BQc@sddlZddlTejdZejdZdfdYZdfdYZd fd YZd fd YZd Z dfdYZ dZ dS(iN(t*sm^(ATOM|HETATM) *([0-9]+) *(\S+) +([A-Z]+) +([a-zA-Z]?) *([-0-9]+) *(-?[0-9.]+) *(-?[0-9.]+) *(-?[0-9.]+)(.*$)sV^REMARK +350 +BIOMT[1-3] *(\d+) +(-?[0-9.]+) +(-?[0-9.]+) +(-?[0-9.]+) +(-?[0-9.]+) *$tAtomcBs>eZdZdddddZdZdZdZRS(s;This object represents information concerning a single atomtXicCs|dkr|jd|_t|jd|_|jd|_|jdj|_|jd|_t|jd|_ t |jd|_ t |jd|_ t |jd |_ t|j |j |j g|_d|_d|_|jd |_n|dkr||_||_|\|_ |_ |_ ||_d |_d |_ d |_d|_d|_d|_d|_nt|j|_d|_d|_g|_dS(s8Fill in information using a match object from a pdb fileiiiiiiiii i tSSNiRs CtHETATMN(tNonetgroupttypetinttnumtnametstriptrestchaintresnumtfloattxtytztarraytcoordst occupancytbfactorttailtchainobjtresobjtconect(tselftpdbmatchRR R ((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyt__init__s< !               cCs d|j|j|j|jfS(Ns(R R RR (R((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyt__repr__4scCs|jdks|jdkrd|jjd|j|jjd|j|j|j |j d|j d|j d|j f }npd|jjd|j|jjd|j|j|j |j d|j d|j d|j|j|j f }|S( s+Get the pdb line corresponding to this atoms%%s%5d %s%3s%2s%4d%12.3f%8.3f%8.3f%s iiiiis/%s%5d %s%3s%2s%4d%12.3f%8.3f%8.3f%6.2f%6.2f%s N( RRRRtljustR R R R RRR(Rtline((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pytpdbline7s6.67cCs@d|j}x"|jD]}|d|j7}qW|d7}|S(sGet a CONECT line for this atoms CONECT%5ds%5ds (R R(Rtstrta((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pytconlineEs   N(t__name__t __module__t__doc__RRRR!R$(((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyR s %  tResiduecBs/eZdZddZdZddZRS(sResidue or nucleotide objectcCsp|dkr3g|_d|_d|_d|_n9||_|dj|_|dj|_|dj|_dS(Ni(RtatomsR R R RR (RR)((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyRPs      cCsd|j|jfS(Ns(R R (R((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyR\sicCss|rHtj|}xW|jD]"}|j|jdkr|SqWn'x$|jD]}|j|krR|SqRWdS(sReturn the first atom with the given name found in the residue. If regexp is true, then get the atom whose name matches the regular expressionN(tretcompileR)tsearchR R(RR tregexptrNR#((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyt getAtomByName_s N(R%R&R'RRRR/(((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyR(Ns tChaincBs,eZdZddZdZdZRS(s Chain objectcCsA|dkr!g|_d|_n||_|jdj|_dS(Ni(RtresiduesR R (RR1((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyRos     cCs d|jS(Ns (R (R((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyRvscCsg|_|dj|_d}x|D]}|j|jkr]td|j|jfn| sv|j|jkr|r|jj|nt}|j|_|j|_|j|_|g|_ d}q&|j j|q&W|jj|dS(Nis3Atmlist does not all have the same chain name %s %si( R1R R t ValueErrorRR tappendR(R R)(RtatmlisttstartR#R ((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyt fromAtomListys$       N(R%R&R'RRRR6(((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyR0ms  tBasePaircBs#eZdZddZdZRS(s=DNA base pair object. Contains 2 residues and a list of atomscCsg|_|dkr!g|_n-||_x!