ó Ì™xTc @ s›dZddlmZddlmZddlmZmZddlm Z d„Z dd„Z dd „Z dd „Z dd „Zdd „Zd d„Zd d„Zd d„Zd d„Zede fde fde fdefdefdefdefdefdefg ƒZd„Zd„Zd„Zd„Zd„Zd „Zd!„Zd"„Zd#„Zd$„Zd%„Zd&„Z d'„Z!d(„Z"d)„Z#d*„Z$d+„Z%d,„Z&d-„Z'd.„Z(d/„Z)d0„Z*d1„Z+d2„Z,d3„Z-d4„Z.d5„Z/d6„Z0ed7d8e0d fd9ed fgfd:d;ed fd<edfd=ed fd>e/d fgfd?d@ed fdAed fdBe!d fgfdCdDed fde d fdEe"d fdFe$e%e&gd fgfdGdHe#d fdIe'd fgfdJdKe(d fdLe)e*e+gd fgfdMdNe.d fgfgƒZ1ge1j2ƒD]Z3e3D]Z4e4dO^qfq\Z5dP„Z6e7dQdR„Z8dSS(Ts This module provides tools for examining a set of vectors and find the geometry that best fits from a set of built in shapes. iÿÿÿÿ(tdivision(tcol(t OrderedDicttIterable(tsqrtc C sPgt|ƒD]?\}}||dD]$}|||j|dtƒf^q%q S(s¼ Creates a list of angles (In degrees) between all two-element combinations in vectors. Parameters ---------- vectors : scitbx.matrix.col Returns ------- list of float itdeg(t enumeratetangletTrue(tvectorstindextv1tv2((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt _bond_angles sicC s~t|ƒdks$t|ƒdkr(dSt|ƒ}ttd„|Dƒƒt|ƒƒ}||krz|dt|ƒfSdS(sê Tetrahedrons have four vertices, with angles between all pairs of vertices uniformly about 104.5 degrees. Parameters ---------- vectors : list scitbx.matrix.col dev_cutoff : float, optional Returns ------- bool iiNcs s'|]}t|ddƒdVqdS(ig Z@N(tabs(t.0ti((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys 2s(tlenR Rtsum(R t dev_cutofftanglest deviation((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_is_tetrahedrons $ & cC s˜t|ƒdkrdSt|ƒ}g}x#|D]}|j|ddƒq/Wttd„|Dƒƒt|ƒƒ}||kr”|dt|ƒfSdS(s$ Triangular planar geometry has three vertices (By definition all on the same equatorial plane). The expected angles are 120 degrees between neighboring vertices. Parameters ---------- vectors : list scitbx.matrix.col dev_cutoff : float, optional Returns ------- bool iNiixcs s|]}|dVqdS(iN((RR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys Os(RR tappendRR(R RRta_120sRR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_is_trigonal_plane7s  & cC s.t|ƒdkrdSt|ƒ}g}g}xc|D][}t|ddƒt|ddƒkr{|j|ddƒq5|j|ddƒq5Wt|ƒdksÜt|ƒdksÜt|ƒdksÜt|ƒdkràdSttd„||Dƒƒt|ƒƒ}||kr*|dt|ƒfSdS(sH Square planar geometry has four vertices, all on the same equatorial plane. The expected angles are 90 degrees between neighboring vertices and 180 degrees between vertices across from one another. Parameters ---------- vectors : list scitbx.matrix.col dev_cutoff : float, optional Returns ------- bool iNiiZi´ics s|]}|dVqdS(iN((RR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys xs(RR RRRR(R RRta_90sta_180sRR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_is_square_planeTs  (H* cC s t|ƒdkrdSt|ƒ}gg}}xc|D][}t|ddƒt|ddƒkr||j|ddƒq6|j|ddƒq6Wt|ƒdks¹t|ƒdkr½dSttd„||Dƒƒt|ƒƒ}||kr|dt|ƒfSdS(s Square bipyramids have five vertices, four on the same equatorial plane with one above. The expected angles are all either 90 degrees or 180 degrees. Parameters ---------- vectors : list scitbx.matrix.col dev_cutoff : float, optional Returns ------- bool iNiiZi´ics s|]}|dVqdS(iN((RR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys šs(RR RRRR(R RRRRRR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_is_square_pyramid}s   ($* cC s/t|ƒdkrdSt|ƒ}gg}}xc|D][}t|ddƒt|ddƒkr||j|ddƒq6|j|ddƒq6Wt|ƒdksÝt|ƒdksÝt|ƒdksÝt|ƒd krádSttd „||Dƒƒt|ƒƒ}||kr+|dt|ƒfSdS( sn Octahedrons have six vertices (Their name comes from their eight faces). The expected angles are all either 90 