B §d;—ã@s‚ddlmZmZmZddlmZddlmZddlmZddlm Z ddlm Z ddl Zddlm Z dd lm Z dd lmZddlZdd lmZddlZdd lmZddlZddlZddlZdd lmZmZmZddlmZddlm Z ddl!m"Z"ddl#m$Z$dd lm Z ddlm%Z&ddlm'Z'ddl(m)Z)ddl(m*Z*Gdd„de+ƒZ,Gdd„de j-ƒZ.Gdd„de+ƒZ/Gdd„de+ƒZ0dS)é)Úabsolute_importÚdivisionÚprint_function)Úext)Ústructure_factors)Úmiller)Úcrystal)ÚsgtbxN)Úadptbx)Úeltbx)Úflex)Úmatrix)Úcount)Ú count_maxÚSorryÚKeep)Ú approx_equal)Ú group_args)Ú is_string)Úneutron_news_1992_table)Ú&format_float_with_standard_uncertainty)Ú covariance)Úrange)Úzipc@seZdZddd„ZdS)Úscattering_type_registry_paramsNcCs||_||_||_||_dS)N)Ú custom_dictÚd_minÚtableÚ'types_without_a_scattering_contribution)Úselfrrrr©r ús/mnt/filia/a/genomebrowser/www/genomebrowser/fleming/tools/molprobity/modules/cctbx_project/cctbx/xray/structure.pyÚ__init__ sz(scattering_type_registry_params.__init__)NNNN)Ú__name__Ú __module__Ú __qualname__r"r r r r!rsrc@sreZdZdZd;dd„Zdd„Zdd „Zd d „Zd d „Zdd„Z e e e e e fdd„Z dd„Z dd„Z ddd„Zd?dd„Zd d!„Zd@d"d#„Zd$d%„ZdAd'd(„ZdBd)d*„ZdCd+d,„ZdDd-d.„ZdEd/d0„ZdFd1d2„ZdGd6d7„ZdHd8d9„Zd:d;„ZdIdd?„Z dKd@dA„Z!dLdBdC„Z"dMdDdE„Z#dNdFdG„Z$dOdHdI„Z%dJdK„Z&dLdM„Z'dNdO„Z(dPdQ„Z)dRdS„Z*dPdTdU„Z+dQdVdW„Z,dRdXdY„Z-dZd[„Z.d\d]„Z/d^d_„Z0d`da„Z1dbdc„Z2ddde„Z3dfdg„Z4dhdi„Z5djdk„Z6dldm„Z7dndo„Z8dpdq„Z9drds„Z:dtdu„Z;dvdw„Zd|d}d~dgddfd€d„Z?d|d}d~dgddfd‚dƒ„Z@d|d}d~dd„gddfd…d†„ZAd|d~dgddfd‡dˆ„ZBd‰dŠ„ZCd‹dŒ„ZDddŽ„ZEdd„ZFdTd’d“„ZGd”d•„ZHdUd–d—„ZIdVd˜d™„ZJdWd›dœ„ZKddž„ZLdŸd „ZMdXd¡d¢„ZNdYd£d¤„ZOdZd¦d§„ZPd¨d©„ZQdªd«„ZRd[d¬d­„ZSd®d¯„ZTd\d°d±„ZUd]d²d³„ZVd´dµ„ZWd¶d·„ZXd¸d¹„ZYd^d»d¼„ZZd_d½d¾„Z[d`d¿dÀ„Z\dadÁd„Z]dbdÃdÄ„Z^dcdÅdÆ„Z_dddÈdÉ„Z`dedÊdË„ZadÇeb cdÌ¡dÍfdÎdÏ„ZddfdÐdÑ„ZedgdÒdÓ„ZfdÔdÕ„ZgdÖdׄZhdØdÙ„ZidÚdÛ„ZjdÜdÝ„ZkdÞdß„Zldàdá„Zmdhdâdã„Zndädå„Zodædç„Zpdidèdé„Zqdjdëdì„Zrdkdîdï„Zsdðdñ„Ztdòdó„Zudldôdõ„Zvdmdöd÷„Zwdndødù„Zxdodúdû„Zydüdý„Zzdþdÿ„Z{dpdd„Z|dd„Z}dd„Z~dd„Zdd „Z€d d „Zdqd d „Z‚drdd„Zƒdsdd„Z„dtdd„Z…dudd„Z†dvdd„Z‡dwdd„Zˆdd„Z‰dd „ZŠd!d"„Z‹dxd#d$„ZŒd%d&„Zd'd(„ZŽdyd+d,„Zdzd-d.„Zdgdddfd/d0„Z‘e’d1d2„ƒZ“e’d{d3d4„ƒZ”d|d5d6„Z•d7d8„Z–d9d:„Z—dS(}Ú structurea!A class to describe and handle information related to a crystal structure. 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||_dS)N)r0)rÚvaluer r r!Ú:set_non_unit_occupancy_implies_min_distance_sym_equiv_zerokszDstructure.set_non_unit_occupancy_implies_min_distance_sym_equiv_zerocCs$t ¡|_t ¡|_d|_d|_dS)z=Remove all scatterers from structure :returns: none TN)r Úxray_scattererr6r r*r7r8r3)rr r r!r/ns  zstructure.erase_scattererscCs2t||j|j|jd}|j ¡|_|j ¡|_|S)zŽCreate a deep copy of the structure with all scatterers :returns: a new cctbx.xray.structure object :rtype: cctbx.xray.structure )r5r+r4)r&r1r0r4r6Ú deep_copyr7)rÚcpr r r!