biopython

v1.71.0

biopython v1.71.0 Bio.PDB.Polypeptide

Polypeptide-related classes (construction and representation).

Simple example with multiple chains,

     >>> from Bio.PDB.PDBParser import PDBParser
     >>> from Bio.PDB.Polypeptide import PPBuilder
     >>> structure = PDBParser().get_structure('2BEG', 'PDB/2BEG.pdb')
     >>> ppb=PPBuilder()
     >>> for pp in ppb.build_peptides(structure):
     ...     print(pp.get_sequence())
     LVFFAEDVGSNKGAIIGLMVGGVVIA
     LVFFAEDVGSNKGAIIGLMVGGVVIA
     LVFFAEDVGSNKGAIIGLMVGGVVIA
     LVFFAEDVGSNKGAIIGLMVGGVVIA
     LVFFAEDVGSNKGAIIGLMVGGVVIA

Example with non-standard amino acids using HETATM lines in the PDB file, in this case selenomethionine (MSE):

     >>> from Bio.PDB.PDBParser import PDBParser
     >>> from Bio.PDB.Polypeptide import PPBuilder
     >>> structure = PDBParser().get_structure('1A8O', 'PDB/1A8O.pdb')
     >>> ppb=PPBuilder()
     >>> for pp in ppb.build_peptides(structure):
     ...     print(pp.get_sequence())
     DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW
     TETLLVQNANPDCKTILKALGPGATLEE
     TACQG

If you want to, you can include non-standard amino acids in the peptides:

     >>> for pp in ppb.build_peptides(structure, aa_only=False):
     ...     print(pp.get_sequence())
     ...     print("%s %s" % (pp.get_sequence()[0], pp[0].get_resname()))
     ...     print("%s %s" % (pp.get_sequence()[-7], pp[-7].get_resname()))
     ...     print("%s %s" % (pp.get_sequence()[-6], pp[-6].get_resname()))
     MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG
     M MSE
     M MSE
     M MSE

In this case the selenomethionines (the first and also seventh and sixth from last residues) have been shown as M (methionine) by the get_sequence method.

Link to this section Summary

Functions

index_to_one()

Index to corresponding one letter amino acid name

index_to_three()

Index to corresponding three letter amino acid name

is_aa()

Return True if residue object/string is an amino acid

one_to_index()

One letter code to index

one_to_three()

One letter code to three letter code

three_to_index()

Three letter code to index

three_to_one()

Three letter code to one letter code

Link to this section Functions

Link to this function index_to_one()

Index to corresponding one letter amino acid name.

 >>> index_to_one(0)
 'A'
 >>> index_to_one(19)
 'Y'
Link to this function index_to_three()

Index to corresponding three letter amino acid name.

 >>> index_to_three(0)
 'ALA'
 >>> index_to_three(19)
 'TYR'
Link to this function is_aa()

Return True if residue object/string is an amino acid.

:param residue: a L{Residue} object OR a three letter amino acid code :type residue: L{Residue} or string

:param standard: flag to check for the 20 AA (default false) :type standard: boolean

 >>> is_aa('ALA')
 True

Known three letter codes for modified amino acids are supported,

 >>> is_aa('FME')
 True
 >>> is_aa('FME', standard=True)
 False
Link to this function one_to_index()

One letter code to index.

 >>> one_to_index('A')
 0
 >>> one_to_index('Y')
 19
Link to this function one_to_three()

One letter code to three letter code.

 >>> one_to_three('A')
 'ALA'
 >>> one_to_three('Y')
 'TYR'
Link to this function three_to_index()

Three letter code to index.

 >>> three_to_index('ALA')
 0
 >>> three_to_index('TYR')
 19
Link to this function three_to_one()

Three letter code to one letter code.

 >>> three_to_one('ALA')
 'A'
 >>> three_to_one('TYR')
 'Y'

For non-standard amino acids, you get a KeyError:

 >>> three_to_one('MSE')
 Traceback (most recent call last):
    ...
 KeyError: 'MSE'