ó Q™xTc @ smddlmZddlmZddlmZddlmZddlmZddlZddlmZddl m Z dd l m Z ddl Z d d ed d d d d d fd d„Zd d ed„Zd„Zdeeedd„Zdeeeddd„Zdedd„Zddddgd„Zdejfd„ƒYZdefd„ƒYZdS( iÿÿÿÿ(tdivision(tsgtbx(tcrystal(tadptbx(txrayN(teltbx(tflex(tadopt_init_argsg333333Ó?ggð¿g…ëQ¸þ‡ÃÀcC sÈg}xP|D]H}tjƒ||}|j|ƒ|dkrO|jdks t‚q W|} | dj} | dj} | dj} |} |d| d_| djjdtdtƒ|d | d _| d jjdtdtƒ|d | d _| d jjdtdtƒ|d | d _| d jjdtdtƒ|| d _| d jjdtdtƒ|| d _| d jjdtdtƒ|d| d_| | d_| djjdtdtƒ|d| d_| | d_| djjdtdtƒ|| d_| | d_| djjdtdtƒ|dkr‚|d | d _| d jjdtdtƒ|d | d _| d jjdtdtƒ|d | d _| d jjdtdtƒ|d | d _| d jjdtdtƒ|d| d_| | d_| djjdtdtƒ|d| d_| | d_| djjdtdtƒnB|dkrÄ|d | d _| d jjdtdtƒ|d | d _| d jjdtdtƒ|| d _| d jjdtdtƒ|d| d_| | d_| djjdtdtƒ|d| d_| | d_| djjdtdtƒ|| d_| | d_| djjdtdtƒndS(Nggð¿iiiitisotanisoiiiiitu_isotu_star(gð¿gð¿gð¿gð¿gð¿gð¿( trandomtappendR tAssertionErrorR tflagst set_use_utTruetFalse(t scattererstrandom_u_iso_scaletrandom_u_iso_mintparameter_namet neg_u_anisot neg_u_isotu_isost scattererR tsctus6tus7tus8tnv((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pytrandom_modify_adp_and_adp_flags s|  %                   c C sÔxÍ|D]Å}tjƒ||}||_|jdkrH|jdksNt‚|rðtjƒ} | dkr®|jjtƒ|dkr›|jjtƒqí|jj|ƒq|dkrÍ|jjtƒn|jj|ƒ|jjtƒn |jj|ƒ|jj|ƒ|jj ƒsFtjƒ} | dkrFd|_qFn|jj ƒs|tjƒ} | dkr|d|_q|n|jj ƒ r|jj ƒ rtjƒ} | dkrÌd|_d |_qÌqqWdS( Nggð¿gà?R R g$À(gð¿gð¿gð¿gð¿gð¿gð¿(g$Àg$Àg$Àg$Àg$Àg$À(g$Àg$Àg$Àg$Àg$Àg$À( R R R RRt set_use_u_isoRtset_use_u_anisoRt use_u_anisot use_u_iso( RR$R#t allow_mixRRRRR tchoice((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pyt!random_modify_adp_and_adp_flags_2Qs<  $            cC s7x0|D](}tj||ƒjƒ|krtSqWtS(N(Rtmin_sym_equiv_distance_infotdistRR(texisting_sitestsym_equiv_sites_of_other_sitetmin_hetero_distancet existing_site((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pythave_suitable_hetero_distance{s   gø?idcC srxkt|ƒD]]}|dkrCtjƒtjƒtjƒf}n,g|D]} tj| ƒt| ƒ^qJ}|j|ƒ} |r—| jƒ r—q ntj| ƒ} t || |ƒs¾q n| j ƒ}|dkrÚ|Sgt ||ƒD]\} } | | ^qê}|j|ƒ}|r/|jƒ r/q ntj|ƒ}t ||g||ƒs]q n||j ƒfSWdS(N( txrangetNoneR t randrangetfloatt site_symmetrytis_point_group_1Rtsym_equiv_sitesR.t exact_sitetzip(tspecial_position_settingsR*R,tgeneral_position_onlytgridtt_centre_of_inversiont max_trialsttrialtsitetgR3R5txtttsite_invtsite_symmetry_invtsym_equiv_sites_inv((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pyt random_site…s2 $,  -  c  C sî|} |dk r5|ddks(t‚| d} nx©t|ƒD]›} |} xkt| ƒD]]} t|| |||||ƒ} | dkrPn|dkr¬| j| ƒq\| j| ƒq\Wt| ƒt|ƒ|krB| SqBWtd‚dS(Niis+Cannot find sites matching all constraints.(R0RR/RER textendtlent RuntimeError(R8R*tn_newR,tgeneral_positions_onlyR:R;R<tmax_back_tracktn_loopt i_back_trackt all_sitesti_newR>((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pyt random_sites§s,      icC s5|j|ƒ}|jƒdks't‚|jƒ}t|j|ƒƒ}xÝt|ƒD]Ï} |r…|d tj|d|ƒg} n%g|D]} tj| |ƒ^qŒ} |j ƒ|j | ƒ} |dkrö|j || ƒ} | |kröqUqön|j| ƒ}|j ƒ|j ƒkr#qUn| SWt d‚dS(Ngñh㈵øä>iisCannot find suitable site.