degrees (Next to each other), or 180 degrees (Across from each other). Another name for this shape is square bipyramidal. Parameters ---------- vectors : list scitbx.matrix.col dev_cutoff : float, optional Returns ------- bool iNiÿÿÿÿiZi´iiii cs s|]}|dVqdS(iN((RR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys ¿s(RR RRRR(R RRRRRR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_is_octahedronŸs   (H* icC s/t|ƒdkrdSt|ƒ}gg}}xc|D][}t|ddƒt|ddƒkr||j|ddƒq6|j|ddƒq6Wt|ƒdksÝt|ƒdksÝt|ƒdksÝt|ƒdkrádSttd„||Dƒƒt|ƒƒ}||kr+|dt|ƒfSdS(sR Trigional pyramids have four vertices. Three vertices form a plane with angles of 120 degrees between each pair. The last vertex resides axial to the plane, at 90 degrees from all of the equatorial vertices. Parameters ---------- vectors : list scitbx.matrix.col dev_cutoff : float, optional Returns ------- bool iNiiZixcs s|]}|dVqdS(iN((RR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys âs(RR RRRR(R RRRRRR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_is_trigonal_pyramidÄs   (H* cC s‰t|ƒdks$t|ƒdkr(dSt|ƒ}t|dd„ƒ\}}}|dkrbdSg}g}x|D]w\}} } |||gk| ||gkkr¸|| f7}qu|||gkru| ||gkru|| f7}ququW|dg} | g|D]} | d^q7} | g|D]} | d ^q(7} ttd „| Dƒƒt| ƒƒ} | |kr…| dt|ƒfSdS( sj Trigonal bipyramids have five vertices. Three vertices form a plane in the middle and the angles between all three are 120 degrees. The two other vertices reside axial to the plane, at 90 degrees from all the equatorial vertices. Parameters ---------- vectors : list scitbx.matrix.col dev_cutoff : float, optional Returns ------- bool iiNtkeycS st|dƒS(Niÿÿÿÿ(R(tx((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pytýsi–i´iZixcs s|]}|dVqdS(iN((RR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys s(RR tmaxRR(R RRtax1tax2t axial_angletbase_to_axialstequatorial_anglesR R RtdeviantsRR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_is_trigonal_bipyramidçs&$  $$ !!& cC s–t|ƒdks$t|ƒdkr(dSt|ƒ}g}xâ|D]Ú}g}x9|D]1}||krT|j|j|dtƒƒqTqTWtg|D]"}t|dƒdkr“|^q“ƒ}tg|D]"}t|dƒdkrÈ|^qȃ} |dkrA| d krA|j|ƒqAqAWt|ƒd kr5dS|\} } | j| dtƒ} g} g}x|D]w\}}}|| | gk|| | gkkr¬| |f7} qi|| | gkri|| | gkri||f7}qiqiW| dg}|g| D]}|d^qû7}|g|D])}tt|d ƒt|d ƒƒ^q7}ttd „|Dƒƒt|ƒƒ}||kr’|dt|ƒfSdS(sh Pentagonal bipyramids have seven vertices. Five vertices form a plane in the middle and the angles between all five are 72 degrees. The two other vertices reside axial to the plane, at 90 degrees from all the equatorial vertices. Parameters ---------- vectors : list scitbx.matrix.col dev_cutoff : float, optional Returns ------- bool iiNRi´iiZiiiiHics s|]}|dVqdS(iN((RR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys Ms( RR RRRRtminRR(R RRtaxialsR tv_anglesR RRRR$R%R&R'R(RR)R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_is_pentagonal_bipyramids<$    #55 $$ !:& cC s t|ƒdkrdSt|ƒ}gg}}xc|D][}t|ddƒt|ddƒkr||j|ddƒq6|j|ddƒq6Wt|ƒdkr½t|ƒdkr½dSttd„||Dƒƒt|ƒƒ}||kr|dt|ƒfSdS(s Triangular prisms are defined by 3 vertices in a triangular pattern on two aligned planes. Unfortunately, the angles are dependent on the length and width of the prism. Need more examples to come up with a better way of detecting this shape. For now, this code is experimental. Parameters ---------- vectors : list scitbx.matrix.col dev_cutoff : float, optional Returns ------- bool iNiÿÿÿÿiUi‡i cs s|]}|dVqdS(iN((RR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys ss(RR RRRR(R