Údeep_copy_scatterersxs   zstructure.deep_copy_scattererscCsp|tkr |}tjj|||d}|tkr,|j}|tkr:|j}ttj||j|j |j d|j ||j |d}|j |_ |S)N)r:r;)r(Úmin_distance_sym_equivÚu_star_toleranceÚassert_min_distance_sym_equiv)r-r)r+r5r4)rrr<Úcustomized_copyr0r4r&r-Ú_min_distance_sym_equivÚ_u_star_toleranceÚ_assert_min_distance_sym_equivr6r1r3)rr(r:r;r+r4Ústrr r r!rF‡s,zstructure.customized_copycCs|jS)zŠGet all scatterers of the structure :returns: a reference to an array of cctbx.xray.scatterer :rtype: cctbx.xray.scatterer[] )r6)rr r r!r)¦szstructure.scattererscCs|jS)N)r0)rr r r!r+®sz@structure.non_unit_occupancy_implies_min_distance_sym_equiv_zerocCsœ||g d¡dkst‚|j}|dkr6t | ¡d¡}n| ¡| ¡ksJt‚|dk rr| t | ¡|¡|| ¡¡n&| ¡| ¡ks†t‚| ||| ¡¡|S)aïSet isotropic mean thermic displacements of scatterers :param value: a single double value to set all u_iso of selected scatterers to :type value: double :param values: an array of double values to set all u_iso of selected scatterers to :type values: double[] :param selection: an array of bools to select scatterers to be updated with new u_iso values :type selection: boolean[] :returns: the modified base object :rtype: cctbx.xray.structure Nr'T) rr,r6r ÚboolÚsizeÚ set_u_isoÚdoubler:)rr=ÚvaluesÚ selectionÚsr r r!rM±s zstructure.set_u_isocCsr||g d¡dkst‚|j}|dk r:|jt |¡|dn4| ¡| ¡ksNt‚|}|t d¡}|j||d|S)aSet isotropic Debye-Waller/temperature/B factors with automatic conversion to u_iso :param value: a single double value to set all b_iso of selected scatterers to :type value: double :param values: an array of double values to set all b_iso of selected scatterers to :type values: double[] :param selection: an array of bools to select scatterers to be updated with new b_iso values :type selection: boolean[] :returns: the modified base object :rtype: cctbx.xray.structure Nr')r=rP)rOrP)rr,r6rMr Úb_as_urL)rr=rOrPrQÚb_isoZ u_iso_valuesr r r!Ú set_b_isoÌszstructure.set_b_isoc CsÚ|j ¡}t|dƒdkr&t |d¡S|dks6|dkr>tdƒ‚d}d}t|ddƒ}t|dd ƒ}xrtd ƒD]f}x`||krÐt  |¡|}|dk} t ||   d¡ƒ|} t|| ƒ|krÆt|| ƒ}| }|d 7}qrWqlW|S) Nggü©ñÒMbP?Tg{®Gáz„?g®Gáz®ï?z'fraction must be between 0.01 and 0.99.g8@gš™™™™™©?gð?ég-Cëâ6?) r6rLÚabsr rKÚ RuntimeErrorÚmaxÚminrÚ random_doubleÚfloatr) rÚfractionZscatterers_sizeÚtolrPÚlÚrÚiÚarrÚselÚdeletedr r r!Úrandom_remove_sites_selectionès&    z'structure.random_remove_sites_selectioncCsX|dk r| ¡ ||¡}t||j|j|jd}|j ¡}| |¡||_|j  ¡|_ |S)N)r+r5r4) Ú sites_fracÚ set_selectedr&r0r1r4r6r@Ú set_sitesr7)rÚ new_sitesrPrAÚnew_scatterersr r r!Úreplace_sites_fracýs    zstructure.replace_sites_fraccCs|j| ¡j|d|dS)N)Ú sites_cart)rhrP)rjr:Ú fractionalize)rrhrPr r r!Úreplace_sites_cart szstructure.replace_sites_cartcCs|j ¡dS)N)r6Ú adjust_u_iso)rr r r!rnszstructure.adjust_u_isocCsˆ|dk r.d|j d¡dkr.t |j ¡|¡}|j ¡}||k}| ||¡}||k}| ||¡}|dkrv|j |¡n|j ||¡dS)aqAdjust site occupancy factor for selected sites to be between occ_min and occ_max. :param occ_max: maximal site occupancy factor :type occ_max: float :param occ_min: minimal site occupancy factor :type occ_min: float :param selection: an array of bools to select scatterers to be adjusted :type selection: boolean[] :returns: none Nz%szarray_family_flex_ext.size_tr) Ú __class__rr rKr6rLÚextract_occupanciesrfÚset_occupancies)rZocc_maxZocc_minrPÚoccrbr r r!