:>"^R7@sdZddlmZddlmZddlZddlmZddlm Z ddl m Z ddl m Z dd lmZmZd d d d ddddddddddddddddgZdZeZiZiZiZiZxSeddD]BZeeZeeZeee>> 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. )print_function) basestringN)generic_protein)SCOPData)Seq) PDBException) calc_dihedral calc_angleZALAZCYSZASPZGLUZPHEZGLYZHISZILEZLYSZLEUZMETZASNZPROZGLNZARGZSERZTHRZVALZTRPZTYRZACDEFGHIKLMNPQRSTVWYcCst|S)zyIndex to corresponding one letter amino acid name. >>> index_to_one(0) 'A' >>> index_to_one(19) 'Y' ) dindex_to_1)indexr 8/tmp/pip-build-ww9dw3qa/biopython/Bio/PDB/Polypeptide.py index_to_oneksrcCst|S)z`One letter code to index. >>> one_to_index('A') 0 >>> one_to_index('Y') 19 ) d1_to_index)sr r r one_to_indexvsrcCst|S)zIndex to corresponding three letter amino acid name. >>> index_to_three(0) 'ALA' >>> index_to_three(19) 'TYR' ) dindex_to_3)ir r rindex_to_threesrcCst|S)zjThree letter code to index. >>> three_to_index('ALA') 0 >>> three_to_index('TYR') 19 ) d3_to_index)rr r rthree_to_indexsrcCst|}t|S)a 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' )rr )rrr r r three_to_ones rcCst|}t|S)zsOne letter code to three letter code. >>> one_to_three('A') 'ALA' >>> one_to_three('Y') 'TYR' )rr)rrr r r one_to_threes rFcCsHt|ts|j}|j}|r7|tkS|tjkSdS)aReturn 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 N) isinstancer get_resnameupperrrprotein_letters_3to1)residuestandardr r ris_aas    r c@s^eZdZdZddZddZddZdd Zd d Zd d Z dS) Polypeptidez5A polypeptide is simply a list of L{Residue} objects.cCs2g}x%|D]}|d}|j|q W|S)zGet list of C-alpha atoms in the polypeptide. :return: the list of C-alpha atoms :rtype: [L{Atom}, L{Atom}, ...] CA)append)selfca_listrescar r r get_ca_lists   zPolypeptide.get_ca_listcCsg}t|}xtd|D]}||}y4|dj}|dj}|dj}Wn<tk r|jd d|jds z,Polypeptide.get_tau_list..ZTAU)r(r-r,rr# get_parentr0) r$r%Ztau_listr atom_listv1v2v3Zv4taur&r r r get_tau_lists  . zPolypeptide.get_tau_listc Csg}|j}xtdt|dD]}||||d||df}dd|D\}}}t|||}|j|||dj} || jd.ZTHETA)r(r-r,r r#r>r0) r$Z theta_listr%rr?r@rArBthetar&r r rget_theta_lists  # zPolypeptide.get_theta_listcCsId}x-|D]%}|tjj|jd7}q Wt|t}|S)znReturn the AA sequence as a Seq object. :return: polypeptide sequence :rtype: L{Seq} X)rrgetrrr)r$rr&seqr r r get_sequence+s  #zPolypeptide.get_sequencecCs<|djd}|djd}d||f}|S)zReturn string representation of the polypeptide. Return , where START and END are sequence identifiers of the outer residues. rr+z)Zget_id)r$startendrr r r__repr__7szPolypeptide.__repr__N) __name__ __module__ __qualname____doc__r(r8rDrFrKrOr r r rr!s  -   r!c@s=eZdZdZddZddZdddZd S) _PPBuilderzBase class to extract polypeptides. It checks if two consecutive residues in a chain are connected. The connectivity test is implemented by a subclass. This assumes you want both standard and non-standard amino acids. cCs ||_dS)z`Initialize the base class. :param radius: distance :type radius: float N)radius)r$rUr r r__init__Lsz_PPBuilder.__init__cCsOt|d|rdS| rGd|jkrGtjd|jdSdSdS)z0Check if the residue is an amino acid (PRIVATE).rTr"z5Assuming residue %s is an unknown modified amino acidFN)r Z child_dictwarningswarnr)r$rZstandard_aa_onlyr r r_acceptTsz_PPBuilder._acceptr+c Cs|j}|j}|j}|dkrC|d}|j}n?|dkr^|j}n$|dkrv|g}n tdg}x|D]} t| } y2t| } x|| |st| } qWWntk rwYnXd} x| D]~} || |rj|| |rj|| | rj| dkrZt} | j | |j | | j | nd} | } qWqW|S)aBuild and return a list of Polypeptide objects. :param entity: polypeptides are searched for in this object :type entity: L{Structure}, L{Model} or L{Chain} :param aa_only: if 1, the residue needs to be a standard AA :type aa_only: int SrMr*z+Entity should be Structure, Model or Chain.N) _is_connectedrYZ get_levelZget_listriternext StopIterationr!r#)r$entityZaa_onlyZ is_connectedacceptlevelmodelZ chain_listZpp_listchainZchain_itprev_resppnext_resr r rbuild_peptidesesB                  z_PPBuilder.build_peptidesN)rPrQrRrSrVrYrhr r r rrTCs   rTc@s1eZdZdZdddZddZdS) CaPPBuilderz)Use CA--CA distance to find polypeptides.g333333@cCstj||dS)zInitialize the class.N)rTrV)r$rUr r rrVszCaPPBuilder.__init__c Csx'||gD]}|jds dSq W|d}|d}|jrY|j}n |g}|jr}|j}n |g}x6|D].}x%|D]} || |jkrdSqWqWdS)Nr"FT)has_id is_disordereddisordered_get_listrU) r$rergrr1pnlistplistr6rfr r rr\s          zCaPPBuilder._is_connectedN)rPrQrRrSrVr\r r r rris ric@s=eZdZdZdddZddZddZd S) PPBuilderz'Use C--N distance to find polypeptides.g?cCstj||dS)zInitialize the class.N)rTrV)r$rUr r rrVszPPBuilder.__init__c Cs2|jdsdS|jds&dS|j}|d}|d}|jr^|j}n |g}|jr|j}n |g}x|D]}x|D]} |j} | j} | | ks| dks| dkr||| r|jr |j| |jr"|j| dSqWqWdS)Nr*Fr) T)rj _test_distrkrlZ get_altlocZdisordered_select) r$rergZ test_distr2r1Zclistror6ccZn_altlocZc_altlocr r rr\s2           $     zPPBuilder._is_connectedcCs|||jkrdSdSdS)z4Return 1 if distance between atoms3sh         pV