tcr_pmhc_interface_analysis.missing_residues module

tcr_pmhc_interface_analysis.missing_residues.add_missing_entities_to_structure(structure: DataFrame, missing_entities: DataFrame) → DataFrame

Create a new dataframe with line indicating missing entities.

tcr_pmhc_interface_analysis.missing_residues.get_missing_atoms(header: str) → list[dict]

Extract residues with missing atoms from the header of a pdb file.

tcr_pmhc_interface_analysis.missing_residues.get_missing_residues(header: str) → list[dict]

Extract all missing residues from the header of a pdb file. Returns residue name, chain id, residue/sequence id, and insert id if available.

tcr_pmhc_interface_analysis.missing_residues.get_missing_residues_and_atoms(header: str) → DataFrame

Create a dataframe of missing information for a structure.

tcr_pmhc_interface_analysis.missing_residues.get_raw_structures_with_missing_residues(pdb_ids: list[str], stcrdab_path: str | None = None) → dict[DataFrame]

Get all raw structure files from the STCRDab or RCSB PDB.

tcr_pmhc_interface_analysis.missing_residues.screen_pmhcs_for_missing_residues(df: DataFrame, raw_structures: dict[DataFrame]) → ndarray

Screen pmhcs for missing residues.

tcr_pmhc_interface_analysis.missing_residues.screen_tcrs_for_missing_residues(df: DataFrame, raw_structure_dfs: dict[DataFrame]) → ndarray

Disgard structures missing residues in TCR variable domains.

tcr_pmhc_interface_analysis.missing_residues.screen_variable(chain: DataFrame, raw_chain: DataFrame) → bool

Screen variable domains for missing residues