5.13. MMTF Topology Parser

Reads topology data from the Macromolecular Transmission Format (MMTF) format. This should generally be a quicker alternative to PDB.

Makes individual models within the MMTF file available via the models attribute on Universe.

Added in version 0.16.0.

Changed in version 0.20.0: Can now read files with optional fields missing/empty

Changed in version 2.0.0: Aliased bfactors topologyattribute to tempfactors. tempfactors is deprecated and will be removed in 3.0 (Issue #1901)

Changed in version 2.8.0: Removed mass guessing (attributes guessing takes place now through universe.guess_TopologyAttrs() API).

Reads the following topology attributes:

Atoms:

  • altLoc

  • atom ID

  • tempfactor

  • bonds

  • charge

  • name

  • occupancy

  • type

Residues:

  • icode

  • resname

  • resid

  • resnum

Segments:

  • segid

  • model

Note

By default, masses will be guessed on Universe creation. This may change in release 3.0. See Guesser modules for more information.

5.13.1. Classes

class MDAnalysis.topology.MMTFParser.MMTFParser(filename)[source]