Úadjust_occupancys    zstructure.adjust_occupancycCst |j ¡d¡S)z–Get a selector array for all scatterers of the structure. :returns: an array to select all scatterers of the structure :rtype: boolean[] T)r rKr6rL)rr r r!Ú all_selection-szstructure.all_selectionrc Csj| ¡}t||j|j|jd}|j ¡}| | ¡j |t   |  ¡|||g¡d¡||_|j  ¡|_ |S)agTranslates all scatterers of this structure by x,y,z. :param x: x component of the translation vector :type x: float :param y: y component of the translation vector :type y: float :param z: z component of the translation vector :type z: float :returns: a new translated copy of the structure :rtype: cctbx.xray.structure )r+r5r4)rk)rkr&r0r1r4r6r@rgr:rlr Ú vec3_doublerLr7)rÚxÚyÚzrkrArir r r!Ú translate5s     zstructure.translatecCs`|dkrt |j ¡d¡}| ¡ |¡}| ¡ |¡}| ¡| ¡krNtdƒ‚t || ¡¡S)a£Calculates pairwise distances between the atoms of this structure and another structure with the same number of scatterers. :param other: the other structure :type other: cctbx.xray.structure :param selection: an array of bools to select scatterers to be taken into calculation :type selection: boolean[] :returns: an array of distances for the selected scatterers :rtype: float[] NTzModels must be of equal 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According to the CIF definition, this item **may** contain dispersion contributions. :param include_inelastic_part: If 'True' contributions due to dispersion are included in F(000). :type include_inelastic_part: boolean :returns: F(000) :rtype: float rz%scattering_type_registry out of date.)r5rÖr r×r6rLrWrÙÚ unique_form_factors_at_d_star_sqrÚrÍr)r®Ú occupancyÚ multiplicityr²rVÚcomplex) rZinclude_inelastic_partZ elastic_partrÛrÖrÙZunique_form_factors_at_originrÔrÜZinelastic_part_realZinelastic_part_imagrr r r!Úf_000‘s(  zstructure.f_000c Csª||g d¡dkst‚|dk r0|dks*t‚|}n|dks=0) to apply to selected scatterers :type rms_difference: float :param mean_distance: a mean distance shift (>=0) to apply to selected scatterers :type mean_distance: float :param selection: an array of bools to select scatterers to be shaken :type selection: boolean[] :param allow_all_fixed: if set to 'True' shaking a structure with all scatterers on fixed special positions will not cause an error :type allow_all_fixed: boolean :param random_double: "random" numbers to use for displacements :type random_double: float[] :returns: 'True' if at least one scatterer was moved, 'False' otherwise :rtype: boolean Nr'rTzNo scatterers selected.z selectedrÊFz0All%s scatterers are fixed on special positions.é )Úassert_less_thanr¸r“)rLrŒ)rrrgà?gíµ ÷Æ°>)rr,r6rLr7r¹rWr r¶rºr»r¼r½rŠr:rlÚ orthogonalizerZrrurfr ÚcolÚsiteÚ special_opr×r|r{Úset_sites_fracre)rÚrms_differencerƒrPZallow_all_fixedrZZtarget_differencer*Z n_variableÚallÚselection_fixedr`r)ÚfracÚorthZ shifts_cartZsite_frac_origÚ site_fracÚ differencer r r!