qp.structure.missing.get_residues

qp.structure.missing.get_residues(path, AA)

Extract residues from a PDB file, including missing residue annotations.

Parses REMARK 465 (missing residues) and REMARK 470 (missing atoms) records to identify gaps in the structure that need to be filled by Modeller.

Non-standard residues (substrates, cofactors, and other HETATM entries except water and selenomethionine) are treated as rigid bodies by Modeller. Their existing coordinates are preserved, but any missing atoms in these residues will not be modeled. A warning is emitted listing the non-standard residue names encountered.

Parameters:

• path (str) – Path to the PDB file.

• AA (dict) – Amino acid lookup table mapping 3-letter codes to 1-letter codes (from define_residues()).

Returns:

Residues separated by chain. Each residue is a tuple of ((sequence_number, insertion_code), one_letter_code, flag), where flag is 'R' for completely absent residues, 'A' for residues with missing atoms, or '' for complete.

Return type:

list of list