ó "˜ĪIc@s~ddlmZddlmZddlmZddlmZddlm Z ddl m Z m Z ddl mZmZdZd d d d d dddddddddddddddgZdZeZiZiZiZiZxSeddƒD]BZeeZeeZeee>> ppb=PPBuilder() >>> for pp in ppb.build_peptides(structure): >>> print pp.get_sequence() tALAtCYStASPtGLUtPHEtGLYtHIStILEtLYStLEUtMETtASNtPROtGLNtARGtSERtTHRtVALtTRPtTYRtACDEFGHIKLMNPQRSTVWYiicCst|S(sU Index to corresponding one letter amino acid name. For example: 0 to A. (t dindex_to_1(tindex((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyt index_to_one/scCst|S(s< One letter code to index. For example: A to 0. (t d1_to_index(ts((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyt one_to_index6scCst|S(sY Index to corresponding three letter amino acid name. For example: 0 to ALA. (t dindex_to_3(ti((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pytindex_to_three=scCst|S(s@ Three letter code to index. For example: ALA to 0. (t d3_to_index(R"((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pytthree_to_indexDscCst|}t|S(sJ Three letter code to one letter code. For example: ALA to A. (R'R(R"R%((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyt three_to_oneKs cCst|}t|S(sJ One letter code to three letter code. For example: A to ALA. (R!R$(R"R%((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyt one_to_threeSs cCsQt|ƒtks!|jƒ}n|jƒ}|r@tj|ƒStj|ƒSdS(s Return 1 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 N(ttypeRt get_resnametupperR'thas_keyR(tresiduetstandard((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pytis_aa[s   t PolypeptidecBsDeZdZd„Zd„Zd„Zd„Zd„Zd„ZRS(s? A polypeptide is simply a list of L{Residue} objects. cCs2g}x%|D]}|d}|j|ƒq W|S(s\ @return: the list of C-alpha atoms @rtype: [L{Atom}, L{Atom}, ...] tCA(tappend(tselftca_listtrestca((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyt get_ca_listrs   cCs‹g}t|ƒ}xrtd|ƒD]a}||}y4|djƒ}|djƒ}|djƒ}Wn1|jd ƒd|jdµstTAU(R9R?R>tmapRR4t get_parentRB( R5R6ttau_listR%t atom_listt vector_listtv1tv2tv3tv4ttauR7((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyt get_tau_list¬s  . c Cs¾g}|jƒ}x„tdt|ƒdƒD]Š}||||d||dg}td„|ƒ}|\}}}t|||ƒ} |j| ƒ||djƒ} | | jdRQRR4RRRB( R5t theta_listR6R%RTRURVRWRXtthetaR7((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pytget_theta_list¾s  # cCsbd}xF|D]>}|jƒ}tj|ƒr;t|}nd}||}q Wt|tƒ}|S(sh Return the AA sequence. @return: polypeptide sequence @rtype: L{Seq} ttX(R,RR.RR(R5R"R7tresnametseq((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyt get_sequenceŠs   cCs<|djƒd}|djƒd}d||f}|S(s‡ Return , where START and END are sequence identifiers of the outer residues. iii’’’’s(tget_id(R5tstarttendR"((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyt__repr__ās( t__name__t __module__t__doc__R9RMR[R_RdRh(((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyR2ns /   t _PPBuildercBs,eZdZd„Zd„Zdd„ZRS(sÆ Base class to extract polypeptides. It checks if two consecutive residues in a chain are connected. The connectivity test is implemented by a subclass. cCs ||_dS(sE @param radius: distance @type radius: float N(tradius(R5Rm((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyt__init__óscCst|ƒrdSdSdS(s&Check if the residue is an amino acid.iiN(R1(R5R/((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyt_acceptśs icCsH|j}|j}|jƒ}|dkrC|d}|jƒ}n?|dkr^|jƒ}n$|dkrv|g}n tdƒ‚g}x¹|D]±} t| ƒ} | jƒ} d} xŠ| D]‚} |rß|| ƒ rß| } qŗn|| | ƒr0| dkr tƒ} | j | ƒ|j | ƒn| j | ƒnd} | } qŗWqW|S(s Build 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 tSitMR;s+Entity should be Structure, Model or Chain.N( t _is_connectedRot get_leveltget_listRtitertnextRAR2R4(R5tentitytaa_onlyt is_connectedtaccepttleveltmodelt chain_listtpp_listtchaintchain_ittprevtppRv((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pytbuild_peptidess:                (RiRjRkRnRoRƒ(((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyRlģs  t CaPPBuildercBs#eZdZdd„Zd„ZRS(s3 Use CA--CA distance to find polypeptides. g333333@cCstj||ƒdS(N(RlRn(R5Rm((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyRn2sc CsĆx'||gD]}|jdƒs dSq W|d}|d}|jƒrY|jƒ}n |g}|jƒr}|jƒ}n |g}x6|D].}x%|D]} || |jkršdSqšWqWdS(NR3ii(thas_idt is_disorderedtdisordered_get_listRm( R5RRvtrREtptnlisttplistRKR‚((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyRr5s          (RiRjRkRnRr(((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyR„.s t PPBuildercBs,eZdZdd„Zd„Zd„ZRS(s1 Use C--N distance to find polypeptides. gĶĢĢĢĢĢü?cCstj||ƒdS(N(RlRn(R5Rm((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyRnOsc Cs;|jdƒsdS|jdƒs&dS|j}|d}|d}|jƒr^|jƒ}n |g}|jƒr‚|jƒ}n |g}x©|D]”}x˜|D]} |jƒ} | jƒ} | | ksį| dksį| dkrŸ||| ƒr/|jƒr |j| ƒn|jƒr(|j| ƒndSqŸqŸWq’WdS(NR;iR:t i(R…t _test_distR†R‡t get_altloctdisordered_select( R5RRvt test_distRFREtclistRŠRKtcctn_altloctc_altloc((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Polypeptide.pyRrRs2           $  cCs|||jkrdSdSdS(s)Return 1 if distance between atomsst              ~B2