B b%@sndZddlZddlmZddlmZddlmZdZddd Z Gd d d Z d d Z ddZ GdddZ dS)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)SVDSuperimposer) PDBException) PPBuilderzlib_%s_z_%s.txt.c Cs|dt||f}t|}g}d}x|D]x}|ddks,|ddkrJq,|}|ddkr|t||} || |d7}q,tdd|dd D} | d | q,WWd QRX|S) 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------cSsg|] }t|qS)float).0xr r 5lib/python3.7/site-packages/Bio/PDB/FragmentMapper.py ^sz#_read_fragments..ZXXXN)_FRAGMENT_FILEopensplitFragmentappendnumpyZarray add_residue) sizelengthdirfilenamefpflistfidlZslfZcoordr r r_read_fragments<s      r!c@sPeZdZdZddZddZddZdd Zd d Zd d Z ddZ ddZ dS)rz)Represent a polypeptide C-alpha fragment.cCs.||_d|_g|_t|dfd|_||_dS)zInitialize fragment object. :param length: length of the fragment :type length: int :param fid: id for the fragment :type fid: int rrdN)rcounter resname_listrZzeros coords_car)selfrrr r r__init__gs zFragment.__init__cCs|jS)zcGet residue list. :return: the residue names :rtype: [string, string,...] )r$)r&r r rget_resname_listyszFragment.get_resname_listcCs|jS)zcGet identifier for the fragment. :return: id for the fragment :rtype: int )r)r&r r rget_idszFragment.get_idcCs|jS)zGet the CA coordinates in the fragment. :return: the CA coords in the fragment :rtype: Numeric (Nx3) array )r%)r&r r r get_coordsszFragment.get_coordscCs<|j|jkrtd|j|||j|j<|jd|_dS)zAdd a residue. :param resname: residue name (eg. GLY). :type resname: string :param ca_coord: the c-alpha coorinates of the residues :type ca_coord: Numeric array with length 3 zFragment boundary exceeded.r N)r#rrr$rr%)r&resnameca_coordr r rrs   zFragment.add_residuecCs|jS)zReturn lengt of the fragment.)r)r&r r r__len__szFragment.__len__cCs&t}||j|j||S)zReturn rmsd between two fragments. :return: rmsd between fragments :rtype: float Examples -------- This is an incomplete but illustrative example:: rmsd = fragment1 - fragment2 )rsetr%runZget_rms)r&otherZsupr r r__sub__s zFragment.__sub__cCsd|j|jfS)zRepresent the fragment object as a string. Returns where L=length of fragment and ID the identifier (rank in the library). z)rr)r&r r r__repr__szFragment.__repr__N) __name__ __module__ __qualname____doc__r'r(r)r*rr-r1r2r r r rrdsrc Csg}xtdt||dD]}t|d}xftd|D]X}|||}|}|drb|d}ntd|rztd|} ||| q6W| |qW|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 rr ZCA CHAINBREAK) rangelenrZ get_resnameZhas_idrZ is_disorderedZ get_coordrr) pprZ frag_listir jZresiduer+Zcar,r r r_make_fragment_lists     r>c Csng}xd|D]\}g}x4tdt|D]"}||}||}|||fq"W||dd}||q W|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 )r9r:rsort) rreflistZmappedr Zrankr<ZrfZrmsZfragmentr r r_map_fragment_lists   rAc@s2eZdZdZdddZddZd d Zd d Zd S)FragmentMapperzAMap polypeptides in a model to lists of representative fragments.rcCsZ|dkrd|_n|dkr d|_ntd||_||_t||||_||_||j|_dS)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 rDrz!Fragment length should be 5 or 7.N) edgerflengthlsizer!r@model_mapfd)r&rJrIrHZfdirr r rr'szFragmentMapper.__init__c Cst}||}i}x|D]}yt||j}t||j}xdtdt|D]R}||} ||jkrbqHqH|t||jkrxqHqH||j} | dkst || || <qHWWqt k r} z| dkrn t | dWdd} ~ XYqXqW|S)zjMap (PRIVATE). :param model: the model that will be mapped :type model: L{Model} rr8N) rZbuild_peptidesr>rHrAr@r9r:rGAssertionErrorr) r&rJZppbZpplrLr;rZmflistr<resindexZwhyr r rrKs*        zFragmentMapper._mapcCs ||jkS)zeCheck if the given residue is in any of the mapped fragments. :type res: L{Residue} )rL)r&rNr r r __contains__7szFragmentMapper.__contains__cCs |j|S)z{Get an entry. :type res: L{Residue} :return: fragment classification :rtype: L{Fragment} )rL)r&rNr r r __getitem__>szFragmentMapper.__getitem__N)rCrDr)r3r4r5r6r'rKrPrQr r r rrBs  $rB)r)r6rZBio.SVDSuperimposerrZBio.PDB.PDBExceptionsrZBio.PDB.Polypeptiderrr!rr>rArBr r r r+s    ([