Bio.PDB.mmtf package

Submodules

• Bio.PDB.mmtf.DefaultParser module
  • StructureDecoder
    • StructureDecoder.__init__()
    • StructureDecoder.init_structure()
    • StructureDecoder.set_atom_info()
    • StructureDecoder.set_chain_info()
    • StructureDecoder.set_entity_info()
    • StructureDecoder.set_group_info()
    • StructureDecoder.set_model_info()
    • StructureDecoder.set_xtal_info()
    • StructureDecoder.set_header_info()
    • StructureDecoder.set_bio_assembly_trans()
    • StructureDecoder.finalize_structure()
    • StructureDecoder.set_group_bond()
    • StructureDecoder.set_inter_group_bond()
• Bio.PDB.mmtf.mmtfio module
  • MMTFIO
    • MMTFIO.__init__()
    • MMTFIO.save()

Module contents

Support for loading 3D structures stored in MMTF files.

Bio.PDB.mmtf.get_from_decoded(decoder)

Return structure from decoder.

class Bio.PDB.mmtf.MMTFParser

Bases: object

Class to get a Biopython structure from a URL or a filename.

static get_structure_from_url(pdb_id)

Get a structure from a URL - given a PDB id.

Parameters:

pdb_id – the input PDB id

Returns:

the structure

static get_structure(file_path)

Get a structure from a file - given a file path.

Parameters:

file_path – the input file path

Returns:

the structure