Ri%tdZddlZddlmZddlmZddlmZdZ ddZ Gdd Z d Z d Z Gd d Zy)aClassify protein backbone structure with 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: http://github.com/csblab/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'. >>> from Bio.PDB.PDBParser import PDBParser >>> from Bio.PDB.FragmentMapper import FragmentMapper >>> parser = PDBParser() >>> structure = parser.get_structure("1a8o", "PDB/1A8O.pdb") >>> model = structure[0] >>> fm = FragmentMapper(model, lsize=10, flength=5, fdir="PDB") >>> chain = model['A'] >>> res152 = chain[152] >>> res157 = chain[157] >>> res152 in fm # is res152 mapped? (fragment of a C-alpha polypeptide) False >>> res157 in fm # is res157 mapped? (fragment of a C-alpha polypeptide) True N) PDBException) PPBuilder)SVDSuperimposerzlib_%s_z_%s.txtc |dztz||fz}t|5}g}d}|D]}|ddk(s|ddk(r|j}|ddk(r#t||} |j | |dz }Ot j |ddD cgc] } t| c} }  jd|  d d d |Scc} w#1swYSxYw) aRead a fragment spec file (PRIVATE). Read a fragment spec file available from http://github.com/csblab/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 /r* z------XXXN) _FRAGMENT_FILEopensplitFragmentappendnparrayfloat add_residue) sizelengthdirfilenamefpflistfidlineslfxcoords N/home/agent/.friday_env/lib/python3.12/site-packages/Bio/PDB/FragmentMapper.py_read_fragmentsr#9s c N*tVn where L=length of fragment and ID the identifier (rank in the library). z)rrr/s r"__repr__zFragment.__repr__s ,t{{DHH.EEEr-N) __name__ __module__ __qualname____doc__r,r0r2r4rr9r@rBr-r"rras.3$! ($Fr-rcg}tt||z dzD]}t|d}t|D]y}|||z}|j}|j dr|d}n t d|j r t d|j} |j|| {|j||S)zDice up a peptide in fragments of length "length" (PRIVATE). :param pp: a list of residues (part of one peptide) :type pp: [L{Residue}, L{Residue}, ...] :param length: fragment length :type length: int r CA CHAINBREAK) rangelenr get_resnamehas_idr is_disordered get_coordrr) ppr frag_listirjresiduer6car7s r"_make_fragment_listrXsI 3r7V#a' (  VR v -AQiG))+G~~d#T]"<00!"<00||~H MM'8 , -   r-cg}|D]c}g}tt|D]}||}||z }|j||f!|j|dd}|j|e|S)aMap flist fragments to closest entry in reflist (PRIVATE). 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}, ...] rr )rLrMrsort) rreflistmappedrrankrTrfrmsfragments r"_map_fragment_listrasF  s7|$ #ABb&C KKb " # 71: h  Mr-c*eZdZdZddZdZdZdZy)FragmentMapperzAMap polypeptides in a model to lists of representative fragments.c|dk(rd|_n|dk(rd|_n td||_||_t ||||_||_|j|j |_y)aCreate instance of FragmentMapper. :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 r z!Fragment length should be 5 or 7.N) edgerflengthlsizer#r[model_mapfd)r+rkrjrifdirs r"r,zFragmentMapper.__init__se a<DI \DIBC C  &ugt<  ))DJJ'r-ct}|j|}i}|D]} t||j}t ||j }t t|D]Q}||} ||jkr|t||jz k\r4||jz } | dk\sJ|| || <S|S#t$r} | dk(rn t| dYd} ~ d} ~ wwxYw)zjMap (PRIVATE). :param model: the model that will be mapped :type model: L{Model} rrKN) rbuild_peptidesrXrirar[rLrMrhr) r+rkppbpplrmrRrmflistrTresindexwhys r"rlzFragmentMapper._maps k  '  6B 6+B =+E4<<@s2w 0AQ%C499} s2w23 !"DII $z)z"(-3 0  62   6,&&s+5 6sBB<< C!CC!c||jvS)zeCheck if the given residue is in any of the mapped fragments. :type res: L{Residue} rmr+rts r" __contains__zFragmentMapper.__contains__4s dgg~r-c |j|S)z{Get an entry. :type res: L{Residue} :return: fragment classification :rtype: L{Fragment} rxrys r" __getitem__zFragmentMapper.__getitem__;swws|r-N)re.)rCrDrErFr,rlrzr|rGr-r"rcrcsK(8"Hr-rc)r~)rFnumpyrBio.PDB.PDBExceptionsrBio.PDB.PolypeptiderBio.SVDSuperimposerrr r#rrXrarcrGr-r"rsK#J.)/ #%PXFXFv64RRr-