biotite.structure.io.pdb.get_structure

biotite.structure.io.pdb.get_structure(pdb_file, model=None, altloc='first', extra_fields=[], include_bonds=False)[source]

Create an AtomArray or AtomArrayStack from a PDBFile.

This function is a thin wrapper around the PDBFile method get_structure() for the sake of consistency with other structure.io subpackages.

Parameters
pdb_filePDBFile

The file object.

modelint, optional

If this parameter is given, the function will return an AtomArray from the atoms corresponding to the given model number (starting at 1). Negative values are used to index models starting from the last model insted of the first model. If this parameter is omitted, an AtomArrayStack containing all models will be returned, even if the structure contains only one model.

altloc{‘first’, ‘occupancy’, ‘all’}
This parameter defines how altloc IDs are handled:
  • 'first' - Use atoms that have the first altloc ID appearing in a residue.

  • 'occupancy' - Use atoms that have the altloc ID with the highest occupancy for a residue.

  • 'all' - Use all atoms. Note that this leads to duplicate atoms. When this option is chosen, the altloc_id annotation array is added to the returned structure.

extra_fieldslist of str, optional

The strings in the list are optional annotation categories that should be stored in the output array or stack. These are valid values: 'atom_id', 'b_factor', 'occupancy' and 'charge'.

include_bondsbool, optional

If set to true, a BondList will be created for the resulting AtomArray containing the bond information from the file. All bonds have BondType.ANY, since the PDB format does not support bond orders.

Returns
arrayAtomArray or AtomArrayStack

The return type depends on the model parameter.