RRta_85sta_135sRR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_is_trigonal_prismRs   ($* t tetrahedralttrigonal_planart square_planartsquare_pyramidalt octahedralttrigonal_pyramidalttrigonal_bipyramidaltpentagonal_bipyramidalttrigonal_prismcG sXg}xK|D]C}t|tƒrCx+|D]}|j|ƒq)Wq |j|ƒq W|S(s² Reduces a list of a mixture of elements and lists down to a single list. Parameters ---------- args : tuple of (object or list of object) Returns ------- list (t isinstancetlistR(targstlsttargtelem((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt _concatenate„s   cC sLtdddgƒtdddgƒtdddgƒtdddgƒgS(s3 Returns ------- list of scitbx.matrix.col iiÿÿÿÿ(R(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt _tetrahedron™scC s ttƒƒS(s3 Returns ------- list of scitbx.matrix.col (t _bipyramidt _square_plane(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt _octahedron¦scC sOtdddgƒttdƒ dddgƒttdƒdddgƒgS(s3 Returns ------- list of scitbx.matrix.col iiiiiÿÿÿÿgà¿gà¿(RR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_trigonal_plane®scC sLtdddgƒtdddgƒtdddgƒtdddgƒgS(s3 Returns ------- list of scitbx.matrix.col iiiÿÿÿÿ(R(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyRDºscC st|tdddgƒƒS(s3 Returns ------- list of scitbx.matrix.col ii(RAR(tbase((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_pyramidÇscC s.t|tdddgƒtdddgƒƒS(s3 Returns ------- list of scitbx.matrix.col iiiÿÿÿÿ(RAR(RG((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyRCÏscC s ttƒƒS(s3 Returns ------- list of scitbx.matrix.col (RHRD(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_square_pyramid×scC s ttƒƒS(s3 Returns ------- list of scitbx.matrix.col (RCRD(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_square_bipyramidßscC s ttƒƒS(s3 Returns ------- list of scitbx.matrix.col (RHRF(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_trigonal_pyramidçscC s ttƒƒS(s3 Returns ------- list of scitbx.matrix.col (RCRF(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_trigonal_bipyramidïsc C s_tgtƒD]}|tdddgƒ^q gtƒD]}|tdddgƒ^q9ƒS(s3 Returns ------- list of scitbx.matrix.col iiiÿÿÿÿ(RARFR(R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_trigonal_prism÷s,cC sÆtdƒdd}tdƒdd}tddtdƒƒd}tddtdƒƒd}tdddgƒt||dgƒt| |dgƒt| | dgƒt|| dgƒgS(s¶ Create a list of vectors in the shape of a planar pentagon. Returns ------- list of scitbx.matrix.col See Also -------- http://mathworld.wolfram.com/Pentagon.html iiii ii(RR(tc_1tc_2ts_1ts_2((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt _pentagons cC s ttƒƒS(s3 Returns ------- list of scitbx.matrix.col (RHRR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_pentagonal_pyramidscC s ttƒƒS(sX Creates a square bipyramid shape. Returns ------- list of scitbx.matrix.col (RCRR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_pentagonal_bipyramid#scC s[ttƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒƒS(sº Creates a square pyramid shape with one vertex replaced with a bidentate coordination group. One vertex is missing in this shape. Returns ------- list of scitbx.matrix.col iiÿÿÿÿ(RARDRR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt _square_pyramid_bidentate_miss_1-s &c C sštdddgƒtdddgƒtdddgƒtdddgƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒgS(sº Creates a square pyramid shape with one vertex replaced with a bidentate coordination group. One vertex is missing in