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 corresponding one letter amino acid name

Index to corresponding three letter amino acid name

Return True if residue object/string is an amino acid

One letter code to index

One letter code to three letter code

Three letter code to index

Three letter code to one letter code

Link to this section Functions

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'

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

One letter code to index.

 >>> one_to_index('A')
 0
 >>> one_to_index('Y')
 19

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

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'