ó Žï Ic@sddlZddlZddlmZddlTdZdZdd„Zddd „ƒYZd „Z d „Z d dd „ƒYZ e dkrddl Z eƒZejde jdƒZedZe edddƒZx=ejedƒD]&ZeGejeƒreeGHqîHqîWndS(iÿÿÿÿN(tSVDSuperimposer(t*sO Classify protein backbone structure according to Kolodny et al's fragment libraries. It can be regarded as a form of objective secondary structure classification. Only fragments of length 5 or 7 are supported (ie. there is a 'central' residue). Full reference: Kolodny R, Koehl P, Guibas L, Levitt M. Small libraries of protein fragments model native protein structures accurately. J Mol Biol. 2002 323(2):297-307. The definition files of the fragments can be obtained from: U{http://csb.stanford.edu/~rachel/fragments/} You need these files to use this module. The following example uses the library with 10 fragments of length 5. The library files can be found in directory 'fragment_data'. >>> model=structure[0] >>> fm=FragmentMapper(lsize=10, flength=5, dir="fragment_data") >>> fm.map(model) >>> fragment=fm[residue] slib_%s_z_%s.txtt.c Csõ|dt||f}t|dƒ}g}d}x±|jƒD]£}|ddks@|ddkrlq@n|jƒ}|ddkr´t||ƒ} |j| ƒ|d7}q@ntjtt |dd!ƒƒ} | j d | ƒq@W|j ƒ|S( sx Read a fragment spec file (available from U{http://csb.stanford.edu/rachel/fragments/} and return a list of Fragment objects. @param size: number of fragments in the library @type size: int @param length: length of the fragments @type length: int @param dir: directory where the fragment spec files can be found @type dir: string t/triRs is------itXXX( t_FRAGMENT_FILEtopent readlinestsplittFragmenttappendtnumpytarraytmaptfloatt add_residuetclose( tsizetlengthtdirtfilenametfptflisttfidtltsltftcoord((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/FragmentMapper.pyt_read_fragments.s"     R cBsVeZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z RS( s3 Represent a polypeptide C-alpha fragment. cCsC||_d|_g|_tj|dfdƒ|_||_dS(s‘ @param length: length of the fragment @type length: int @param fid: id for the fragment @type fid: int iitdN(Rtcountert resname_listR tzerost coords_caR(tselfRR((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/FragmentMapper.pyt__init__Zs   cCs|jS(sQ @return: the residue names @rtype: [string, string,...] (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/FragmentMapper.pytget_resname_listkscCs|jS(sB @return: id for the fragment @rtype: int (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/FragmentMapper.pytget_idrscCs|jS(s\ @return: the CA coords in the fragment @rtype: Numeric (Nx3) array (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/FragmentMapper.pyt get_coordsyscCsU|j|jkr!tdƒ‚n|jj|ƒ||j|j<|jd|_dS(sÌ @param resname: residue name (eg. GLY). @type resname: string @param ca_coord: the c-alpha coorinates of the residues @type ca_coord: Numeric array with length 3 sFragment boundary exceeded.iN(RRt PDBExceptionR R R"(R#tresnametca_coord((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/FragmentMapper.pyR€s cCs|jS(sA @return: length of fragment @rtype: int (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/FragmentMapper.pyt__len__ŽscCs3tƒ}|j|j|jƒ|jƒ|jƒS(s® Return rmsd between two fragments. Example: >>> rmsd=fragment1-fragment2 @return: rmsd between fragments @rtype: float (RtsetR"truntget_rms(R#tothertsup((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/FragmentMapper.pyt__sub__•s  cCsd|j|jfS(sƒ Returns where L=length of fragment and ID the identifier (rank in the library). s(RR(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/FragmentMapper.pyt__repr__¤s( t__name__t __module__t__doc__R$R%R&R'RR+R1R2(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/FragmentMapper.pyR Vs       c Cság}xÔtdt|ƒ|dƒD]µ}t|dƒ}xtd|ƒD]}|||}|jƒ}|jdƒr…|d}n tdƒ‚|jƒr¬tdƒ‚n|jƒ} |j|| ƒqIW|j |ƒq$W|S(sÛ Dice up a peptide in fragments of length "length". @param pp: a list of residues (part of one peptide) @type pp: [L{Residue}, L{Residue}, ...] @param length: fragment length @type length: int iiiÿÿÿÿtCAt CHAINBREAK( trangetlenR t get_resnamethas_idR(t is_disorderedt get_coordRR ( tppRt frag_listtiRtjtresidueR)tcaR*((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/FragmentMapper.pyt_make_fragment_list¬s $     c Csg}x€|D]x}g}xDtdt|ƒƒD]-}||}||}|j||fƒq/W|jƒ|dd}|j|ƒq W|S(sN Map all frgaments in flist to the closest (in RMSD) fragment in reflist. Returns a list of reflist indices. @param flist: list of protein fragments @type flist: [L{Fragment}, L{Fragment}, ...] @param reflist: list of reference (ie. library) fragments @type reflist: [L{Fragment}, L{Fragment}, ...] ii(R8R9R tsort( RtreflisttmappedRtrankR@trftrmstfragment((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/FragmentMapper.pyt_map_fragment_listÈs     tFragmentMappercBs;eZdZdddd„Zd„Zd„Zd„ZRS(sK Map polypeptides in a model to lists of representative fragments. iiRcCs…|dkrd|_n$|dkr0d|_n tdƒ‚||_||_t|||ƒ|_||_|j|jƒ|_dS(s @param model: the model that will be mapped @type model: L{Model} @param lsize: number of fragments in the library @type lsize: int @param flength: length of fragments in the library @type flength: int @param fdir: directory where the definition files are found (default=".") @type fdir: string iiiis!Fragment length should be 5 or 7.N( tedgeR(tflengthtlsizeRRFtmodelt_maptfd(R#RQRPROtfdir((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/FragmentMapper.pyR$æs        c Csútƒ}|j|ƒ}i}xÕ|D]Í}y³t||jƒ}t||jƒ}xˆtdt|ƒƒD]q}||} ||jkrqhqh|t|ƒ|jkr¬qhqh||j} | dksËt ‚|| || RtmflistR@trestindex((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/FragmentMapper.pyRRs&     cCs|jj|ƒS(s' @type res: L{Residue} (RSthas_key(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/FragmentMapper.pyR]!scCs |j|S(sm @type res: L{Residue} @return: fragment classification @rtype: L{Fragment} (RS(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/FragmentMapper.pyt __getitem__'s(R3R4R5R$RRR]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/FragmentMapper.pyRMâs  t__main__tXiii it levitt_datatR(((tosR tBio.SVDSuperimposerRtBio.PDBR5RRR RDRLRMR3tsyst PDBParsertpt get_structuretargvtstmtfmt Selectiontunfold_entitiesRR](((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/FragmentMapper.pyts*    (V  O