this shape. Returns ------- list of scitbx.matrix.col iiiÿÿÿÿi(RR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt _square_pyramid_bidentate_miss_2<s &c C sštdddgƒtdddgƒtdddgƒtdddgƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒgS(sº Creates a square pyramid shape with one vertex replaced with a bidentate coordination group. One vertex is missing in this shape. Returns ------- list of scitbx.matrix.col iiiÿÿÿÿi(RR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt _square_pyramid_bidentate_miss_3Ns &cC s[ttƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒƒS(s• Creates a square pyramid shape with one vertex replaced with a bidentate coordination group. Returns ------- list of scitbx.matrix.col iiÿÿÿÿ(RARIRR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_square_pyramid_bidentate`s &cC s[ttƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒƒS(s™ Creates a pentagonal pyramid shape with one vertex replaced with a bidentate coordination group. Returns ------- list of scitbx.matrix.col iiÿÿÿÿ(RARSRR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_pentagonal_pyramid_bidentateos &cC s­tttdƒdtdƒddgƒttdƒ dtdƒ ddgƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒtƒd ŒS(sº A planar pentagon with bidentate atoms coordinating directly above and below. One vertex from the plane is missing in this shape. Returns ------- list of scitbx.matrix.col iiiÿÿÿÿ(RARRRR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_pentagonal_bibidentate_miss_1~s &(&(cC s­tttdƒdtdƒddgƒttdƒ dtdƒ ddgƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒtƒdŒS(sº A planar pentagon with bidentate atoms coordinating directly above and below. One vertex from the plane is missing in this shape. Returns ------- list of scitbx.matrix.col iiiÿÿÿÿ(RARRRR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_pentagonal_bibidentate_miss_2s &(&(c C sÈtƒ}tttdƒdtdƒddgƒttdƒ dtdƒ ddgƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒ|d|d|d|dƒS(sº A planar pentagon with bidentate atoms coordinating directly above and below. One vertex from the plane is missing in this shape. Returns ------- list of scitbx.matrix.col iiiÿÿÿÿiii(RRRARR(tpentagon((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_pentagonal_bibidentate_miss_3 s &(&(cC sƒttƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒttdƒ dtdƒ ddgƒƒS(sÈ A planar pentagon with bidentate atoms coordinating directly above and below. One vertex from a bidentate coordinator is missing in this shape. Returns ------- list of scitbx.matrix.col iiiÿÿÿÿ(RARRRR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_pentagonal_bibidentate_miss_4µs &(cC sttƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒttdƒdtdƒddgƒƒS(sÈ A planar pentagon with bidentate atoms coordinating directly above and below. One vertex from a bidentate coordinator is missing in this shape. Returns ------- list of scitbx.matrix.col iiiÿÿÿÿ(RARRRR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_pentagonal_bibidentate_miss_5Ås &(c C s©ttƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒttdƒdtdƒddgƒttdƒ dtdƒ ddgƒƒS(s„ A planar pentagon with bidentate atoms coordinating directly above and below. Returns ------- list of scitbx.matrix.col iiiÿÿÿÿ(RARRRR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_pentagonal_bibidentateÕs &(&cC sLtdddgƒtdddgƒtdddgƒtdddgƒgS(sa An octahedron missing