pestifer.molecule.asymmetricunit module

A class for building the asymmetric unit from a PDB file

class pestifer.molecule.asymmetricunit.AsymmetricUnit(parsed: PDBRecordDict | DataContainer = None, sourcespecs: dict = {}, objmanager: ObjManager = {}, chainIDmanager: ChainIDManager = <pestifer.molecule.chainidmanager.ChainIDManager object>, psf: str | Path = None)[source]

Bases: object

A class for building the asymmetric unit from a PDB/mmCIF file.

Parameters:

  • parsed (PDBRecordDict or DataContainer) – The parsed PDB or mmCIF data. A PDBRecordDict is returned by pidibble.pdbparse.PDBParser(spec).parse().parsed, and a DataContainer is returned by ~pestifer.util.cifutil.CIFload(filepath).

  • sourcespecs (dict, optional) – Specifications for the source of the data, including exclusions and sequence specifications.

  • objmanager (ObjManager, optional) – An object manager to handle the objects in the asymmetric unit. Defaults to a new instance of ObjManager.

  • chainIDmanager (ChainIDManager, optional) – A manager for chain IDs. Defaults to a new instance of ChainIDManager.

  • psf (str or Path, optional) – Path to a PSF file to use for additional information about the structure. Defaults to None. If set, it must be congruent to the PDB/mmCIF data.

add_segment(seg)[source]

Adds a segment to the asymmetric unit.

Parameters:

seg (Segment) – The segment to add to the asymmetric unit.

describe()[source]
ingest_grafts(grafts: GraftList, residues: ResidueList, links: LinkList)[source]

Ingests grafts into the asymmetric unit.

Parameters:

  • grafts (GraftList) – The list of grafts to ingest.

  • residues (ResidueList) – The list of residues in the asymmetric unit.

  • links (LinkList) – The list of links in the asymmetric unit.

set_coords(altstruct: PDBRecordDict)[source]

Sets the coordinates of the asymmetric unit from an alternative structure.

Parameters:

altstruct (dict) – The alternative structure containing atomic coordinates.

set_parent_molecule(parent_molecule)[source]

Sets the parent molecule of the asymmetric unit.

Parameters:

parent_molecule (Any) – The parent molecule to set for the asymmetric unit.