pdb_io.PolypeptideEntry

class pdb_io.PolypeptideEntry(pdb_id: str, model: int, chain: ~Bio.PDB.Chain.Chain, polypeptide: <module 'Bio.PDB.Polypeptide' from '/home/docs/checkouts/readthedocs.org/user_builds/motif-conformation-finder/envs/latest/lib/python3.11/site-packages/Bio/PDB/Polypeptide.py'>)[source]

Bases: object

Object representing a contiguous polymer of amino acids, with methods to extract amino acid sequences from it

pdb_id

pdb entity ID of the protein structure

Type:: str

model

pdb model number

Type:: int

chain

protein chain entity object

Type:: PDB.Chain.Chain

polypeptide

a contiguous chain of amino acids from the protein chain entry

Type:: PDB.Polypeptide

__init__(pdb_id: str, model: int, chain: ~Bio.PDB.Chain.Chain, polypeptide: <module 'Bio.PDB.Polypeptide' from '/home/docs/checkouts/readthedocs.org/user_builds/motif-conformation-finder/envs/latest/lib/python3.11/site-packages/Bio/PDB/Polypeptide.py'>) → None

Methods

`__init__`(pdb_id, model, chain, polypeptide)
`find_motif`(motif)	find each instance of the sequence motif in the polypeptides

Attributes

`sequence`	returns: amino acid sequence of the polypeptide instance :rtype: str
`pdb_id`
`model`
`chain`
`polypeptide`

find_motif(motif: str) → Generator[list[Bio.PDB.Residue.Residue], None, None][source]

find each instance of the sequence motif in the polypeptides

Parameters:: motif (str) –
Yields:: list[PDB.Residue.Residue] – residues matching the motif from each polypeptide

property sequence: str: returns: amino acid sequence of the polypeptide instance :rtype: str