Úshake_sites_in_place´st                zstructure.shake_sites_in_placec s~ˆdkr dSˆj}| ¡ ¡ˆj ¡ks,t‚ˆ ¡j‰ˆ ¡j‰ˆdkrTtj dd‰t j ‰xt ˆjƒD] \}‰ˆˆj ƒ‰ | |¡‰ ˆ  ¡‰ˆ ¡}|dkr qh|dkrȇ‡‡‡‡‡‡ fdd„}|ƒqh|dkrRg}xhdD]`}xZdD]R} tˆ ˆ ¡ƒ} | d|7<| d | 7<| ˆˆˆˆ | ¡ƒˆ ƒƒ¡qæWqÜWt|ƒd ksRt‚d‰d} xjtd ƒD]^} || } xNt| d d ƒD]<}||}|  |¡}| ¡}ˆdks²|| kr€|‰|} q€WqdWˆdk sÔt‚| dksât‚d}d}x2|D]*‰ ˆ  ¡}|dks||krðˆ }|}qðW|dk s,t‚‡‡‡‡‡‡‡‡ ‡ ‡ f d d „}|ƒqh‡‡‡‡‡‡‡‡‡ ‡ f dd„}|ƒqhWdS)a1Shifts the coordinates of all scatterers in this structure. :param shift_length: the distance to shift each scatterer with :type shift_length: float :param mersenne_twister: a mersenne twister to use as entropy source :type mersenne_twister: flex.mersenne_twister :returns: none rN)Úseedr¸csnˆ}xd|dkrhxNtdƒD]B}ˆˆˆˆ ¡ƒ|ƒƒ}ˆ|}ˆj|d}| ¡r|ˆ_dSqW|d9}qWdS)Nrrë)rïgà?)rÚrandom_double_point_on_sphereÚ site_symmetryÚis_point_group_1rï)ÚslÚi_trialÚ shift_fracÚsite_modÚss_mod)rîrõÚmersenne_twisterrrÚ shift_lengthr÷r r!Úfind_3$s  z.structure.shift_sites_in_place..find_3r“)éÿÿÿÿrr'r'é écs’ˆ}xˆ|dkrŒxrtddD]d}ˆjˆ ¡dtjd}ˆˆ|ˆ  ¡|ƒƒ}ˆ|}ˆj|d}| ¡ˆ ¡kr|ˆ_dSqW|d9}qWdS)Nrrë)rìr“)Úangle)rïgà?) rÚ$axis_and_angle_as_r3_rotation_matrixrZÚmathÚpiÚ normalizerürðrï)rþrÿr_rrr) Úaxisrîrõrrrrr÷ÚssÚvr r!Úfind_2Ps  z.structure.shift_sites_in_place..find_2csÔˆ}xÊ|dkrΈ ¡dkr$ddg}nddg}x–|D]Ž}tˆ ˆ¡ƒ}|d|7<ˆˆˆˆ |¡ƒˆƒƒ}| ¡dks~t‚ˆˆ| ¡ˆƒƒ}ˆ|}ˆj|d}| ¡ˆ  ¡kr2|ˆ_ dSq2W|d9}qWdS)Nrgà?r'r)rï) rZÚlistÚindependent_paramsÚ all_paramsÚlengthr,r rürðrï)rþÚusÚuÚindeprrrr) rîÚconstrrõrrörrrr÷rr r!Úfind_1_s"     z.structure.shift_sites_in_place..find_1)r7r¹rLr6r,r:rlrír rr rîr¥rïr»r¼r½rrrŠrrÀrÚcrossr)rrrZsstÚi_scÚnprZ plane_vectorsÚs0r}rÚ axis_lengthr`ÚviÚjZvjrrZv_maxZl_maxr^rrr ) rrîrrõrrörrrr÷rrr!Úshift_sites_in_place sl               zstructure.shift_sites_in_placecCs<|j ¡t d¡}t |¡}t |¡}t |¡}|||fS)zÔGet the minimal, maximal and mean isotropic Debye-Waller/temperature/B factors of all scatterers in this structure. :returns: minimal b_iso, maximal b_iso, mean b_iso :rtype: float, float, float r')r6Ú extract_u_isor rRr rYrXr‚)rZb_isosrŸržr¡r r r!Úb_iso_min_max_meants    zstructure.b_iso_min_max_meancCs d|_dS)NT)r8)rr r r!Ú discard_scattering_type_registrysz*structure.discard_scattering_type_registrycCs t |j¡S)N)rÚn_undefined_multiplicitiesr6)rr r r!r&„sz$structure.n_undefined_multiplicitiescCs |j ¡S)N)r6Ú extract_sites)rr r r!re‡szstructure.sites_fraccCs |j ¡S)N)r6Úextract_use_u_iso)rr r r!r‡Šszstructure.use_u_isocCs |j ¡S)N)r6Úextract_use_u_aniso)rr r r!r‰szstructure.use_u_anisocCs&| ¡|j ¡kst‚|j |¡dS)zùSet the the fractional coordinates of all sites of the structure to 'sites_frac'. :param sites_frac: a list of the fractional coordinates for all scatterers :type sites_frac: scitbx.array_family.flex.vec3_double :returns: none N)rLr6r,rg)rrer r r!rñs zstructure.set_sites_fraccCs| ¡j| ¡dS)zÃGet the the cartesian coordinates of all sites of the structure. :returns: a list of the sites of the structure in cartesian coordinates :rtype: scitbx.array_family.flex.vec3_double )re)r:ríre)rr r r!rkœszstructure.sites_cartcCs| | ¡j|d¡dS)z÷Set the the cartesian coordinates of all sites of the structure to 'sites_cart'. :param sites_cart: a list of the cartesian coordinates for all scatterers :type sites_cart: scitbx.array_family.flex.vec3_double :returns: none )rkN)rñr:rl)rrkr r r!