ó Z÷ Ic@sžddlZddlZdZd„Zd„Zd„ZeZd„Zd„Zd„Z d „Z d dd „ƒYZ e d kršdd l mZe dddƒZe dddƒZe dddƒZe dddƒZejƒeGHe eeeƒGHe eeeeƒZedks!t‚dGeGHeeeƒZeeeƒZeGHejeƒGHejeƒGHejejeƒƒGHeeGHedGHedGHeeGHedGHedGHeeGHedGHedGHeeGHedGHedGHejƒGHejƒGHded>> m=rotaxis(pi, Vector(1,0,0)) >>> rotated_vector=any_vector.left_multiply(m) @type theta: float @param theta: the rotation angle @type vector: L{Vector} @param vector: the rotation axis @return: The rotation matrix, a 3x3 Numeric array. iiii(ii(ii(ii(ii(ii(ii(ii(ii(ii(ii(tcopyRRRtsint get_arraytzeros( tthetatvectortctsR R R Rtrot((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Vector.pyt rotaxis2mIs"   cCs–|jƒ|jƒ||jƒdkr7tjdƒS||}|jƒ|jƒ}d|_tjdƒ}|dtj|tj|ƒƒ}|S(s  Return a (left multiplying) matrix that mirrors p onto q. Example: >>> mirror=refmat(p,q) >>> qq=p.left_multiply(mirror) >>> print q, qq # q and qq should be the same @type p,q: L{Vector} @return: The mirror operation, a 3x3 Numeric array. gñh㈵øä>iii(ii(RRRtidentityRtshapetdott transpose(tptqtpqtbtitref((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Vector.pytrefmatss       #cCs*tjt|| ƒt|| ƒƒ}|S(sL Return a (left multiplying) matrix that rotates p onto q. Example: >>> r=rotmat(p,q) >>> print q, p.left_multiply(r) @param p: moving vector @type p: L{Vector} @param q: fixed vector @type q: L{Vector} @return: rotation matrix that rotates p onto q @rtype: 3x3 Numeric array (RR'R/(R)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/Vector.pytrotmat‹s&cCs!||}||}|j|ƒS(sÜ Calculate the angle between 3 vectors representing 3 connected points. @param v1, v2, v3: the tree points that define the angle @type v1, v2, v3: L{Vector} @return: angle @rtype: float (R (tv1tv2tv3((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Vector.pyt calc_angleŸs  c Cs†||}||}||}||}||}||} |j|ƒ} y#|j| ƒdkrm| } nWntk rnX| S(së Calculate the dihedral angle between 4 vectors representing 4 connected points. The angle is in ]-pi, pi]. @param v1, v2, v3, v4: the four points that define the dihedral angle @type v1, v2, v3, v4: L{Vector} gü©ñÒMbP?(R tZeroDivisionError( R1R2R3tv4tabtcbtdbtutvtwR ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Vector.pyt calc_dihedral®s       RcBs¿eZdZddd„Zd„Zd„Zd„Zd„Zd„Z d„Z d„Z d „Z d „Z d „Zd „Zd „Zd„Zd„Zd„Zd„Zd„Zd„ZRS(s 3D vectorcCsm|dkrK|dkrKt|ƒdkr3d‚ntj|dƒ|_ntj|||fdƒ|_dS(Nis0Vector: x is not a list/tuple/array of 3 numberstd(tNonetlenRtarrayt_ar(tselfR 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/Vector.pyt__init__Ês  cCs#|j\}}}d|||fS(Ns(RB(RCR 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/Vector.pyt__repr__ÔscCs|j }t|ƒS(sReturn Vector(-x, -y, -z)(RBR(RCta((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Vector.pyt__neg__Øs cCsBt|tƒr"|j|j}n|jtj|ƒ}t|ƒS(s$Return Vector+other Vector or scalar(t isinstanceRRBRRA(RCtotherRF((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Vector.pyt__add__ÝscCsBt|tƒr"|j|j}n|jtj|ƒ}t|ƒS(s$Return Vector-other Vector or scalar(RHRRBRRA(RCRIRF((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Vector.pyt__sub__åscCst|j|jƒS(s"Return Vector.Vector (dot product)(tsumRB(RCRI((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Vector.pyt__mul__íscCs |jtj|ƒ}t|ƒS(sReturn Vector(coords/a)(RBRRAR(RCR RF((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Vector.pyt__div__ñsc Csït|tƒrË|j\}}}|j\}}}tjjtj||f||ffƒƒ}tjjtj||f||ffƒƒ } tjjtj||f||ffƒƒ} t|| | ƒS|jtj|ƒ}t|ƒSdS(s5Return VectorxVector (cross product) or VectorxscalarN(RHRRBRtlinalgtdetRA( RCRIRFR,R!R>tetftc1tc2tc3((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Vector.pyt__pow__ös-.-cCs |j|S(N(RB(RCR-((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Vector.pyt __getitem__scCs||j|sp   +  (    p