two adjacent points. Returns ------- list of scitbx.matrix.col iiiÿÿÿÿ(R(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_see_sawås cC s:tdddgƒtdddgƒtdddgƒgS(s‰ Better name? Imagine 3 orthogonal vectors pointed in the x, y, and z directions. Returns ------- list of scitbx.matrix.col ii(R(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt _three_legsôs it three_legsttrigonal_planeit tetrahedront square_planettrigonal_pyramidtsee_sawitsquare_pyramidttrigonal_bipyramidR\it octahedrontpentagonal_pyramidtsquare_pyramid_bidentate_missitpentagonal_bipyramidtsquare_pyramid_bidentateitpentagonal_pyramid_bidentatetpentagonal_bibidentate_missi tpentagonal_bibidentateicC s÷t|ƒt|ƒkst‚gt|ƒD]6\}}||dD]}|j|dtƒ^qCq+}gt|ƒD]6\}}||dD]}|j|dtƒ^qŒqt}|jƒ|jƒttd„t||ƒDƒƒt|ƒƒ}|S(sñ Calculates the root mean square of the angle deviation (in degrees) between two lists of vectors. Parameters ---------- vectors_a : list of scitbx.matrix.col vectors_b : list of scitbx.matrix.col Returns ------- float iRcs s#|]\}}||dVqdS(iN((RRtj((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys Hs( RtAssertionErrorRRRtsortRRtzip(t vectors_at vectors_bR tvectvec_otangles_atangles_btangle_deviation((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyt_angles_deviation-s00  g333333@c  sºg}xNt|ƒD]@\}‰t‡fd†||dDƒƒr|jˆƒqqWg‰x3|D]+‰ˆjƒ|krdˆjˆjƒqdqdWg}|rgtˆƒ}|tkr»|Sx}t|D]q\}}} t|tƒrt ‡fd†|Dƒƒ} nt ˆ|ƒƒ} | | krÆ|j|| fƒqÆqÆW|r¶|j dd„ƒ|dg}q¶nOxLt j ƒD]>\}}|ˆƒ} | rt| d} |j|| fƒqtqtW|S(s2 Searches through a list of geometries to find those that fit nearby_atom. Geometries are recognized by generating a list of all combinations of angles between the vectors and comparing them against the angles among the vectors of the ideal geometry. Parameters ---------- nearby_atoms: list of mmtbx.ions.environment.atom_contact A list of atom contacts, indicating the vertices of the shape to be recognized. minimizer_method: bool, optional Optional parameter to use the new, more efficient version of geometry recognition. The old method will be depreciated in later versions of cctbx. cutoff: float, optional A cutoff distance, past which vectors are not included in geometry calculations. Returns ------- list of tuples of str, float A list of found geometries. Each tuple contains the name of the geometry in string form followed by the deviation from ideal angles. See Also -------- mmtbx.ions.geometry.SUPPORTED_GEOMETRY_NAMES, mmtbx.ions.geometry.SUPPORTED_GEOMETRIES_OLD c3 s$|]}ˆj|ƒdkVqdS(gà?N(t distance_from(Rtother(tcontact(sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys ssic3 s!|]}tˆ|ƒƒVqdS(N(R~(RR(tfiltered(sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pys †sR cS s|dS(Niÿÿÿÿ((R!((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyR"Žsi(RtallRtdistancetvectorRtSUPPORTED_GEOMETRIESR;RR+R~RutSUPPORTED_GEOMETRIES_OLDtitems( t nearby_atomstminimizer_methodtcutofftnon_overlappingR t geometriest n_vectorstnametfunct rmsa_cutofftrmsatvalR((RR‚sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pytfind_coordination_geometryMs:$      N(9t__doc__t __future__Rt scitbx.matrixRt collectionsRRtmathRR RRRRRRR*R.R1R‡RARBRERFRDRHRCRIRJRKRLRMRRRSRTRURVRWRXRYRZR[R]R^R_R`RaRbR†tvaluestvalstlst_itSUPPORTED_GEOMETRY_NAMESR~tFalseR”(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/geometry.pyts¬    ) " % # / < &                                          0