Úset_sites_cart¤s zstructure.set_sites_cartcCs2t ¡}x$|j ¡D]}| | ¡ ¡¡qW|S)N)r Ú std_stringr6Úextract_scattering_typesrŠÚstripÚupper)rrŽÚsctr r r!Úscattering_types¯szstructure.scattering_typescCs|jj| ¡dS)N)r:)r6r¤r:)rr r r!r¤µsz#structure.extract_u_cart_plus_u_isocCs|jj| ¡dS)N)r:)r6r•r:)rr r r!r•¹sz"structure.extract_u_iso_or_u_equivcCs| ¡t d¡S)Ngð?)r•r r–)rr r r!Úb_iso_or_b_equiv½szstructure.b_iso_or_b_equivcCs |j |¡S)N)r6Ú scale_adps)rÚ scale_factorr r r!r2Àszstructure.scale_adpscCs|jdd ¡S)NÚneutron)r)r5rÌ)rr r r!Ú'switch_to_neutron_scattering_dictionaryÃsz1structure.switch_to_neutron_scattering_dictionarycCsF|j ¡}t ¡}x.|D]&}| ¡dkr4| d¡q| d¡qW|S)zµGet a selector array for all hydrogen and deuterium scatterers of the structure. :returns: an array to select all H and D scatterers of the structure :rtype: boolean[] )ÚHÚDTF)r6r,r rKr-rŠ)rr0rŽr/r r r!Ú hd_selectionÉs   zstructure.hd_selectionc Csè|r|rtdƒ‚|j ¡}| ¡}t ¡}x¸t|ƒD]¬\}}|rb||jdd…dkrb| d¡q4|rˆ||jdd…dkrˆ| d¡q4|r¾x0dD]} ||jdd…| kr’Pq’W| d¡q4|  ¡dkrÖ| d¡q4| d ¡q4W|S) a_Get a selector array for heavy (= non H or D) scatterers of the structure. :param ignore_atoms_with_alternative_conformations: select normal atoms/conformations only :type ignore_atoms_with_alternative_conformations: boolean :param include_only_atoms_with_alternative_conformations: select only scatterers with alternative conformations :type include_only_atoms_with_alternative_conformations: boolean :param only_protein: select only protein scatterers :type only_protein: boolean :returns: an array to select the desired scatterers of the structure :rtype: boolean[] z/Mutually exclusive alternative location optionsrrëú F)ÚALAÚCYSÚASPÚGLUÚPHEÚGLYÚHISÚILEÚLYSÚLEUÚMETÚASNÚPROÚGLNÚARGÚSERÚTHRÚVALÚTRPÚTYRé )r6r7T) rr6r,r)r rKr¥ÚlabelrŠr-) rÚ+ignore_atoms_with_alternative_conformationsÚ1include_only_atoms_with_alternative_conformationsZ only_proteinr0r)rŽr`r/Úresnamer r r!Úheavy_selection×s2      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(This is just an alias for atom_names_selection.) :param atom_names: list of labels of scatterers to select :type atom_names: list(string) :param ignore_atoms_with_alternative_conformations: select normal atoms/conformations only :type ignore_atoms_with_alternative_conformations: boolean :param include_only_atoms_with_alternative_conformations: select only scatterers with alternative conformations :type include_only_atoms_with_alternative_conformations: boolean :returns: an array to select the desired scatterers of the structure :rtype: boolean[] )rZrPrQ)r\)rrZrPrQr r r!Úbackbone_selectionFszstructure.backbone_selectionÚCBcCs|j|||dS)a¾Get a selector array for scatterers of the main chain of the structure. 