|D]}|jj|jq1Wt|jdkrt|jdkrdGHndS(Niis9WARNING: creating base-pair with neither 0 nor 2 residues(R)RR1textendtlen(RR1tr((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyRs     *cCs"d|jdj|jdjfS(Nsii(R1R (R((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyRsN(R%R&R'RRR(((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyR7s cCs|jddkr&|jddkp |jddkrL|jddkp |jddkrr|jddkp |jddkr|jddkp |jdkr|jdkp |jdkr|jdkp |jdkr|jd kp |jd ko |jdkS( s5Check if two DNA/RNA residues make a correct basepairitAtTtGtCtTHYtADNtCYTtGUA(R (tr1tr2((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pytgoodPairs&&&&t StructurecBseZdZddZdZdZdZdZdZ dZ dZ d Z d d d Z d Zd dZdZd dZdZRS(s8Class containing an molecule or multi-molecule structurecCs*|j|dkr&|j|ndS(N(tinitvarsRtstructFromFile(Rtinfile((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyRs  cCs`xYtt|jD]B}|d|j|_x%|j|jD]}|d|_qAWqWdS(sRenumber the residuesiN(trangeR9R1R R)R(RtcR#((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pytrenumResscCs#g|_i}x|jD]}|j|jkrh||jjj|||jjj|jnat||j<|jj||j|j||j_|g||j_|j||j_x|jD]}|j|_qWqWg|_g|jD]}|jj|j^qdS(N( tchainsR1R tkeysR3R)R8R0R (Rt chainnamesR:R#((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pytresetFromResiduess  cCsg|_g|_x|jD]}|jj|jx=|jD]2}|j|_x|jD]}|j|_q[Wq?Wg|jD]}|jj|j^qqWdS(Ni(R1R)RMR8R R (RRKR:R#((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pytresetFromChainss  -cCstg|jD]}|j^q }t|dd}tj|\}}t| }||}|dd|f}tt|dddf|dddf|dddf}|dkrdddg}|dd|f}n||fS(sPerform a principal component analysis on the atom coordinates. Returns eigenvals and eigenvecs. Sorted from largest to smallest eigenvaluetrowvariNii( RR)Rtcovtlinalgteigtargsorttdottcross(RR#tMtcovmattevaltevectindtcheck((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pytPCAs%  H cCsAt|j}x+|jD] }t|j|d|_qWdS(s4Rotate entire structure by the given rotation matrixiN(tmatrixR<R)RR(RRYtrotmatR#((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pytrotateMscCs+x$|jD]}|j|kr |Sq WdS(N(R)R R(RR R#((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyt atomByBumscCs+x$|jD]}|j|kr |Sq WdS(N(RMR (RR RK((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyt chainByName scCs:g|_g|_g|_g|_g|_g|_dS(sInitialize various variablesN(t startlinestendlinesRMR1R)t transforms(R((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyRGs      iic Cs|rt|d}nt|d}|jd|x|jD]}|j|qBWt|jdkrg|jD]}|j|j^qxnxL|jD]A}x8|jD]-}x$|jD]}|j|jqWqWqWg|jD]*}|jdkr|j|j^qg|jD]0}t|j dkr+|j|j ^q+x|j D]}|j|qiW|jd|j dS(NR#twsMODEL %4d isENDMDL (topentwriteReR9RMR)R!R1RRRR$Rftclose( RtoutfileR3tidenttOFtlR#RKR:((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyt outputPDB!s$,8> cCst|}|j}|jg|_d}x|D]}tj|}|dkr6t|jd}gt ddD]}t |j|^q~} t |jd} |t |jkr|jj | g| ggn8|j|ddj | |j|ddj | |j j |q8ntj|}|dkr\|sj|j j |q8|d dkr|| _q8|d dkrF|jt|dd !} | dkrd Gt|dd !GHqVx|t d D][} |d d| d d| !}y#| jj |jt|Wqtk r>PqXqWq8|jj |q8nt|}|st|g}t|g} |jj ||jj | d}n|j|jd jkrSt|g}|jj ||j|jd jkr@t|g} |jjdkrP|jj | qPqc| jj |n|jj ||jj ||jjdkr| |_n||_g|_x9|jD].}t|d|dcCs:|jdd}x!|jD]}|j||_qWdS(s'Move entire structure to shift COM to 0RiN(RR)R(RRR#((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pytrecentersN(R%R&R'RRRLRPRQR_RbRcRdRGRpRHRRyRR(((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyRFs          % Q   cCs%t}dg|_dg|_|S(syMake a barebones structure with nothing in it, but containing appropriate start/end stuff so that it can be output to pdbsHEADER structure sEND (RFReRf(tstruct((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pytmakeBareStructs   ( R*tnumpyR+RwRuRR(R0R7RERFR(((sN/home/lenafabr/Stanford/Spakowitz/proj/shearableWLC/public/scripts/pdbutils.pyts   A'