ó ¾÷ Ic@sQddlmZmZmZmZddlmZmZdd!d„ƒYZe dkrMedddgd d d gd d dgdddggdƒZ edddgdddgdddgdddggdƒZ eƒZ e j e e ƒe jƒe jƒZe jƒ\ZZee eƒeZe jƒZeGHHeGHHdeGHnd S("iÿÿÿÿ(tdott transposetsqrttarray(tsvdtdettSVDSuperimposercBs_eZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z RS( s® SVDSuperimposer finds the best rotation and translation to put two point sets on top of each other (minimizing the RMSD). This is eg. useful to superimpose crystal structures. SVD stands for Singular Value Decomposition, which is used to calculate the superposition. Reference: Matrix computations, 2nd ed. Golub, G. & Van Loan, CF., The Johns Hopkins University Press, Baltimore, 1989 cCs|jƒdS(N(t_clear(tself((s–/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/SVDSuperimposer.pyt__init__scCsCd|_d|_d|_d|_d|_d|_d|_dS(N(tNonetreference_coordstcoordsttransformed_coordstrotttrantrmstinit_rms(R((s–/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/SVDSuperimposer.pyRs      cCs5||}|jd}ttt||ƒƒ|ƒS(s2Return rms deviations between coords1 and coords2.i(tshapeRtsum(Rtcoords1tcoords2tdifftl((s–/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/SVDSuperimposer.pyt_rms%s  cCs|jƒ||_||_|j}|j}||ks_|d|dkoYdkn rntdƒ‚n|d|_dS(s  Set the coordinates to be superimposed. coords will be put on top of reference_coords. o reference_coords: an NxDIM array o coords: an NxDIM array DIM is the dimension of the points, N is the number of points to be superimposed. iis%Coordinate number/dimension mismatch.iN(RR R Rt Exceptiontn(RR R Rtm((s–/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/SVDSuperimposer.pytset-s     1c Cs/|jdks|jdkr-tdƒ‚n|j}|j}t|ƒ|j}t|ƒ|j}||}||}tt|ƒ|ƒ}t|ƒ\}}}ttt|ƒt|ƒƒƒ|_ t |j ƒdkr|d |ds."o