnalysis.coordinates.timestep
• 6.30. Base classes — MDAnalysis.coordinates.base
• 6.31. Common functions for coordinate reading — MDAnalysis.coordinates.core
• 6.32. Serialization of Coordinate Readers
• 6.33. ChainReader — MDAnalysis.coordinates.chain
• 6.34. XDR based trajectory files — MDAnalysis.coordinates.XDR
• XDRBaseReader
• XDRBaseWriter
• offsets_filename()
• read_numpy_offsets()

In particular, all trajectory readers have to be serializable and they should pass all tests available in the MDAnalysisTests.coordinates.base.MultiframeReaderTest or MDAnalysisTests.coordinates.base.BaseReaderTest.