( R3tdistance_movedRt unit_celltlistt orthogonalizeR/R tgausst special_opt fractionalizetdistanceRH(R8R>t gauss_sigmat max_distancet vary_z_onlyR<R3RRt site_cartR=tmodified_site_cartR@t modified_siteRXtmodified_site_symmetry((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pytrandom_modify_siteÈs* %    tOtMgtSitCacC s,tjd|dtjd|ƒt|ƒƒS(Ntsequencet permutationtsize(Rtselectt random_size_tRG(Rgtchoices((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pytrandom_elementsâs txray_structurecB s¼eZdddddddddeddddedddeededd„Zdddd„Zdedd „Zd „Zddd „Z d„Z d„Z d„Z ded„Z RS(gI@gø?ig333333ã?g333333Ó?gš™™™™™¹?c C s/t|tƒddƒ|dkrX|dkrCtjddƒ}qjtjd|ƒ}n|dksjt‚||_|dk r»|jdk s”t‚|jdks©t‚t |ƒ|_n|jdk rp|jdkr+|jdk sît‚|jd krd g|j|_qmt d |jƒ|_qp|jdkrOt |jƒ|_qpt |jƒ|jkspt‚n|dkr¥|j |j||j ƒj ƒƒ}ntjd|d|ƒ}| dkrÒ|} ntj|d| d d dtƒ}tjj||ƒ|jdk r+|j|j|ƒndS(sø Initialise the random xray_structure class. :param space_group_info: a space group descriptor :type space_group_info: sgtbx.space_group_info :param space_group_symbol: international space group symbol or number :type space_group_symbol: string or integer :param unit_cell: the cell parameters of the random structure :type unit_cell: uctbx.unit_cell or tuple(a, b, c, alpha, beta, gamma) :param elements: A list of elements to use. Example: "['Si', 'Si', 'O', 'Al']" If elements='const' then ???. If elements='random' then random scatterers will be used. :type elements: list(strings) :param sites_frac: a list of the fractional coordinates for all scatterers :type sites_frac: scitbx.array_family.flex.vec3_double :param n_scatterers: number of scatterers :type n_scatterers: integer :param volume_per_atom: the volume an atom should occupy in cubic angstroms :type volume_per_atom: float :param min_distance: minimal distance between atoms :type min_distance: float :param min_distance_sym_equiv: minimal distance between symmetrical equivalent atoms :type min_distance_sym_equiv: float :param general_positions_only: if 'True' atoms will be placed on general positions only :type general_positions_only: boolean :param random_f_prime_d_min: ??? :type random_f_prime_d_min: float :param random_f_prime_scale: ??? :type random_f_prime_scale: float :param random_f_double_prime: ??? :type random_f_double_prime: float :param random_f_double_prime_scale: ??? :type random_f_double_prime_scale: float :param random_u_iso: if 'True' the isotropic temperature factors of all atoms will be randomised :type random_u_iso: boolean :param random_u_iso_min: minimum value of u_iso for random u values :type random_u_iso: float :param random_u_iso_scale: ??? :type random_u_iso_scale: float :param u_iso: a fixed value of u_iso to apply to all atoms :type u_iso: float :param use_u_iso: if 'True' the atoms will have isotropic temperature factors :type use_u_iso: boolean :param use_u_aniso: if 'True' the atoms will have anisotropic temperature factors :type use_u_aniso: boolean :param random_u_cart_scale: ??? :type random_u_cart_scale: float :param random_occupancy: if 'True' the atom sites will have a random occupancy :type random_occupancy: boolean :param random_occupancy_min: minimal occupancy for a site :type random_occupancy_min: float texcludetspace_group_infoRRtmin_distance_sym_equivt sites_fracR$tsymbolsP 1tconstR Rgtu_star_toleranceitassert_min_distance_sym_equivN(sspace_group_infos unit_cellsmin_distance_sym_equivs sites_fracs use_u_iso(Rrsrandom(RtlocalsR0RRnRt use_u_iso_telementst n_scatterersRGRktany_compatible_unit_celltgrouptorder_zRtsymmetryR8RRt structuret__init__tbuild_scatterers(tselfRntspace_group_symbolRRRwRpRxtvolume_per_atomt min_distanceRoRJtrandom_f_prime_d_mintrandom_f_prime_scaletrandom_f_double_primetrandom_f_double_prime_scalet random_u_isoRRR R$R#trandom_u_cart_scaletrandom_occupancytrandom_occupancy_mintcrystal_symmetryR8((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pyR~ésRO    ! #     cC s…g|jƒD]}|j^q }|dkrptd|d|dt|ƒd|jd|jd|d|ƒ}n.t|ƒt|ƒksŽt‚|t|ƒ}t|ƒ|j ks¹t‚i}x6|D].