Ri7dZddlZddlmZddlmZddlmZddlmZddlmZddl m Z dd l m Z dd l m Z eeej d \ZZeZiZiZiZiZed D] ZeeZeeZeee<eee<eee<eee<"dZdZdZdZddZ ddZ!Gdde"Z#GddZ$Gdde$Z%Gdde$Z&y)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)Seqc |dS)N)xs K/home/agent/.friday_env/lib/python3.12/site-packages/Bio/PDB/Polypeptide.pyrAs 1Q4)keyct|S)zyIndex to corresponding one letter amino acid name. >>> index_to_one(0) 'A' >>> index_to_one(19) 'Y' ) dindex_to_1)indexs r index_to_onerSs u rct|S)z`One letter code to index. >>> one_to_index('A') 0 >>> one_to_index('Y') 19 ) d1_to_indexss r one_to_indexr^ q>rct|S)zIndex to corresponding three letter amino acid name. >>> index_to_three(0) 'ALA' >>> index_to_three(19) 'TYR' ) dindex_to_3)is rindex_to_threer!irrct|S)zjThree letter code to index. >>> three_to_index('ALA') 0 >>> three_to_index('TYR') 19 ) d3_to_indexrs rthree_to_indexr$trrct|ts|jd}|j}|r|tvS|t vS)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_resnameupperrrresiduestandards ris_aar.sG& gs #((*3/mmoG...777rct|ts|jd}|j}|r|tvS|t vS)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+s r is_nucleicr0sG. gs #((*3/mmoG...777rc4eZdZdZdZdZdZdZdZdZ y) Polypeptidez5A polypeptide is simply a list of L{Residue} objects.cDg}|D]}|d}|j||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_listrescas r get_ca_listzPolypeptide.get_ca_lists4  CTB NN2  rcg}t|}t|D]}||} |dj}|dj}|dj}|dkDr+||d z } |dj} t | |||} nd} ||d z kr+||d z} | dj} t |||| } nd} |j | | f| |j d<| |j d<|S#t$r3|j dd|j d<d|j d<YwxYw#t$rd} YwxYw#t$rd} YwxYw) z+Return the list of phi/psi dihedral angles.Nr4C)NNNPHIPSIrr )lenrange get_vector Exceptionr5xtrar )r6ppllngr r8nr9crpcpphirnnnpsis rget_phi_psi_listzPolypeptide.get_phi_psi_lists$is& "Aq'C H'')Y))+H'')1u!a%[C++-B'Ar15C C!G}!a%[C++-B'2q"5C  JJSz "!CHHUO!CHHUOM& "N C  <("&"&  !C!Cs59C7)!D6!E78D32D36 EE EEc<|j}g}tt|dz D]o}||||dz||dz||dzf}d|D\}}}}t||||} |j | ||dzj } | | j d<q|S)z?List of tau torsions angles for all 4 consecutive Calpha atoms.r c3<K|]}|jywNrB.0as r z+Polypeptide.get_tau_list..s@alln@TAU)r:rAr@r r5 get_parentrD) r6r7tau_listr atom_listv1v2v3v4taur8s r get_tau_listzPolypeptide.get_tau_lists""$s7|a'( "A WQU^WQU^WQQRU^TI@i@NBBBB/C OOC !a%.++-C!CHHUO "rc*g}|j}tt|dz D]f}||||dz||dzf}d|D\}}}t|||}|j |||dzj } || j d<h|S)z8List of theta angles for all 3 consecutive Calpha atoms.rRr c3<K|]}|jywrTrUrVs rrYz-Polypeptide.get_theta_list.. s.s* JM ) - -coo.? E s.0)joinr )r6rs r get_sequencezPolypeptide.get_sequences* GG QU  1v rcl|djd}|djd}d|d|dS)zReturn string representation of the polypeptide. Return , where START and END are sequence identifiers of the outer residues. rr z)get_id)r6startends r__repr__zPolypeptide.__repr__sC Q #2hoo"$UG5Q77rN) __name__ __module__ __qualname____doc__r:rOrdrjrqrxr rrr2r2s$? +Z   8rr2c$eZdZdZdZdZddZy) _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. c||_y)z`Initialize the base class. :param radius: distance :type radius: float Nradiusr6rs r__init__z_PPBuilder.__init__2s  rct||ry|s5d|jvr'tjd|j zyy)z0Check if the residue is an amino acid (PRIVATE).)r-Tr4z5Assuming residue %s is an unknown modified amino acidF)r. child_dictwarningswarnr))r6r,standard_aa_onlys r_acceptz_PPBuilder._accept:sL #3 4!dg.@.@&@ MMG%%'( rcJ|j}|j}|j}|dk(r|d}|j}n*|dk(r|j}n|dk(r|g}n t dg}|D]} t | } t | } || |st | } || |sd} | D]a} || |rR|| |rI|| | r@| ,t} | j| |j| | j| nd} | } c|S#t$rYwxYw)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_connectedr get_levelget_listriternext StopIterationr2r5)r6entityaa_only is_connectedacceptlevelmodel chain_listpp_listchainchain_itprev_resppnext_ress rbuild_peptidesz_PPBuilder.build_peptidesKsD))   " C<1IE)J c\*J c\ JLM M $EE{H > 73#H~H!73 B$ $8W-x1$Xx8z(] (+r*IIh'B# $ $4)!  s(D D"!D"N)r )ryrzr{r|rrrr rrr~r~)s"1rr~ceZdZdZddZdZy) CaPPBuilderz)Use CA--CA distance to find polypeptides.c0tj||yzInitialize the class.Nr~rrs rrzCaPPBuilder.__init__D&)rc&||fD]}|jdry|d}|d}|jr|j}n|g}|jr|j}n|g}|D]}|D]} || z |jksy y)Nr4FT)has_id is_disordereddisordered_get_listr) r6rrrrGpnlistplistrMrs rrzCaPPBuilder._is_connectedsH% A88D>  TN TN ?? ))+ECE ?? ))+ECE B Gt{{*  rN)g333333@)ryrzr{r|rrr rrrrs3*rrc$eZdZdZddZdZdZy) PPBuilderz'Use C--N distance to find polypeptides.c0tj||yrrrs rrzPPBuilder.__init__rrc |jdsy|jdsy|j}|d}|d}|jr|j}n|g}|jr|j}n|g}|D]}|D]} |j } | j } | | k(s | dk(s| dk(s3||| s=|jr|j | |jr|j | yy)Nr=Fr< T)r _test_distrr get_altlocdisordered_select) r6rr test_distrHrGclistrrMccn_altlocc_altlocs rrzPPBuilder._is_connectedss#s#OO SM SM ?? ))+ECE ?? ))+ECE $B $==?==?x'8s?h#o R(??,//9??,//9# $ $ rc*||z |jkryy)z4Return 1 if distance between atomsrs+Z1:1:.&) 1+113H IS     rA QB QBKOKNKOKN 888@k8$k8\SSl*:/ /r