o Rŀg7@sPdZddlZddlmZddlmZddlmZddlmZddlmZddl m Z dd l m Z dd l m Z eeed d d \ZZeZiZiZiZiZedD]ZeeZeeZeee<eee<eee<eee<qRddZddZddZddZd$ddZ d$ddZ!Gddde"Z#GdddZ$Gd d!d!e$Z%Gd"d#d#e$Z&dS)%aPolypeptide-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. N)nucleic_letters_3to1)nucleic_letters_3to1_extended)protein_letters_3to1)protein_letters_3to1_extended) PDBException) calc_angle) calc_dihedral)SeqcCs|dS)N)xr r G/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/Polypeptide.pyAsr)keycCt|S)zyIndex to corresponding one letter amino acid name. >>> index_to_one(0) 'A' >>> index_to_one(19) 'Y' ) dindex_to_1)indexr r r index_to_oneSrcCr)z`One letter code to index. >>> one_to_index('A') 0 >>> one_to_index('Y') 19 ) d1_to_indexsr r r one_to_index^rrcCr)zIndex to corresponding three letter amino acid name. >>> index_to_three(0) 'ALA' >>> index_to_three(19) 'TYR' ) dindex_to_3)ir r r index_to_threeirrcCr)zjThree letter code to index. >>> three_to_index('ALA') 0 >>> three_to_index('TYR') 19 ) d3_to_indexrr r r three_to_indextrrFcC2t|ts |d}|}|r|tvS|tvS)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 <3s) isinstancestr get_resnameupperrrresiduestandardr r r is_aas  r(cCr)a Return True if residue object/string is a nucleic acid. :param residue: a L{Residue} object OR a three letter code :type residue: L{Residue} or string :param standard: flag to check for the 8 (DNA + RNA) canonical bases. Default is False. :type standard: boolean >>> is_nucleic('DA ') True >>> is_nucleic('A ') True Known three letter codes for modified nucleotides are supported, >>> is_nucleic('A2L') True >>> is_nucleic('A2L', standard=True) False r )r!r"r#r$rrr%r r r is_nucleics  r)c@s@eZdZdZddZddZddZdd Zd d Zd d Z dS) Polypeptidez5A polypeptide is simply a list of L{Residue} objects.cCs$g}|D] }|d}||q|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_listc CsBg}t|}t|D]}||}z|d}|d}|d}Wnty<|dd|jd<d|jd<Yq w|dkrb||d }z|d} t| |||} Wn tyad} Ynwd} ||d kr||d } z| d} t|||| } Wn tyd} Ynwd} || | f| |jd<| |jd<q |S) z+Return the list of phi/psi dihedral angles.Nr+C)NNNPHIPSIrr )lenrange get_vector Exceptionr,xtrar)r-ppllngrr/nr0crpcpphirnnnpsir r r get_phi_psi_listsH                zPolypeptide.get_phi_psi_listc Cs|}g}tt|dD]:}||||d||d||df}dd|D\}}}}t||||} || ||d} | | jd<q|S)z?List of tau torsions angles for all 4 consecutive Calpha atoms.r cs|]}|VqdSNr8.0ar r r z+Polypeptide.get_tau_list..TAU)r1r7r6rr, get_parentr:) r-r.tau_listr atom_listv1v2v3v4taur/r r r get_tau_lists(  zPolypeptide.get_tau_listc Csg}|}tt|dD]3}||||d||df}dd|D\}}}t|||}||||d} || jd<q|S)z8List of theta angles for all 3 consecutive Calpha atoms.rGr csrHrIrJrKr r r rN rOz-Polypeptide.get_theta_list..THETA)r1r7r6rr,rQr:) r- theta_listr.rrSrTrUrVthetar/r r r get_theta_lists   zPolypeptide.get_theta_listcCsddd|D}t|S)znReturn the AA sequence as a Seq object. :return: polypeptide sequence :rtype: L{Seq} css |] }t|dVqdS)XN)rgetr#)rLr/r r r rNs z+Polypeptide.get_sequence..)joinr )r-rr r r get_sequences zPolypeptide.get_sequencecCs2|dd}|dd}d|d|dS)zReturn string representation of the polypeptide. Return , where START and END are sequence identifiers of the outer residues. rr z)get_id)r-startendr r r __repr__szPolypeptide.__repr__N) __name__ __module__ __qualname____doc__r1rErYr]rbrhr r r r r*s - r*c@s*eZdZdZddZddZd ddZd 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 Nradiusr-ror r r __init__2s z_PPBuilder.__init__cCs8t||drdS|sd|jvrtd|dSdS)z0Check if the residue is an amino acid (PRIVATE).)r'Tr+z5Assuming residue %s is an unknown modified amino acidF)r( child_dictwarningswarnr#)r-r&standard_aa_onlyr r r _accept:s z_PPBuilder._acceptr c Cs|j}|j}|}|dkr|d}|}n|dkr |}n |dkr(|g}ntdg}|D]U} t| } zt| } || |sIt| } || |r@Wn tySYq0wd} | D],} || |r|| |r|| | r| durzt} | | | | | | nd} | } qXq0|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 SrMr3z+Entity should be Structure, Model or Chain.N) _is_connectedrv get_levelget_listriternext StopIterationr*r,)r-entityaa_only is_connectedacceptlevelmodel chain_listpp_listchainchain_itprev_resppnext_resr r r build_peptidesKsP         z_PPBuilder.build_peptidesN)r )rirjrkrlrqrvrr r r r rm)s rmc@s"eZdZdZdddZddZdS) CaPPBuilderz)Use CA--CA distance to find polypeptides.333333@cCt||dSzInitialize the class.Nrmrqrpr r r rqzCaPPBuilder.__init__c Cs||fD] }|dsdSq|d}|d}|r |}n|g}|r,|}n|g}|D]}|D] } || |jkrBdSq5q1dS)Nr+FT)has_id is_disordereddisordered_get_listro) r-rrrr=pnlistplistrCrr r r rys&    zCaPPBuilder._is_connectedN)r)rirjrkrlrqryr r r r rs  rc@s*eZdZdZd ddZddZddZd S) PPBuilderz'Use C--N distance to find polypeptides.?cCrrrrpr r r rqrzPPBuilder.__init__c Cs|dsdS|dsdS|j}|d}|d}|r"|}n|g}|r.|}n|g}|D]6}|D]1} |} | } | | ksM| dksM| dkrh||| rh|r[|| |rd|| dSq7q3dS)Nr3Fr2 T)r _test_distrr get_altlocdisordered_select) r-rr test_distr>r=clistrrCccn_altlocc_altlocr r r rys6       zPPBuilder._is_connectedcCs|||jkr dSdS)z4Return 1 if distance between atomsr=r r r rszPPBuilder._test_distN)r)rirjrkrlrqryrr r r r rs   #r)F)'rlrsBio.Data.PDBDatarrrrBio.PDB.PDBExceptionsrBio.PDB.vectorsrrBio.Seqr zipsorteditemsaa3aa1standard_aa_namesrrrrr7rn1n3rrrrr(r)listr*rmrrr r r r sB-              nV