} |j | ƒsÆt j j | ƒ|| gð?iidtu_scalegü©ñÒMbP?(5RR>R0RPRGRƒRJRRSRxthas_keyRtxray_scatteringtbest_approximationRgR7RRtstrtapply_symmetryRRt space_groupRoR„t at_d_star_sqR R…R†R‡tfptfdpRvRtset_use_u_iso_onlyR RˆRRR#tset_use_u_aniso_onlyRt random_u_cartR‰taverage_u_startu_cart_as_u_starR tu_star_as_u_cartt eigenvaluestminRŠR‹t occupancyt add_scatterer(R€RwRpR:R;RR*RNtsf_dicttelementR—R˜t n_existingti_labelR>R3tf0R trun_away_countertu_cartRŸ((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pyRis‚"                          idcC st||||||ƒS(N(R`(R€R>RYRZR[R<((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pyR`±scC stdtj||ƒƒS(Ngš™™™™™¹?(tmaxR RU(R€R RY((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pytrandom_modify_u_iso¸sgð?ic C sùxét|ƒD]Û}g}xtt|ƒƒD]{}||}||} tj||ƒ} | ||| kry|| } n!|| || krš|| } n|j| ƒq,Wtj|jƒ|ƒ} tj| ƒ} t | ƒdkr |Sq Wt d‚dS(Ngü©ñÒMbP?sCannot find suitable u_star.( R/RGR RUR RRžRRRŸR RH( R€R RYtmax_relative_differenceR<R=tmodified_u_startitutmax_difft modified_uR©RŸ((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pytrandom_modify_u_star»s     cC s#td|ttjd|ƒƒƒS(Ngš™™™™™¹?i(RªtabsR RU(R€R¡RY((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pytrandom_modify_occupancyÏscC s+|dkst‚tdtj||ƒƒS(Nigš™™™™™¹¿(RR R RU(R€R—RY((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pytrandom_modify_fpÒscC s+|dkst‚tdtj||ƒƒS(Nigš™™™™™¹?(RRªR RU(R€R˜RY((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pytrandom_modify_fdpÖscC s;|jƒ}x(|jƒD]}|dkrL|j|j|d|ƒ|_q|dkr‚|jjƒr‚|j|j|ƒ|_q|dkr¸|jjƒr¸|j |j |ƒ|_ q|dkrß|j |j |ƒ|_ q|dkr|j |j|ƒ|_q|dkr-|j|j|ƒ|_qt‚qW|S(NR>R[R R R¡R—R˜(tdeep_copy_scatterersRR`R>RR$R«R R#R²R R´R¡RµR—R¶R˜RH(R€RRYR[tmodified_structureR((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pytrandom_modify_parametersÚs"      NgUUUUUUÕ?(t__name__t __module__R0RRR~RR`R«R²R´RµR¶R¹(((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pyRlçsJ k E      twyckoff_pair_generatorcB s)eZdddddd„Zd„ZRS(ièiRri cC s\t|tƒƒtjdtjd|jd|ƒd|ƒd|ƒ|_|jƒ|_dS(NRŒRRtvolumeRnRo(RRuRR8R|Ryt wyckoff_table(R€Rntunit_cell_volumeRotmin_cross_distanceRŽtmax_trials_per_position((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pyR~õs      c c sCx<t|jjƒƒD]%}|jjd|jd|ƒ}tj|ƒ}xït|jjƒƒD]Ø}xÏt|jƒD]¾}|jjd|jd|ƒjƒ}tj ||ƒ}|j ƒ|j krut j d|jdtjg|jƒ|gD]!}t jd|jd|ƒ^qñƒƒ} | |j ƒfVPququWq_WqWdS(NR8t i_positionRRŽR>(R/R¾Rgtrandom_site_symmetryR8RR5RÁR6R(R)RÀRR}Rtxray_scattererRRŽ( R€RÂtsite_symmetry_it equiv_sites_it j_positiontn_trialtsite_jt dist_infoR>R}((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pytloops&       =(RºR»R~RË(((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pyR¼ós  (t __future__RtcctbxRRRRtcctbx.eltbx.xray_scatteringRtcctbx.array_familyRtlibtbxRR R0R R'R.RRERPR`RkR}RltobjectR¼(((sP/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/development/random_structure.pytsH   E #    ÿ