Bio.PDB.PICIO module

PICIO: read and write Protein Internal Coordinate (.pic) data files.

Bio.PDB.PICIO.read_PIC(file: <class 'TextIO'>, verbose: bool = False) → Bio.PDB.Structure.Structure

Load Protein Internal Coordinate (.pic) data from file.

PIC file format:

  • comment lines start with #

  • (optional) PDB HEADER record

    • idcode and deposition date recommended but optional

    • deposition date in PDB format or as changed by Biopython

  • (optional) PDB TITLE record

  • repeat:

    • Biopython Residue Full ID - sets residue IDs of returned structure

    • (optional) PDB N, CA, C ATOM records for chain start

    • (optional) PIC Hedra records for residue

    • (optional) PIC Dihedra records for residue

    • (optional) BFAC records listing AtomKeys and b-factors

An improvement would define relative positions for HOH (water) entries.

N.B. dihedron (i-1)C-N-CA-CB is ignored in assembly if O exists.

C-beta is by default placed using O-C-CA-CB, but O is missing in some PDB file residues, which means the sidechain cannot be placed. The alternate CB path (i-1)C-N-CA-CB is provided to circumvent this, but if this is needed then it must be adjusted in conjunction with PHI ((i-1)C-N-CA-C) as they overlap. (i-1)C-N-CA-CB is included by default in .pic files for consistency and informational (e.g. statistics gathering) purposes, as otherwise the dihedron would only appear in the few cases it is needed for.

Parameters

  • file (Bio.File) – file name or handle

  • verbose (bool) – complain when lines not as expected

Returns

Biopython Structure object, Residues with .internal_coord attributes but no coordinates except for chain start N, CA, C atoms if supplied, OR None on parse fail (silent unless verbose=True)

Bio.PDB.PICIO.enumerate_atoms(entity)

Ensure all atoms in entity have serial_number set.

Bio.PDB.PICIO.pdb_date(datestr: str) → str

Convert yyyy-mm-dd date to dd-month-yy.

Bio.PDB.PICIO.write_PIC(entity, file, pdbid=None, chainid=None)

Write Protein Internal Coordinates (PIC) to file.

See read_PIC() for file format. Recurses to lower entity levels (M, C, R).

Parameters

  • entity (Entity) – Biopython PDB Entity object: S, M, C or R

  • file (Bio.File) – file name or handle

  • pdbid (str) – PDB idcode, read from entity if not supplied

  • chainid (char) – PDB Chain ID, set from C level entity.id if needed

Raises

  • PDBException – if entity level not S, M, C, or R

  • Exception – if entity does not have .level attribute