scoring_base – Helper functions for scoring¶

CleanHydrogens(ent, clib)¶

Scoring helper - Returns copy of ent without hydrogens

Non-standard hydrogen naming can cause trouble in residue property assignment which is done by the ost.conop.RuleBasedProcessor when loading. In fact, residue property assignment is not done for every residue that has unknown atoms according to the chemical component dictionary. This function therefore re-processes the entity after removing hydrogens.

Parameters:

• ent (ost.mol.EntityHandle/ost.mol.EntityView) – Entity to clean

• clib (ost.conop.CompoundLib) – Compound library to perform re-processing after hydrogen removal.

Returns:

Cleaned and re-processed ent

MMCIFPrep(mmcif_path, biounit=None, extract_nonpoly=False, fault_tolerant=False, allow_heuristic_conn=False, extract_seqres_mapping=False)¶

Scoring helper - Prepares input from mmCIF

Only performs gentle cleanup of hydrogen atoms. Further cleanup is delegated to scoring classes.

Depending on input flags, the following outputs can be retrieved:

• poly_ent (ost.mol.EntityHandle): An OpenStructure entity with only polymer chains.

• non_poly_entities (list of ost.mol.EntityHandle): OpenStructure entities representing all non-polymer (ligand) entities.

• seqres (ost.seq.SequenceList): Seqres sequences with entity id as sequence names and the respective canonical seqres as sequence.

• trg_seqres_mapping (dict): Dictionary with chain names in poly_ent as keys and the respective entity ids as values.

Parameters:

• mmcif_path (str) – Path to mmCIF file that contains polymer and optionally non-polymer entities

• biounit (str) – If given, construct specified biounit from mmCIF AU

• extract_nonpoly (bool) – Controls return value

• fault_tolerant (bool) – Passed as parameter to ost.io.LoadMMCIF()

• allow_heuristic_conn (bool) – Only relevant if extract_nonpoly is True. The chemical component dictionary is relevant for connectivity information. By default, we enforce the presence of each non-polymer in the dictionary to ensure correct connectity. If you enable this flag, you allow the use of a distance based heuristic as fallback. With all its consequences in ligand matching.

• extract_seqres_mapping (bool) – Controls return value

Returns:

poly_ent if extract_nonpoly/extract_seqres_mapping are False. (poly_ent, non_poly_entities) if extract_nonpoly is True. (poly_ent, seqres, trg_seqres_mapping) if extract_seqres_mapping is True. (poly_ent, non_poly_entities, seqres, trg_seqres_mapping) if both flags are True.

PDBPrep(pdb_path, fault_tolerant=False)¶

Scoring helper - Prepares scoring input from PDB

Only performs gentle cleanup of hydrogen atoms. Further cleanup is delegated to scoring classes. There is no logic to extract ligands from PDB files. Ligands must be provided separately as SDF files in these cases.

Parameters:

• pdb_path (str) – Path to PDB file that contains polymer entities

• fault_tolerant (bool) – Passed as parameter to ost.io.LoadPDB()

Returns:

EntityHandle from loaded file.