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(This is just an alias for atom_names_selection with a different default selection.) :param atom_names: list of labels of scatterers to select :type atom_names: list(string) :param ignore_atoms_with_alternative_conformations: select normal atoms/conformations only :type ignore_atoms_with_alternative_conformations: boolean :param include_only_atoms_with_alternative_conformations: select only scatterers with alternative conformations :type include_only_atoms_with_alternative_conformations: boolean :returns: an array to select the desired scatterers of the structure :rtype: boolean[] )rZrPrQ)r\)rrZrPrQr r r!Úpeptide_dihedral_selectionvsz$structure.peptide_dihedral_selectioncst ‡fdd„| ¡Dƒ¡S)a1Get a selector array for scatterers of specified element type(s) of the structure. :param elements: tuple of element symbols to select :type elements: list(string) or set(string) or tuple(string) :returns: an array to select the desired scatterers of the structure :rtype: boolean[] csg|]}| ¡ ¡ˆk‘qSr )Úelement_symbolr-)r«r)Úelementsr r!r­—sz/structure.element_selection..)r rKr))rrbr )rbr!Úelement_selectionŽs zstructure.element_selectioncst ‡fdd„| ¡Dƒ¡S)a'Get a selector array for scatterers of specified labels from the structure. :param labels: tuple of scatterer labels to select :type labels: list(string) or set(string) or tuple(string) :returns: an array to select the desired scatterers of the structure :rtype: boolean[] csg|]}|jˆk‘qSr )rO)r«r)Úlabelsr r!r­£sz-structure.label_selection..)r rKr))rrdr )rdr!Úlabel_selectionšs zstructure.label_selectioncs6tˆƒrddl}| ˆ¡‰t ‡fdd„| ¡Dƒ¡S)aCGet a selector array for scatterers of specified labels (via regular expression) from the structure. :param label_regex: a regular expression matching scatterer labels to select :type label_regex: string or re :returns: an array to select the desired scatterers of the structure :rtype: boolean[] rNcsg|]}ˆ |j¡dk ‘qS)N)ÚsearchrO)r«r)Ú label_regexr r!r­²sz3structure.label_regex_selection..)rÚreÚcompiler rKr))rrgrhr )rgr!Úlabel_regex_selection¥s  zstructure.label_regex_selectioncCsJt |j ¡d¡}y| t |¡d¡Wntk rDtdƒ‚YnX|S)arGet a selector array for scatterers with specified index from the structure. For example you can select scatterers 1,4 and 5 by passing (1,4,5) as argument. :param selected_scatterers: list of scatterers to select :type selected_scatterers: list(int) :returns: an array to select the desired scatterers of the structure :rtype: flex.bool[] FTzVTried to select a scatterer by index with index => of scatterers for this structuture.)r rKr6rLrfr¶rWÚ IndexError)rZselected_scatterersrŽr r r!Úby_index_selectionµs zstructure.by_index_selectionTc Csx|dkrt |j ¡d¡ ¡}|j| ¡| ¡|||| ¡|  ¡d}|j |jd|rt|  ¡}|  ¡|j |ddS)NT)rkreÚrotÚtransrPr:Úatomic_weights)re)r))r rKr6rLÚ iselectionÚapply_rigid_body_shift_objrkrer:rorñr)r/r2)rrmrnrPÚrecompute_site_symmetriesZrbs_objr)r r r!Úapply_rigid_body_shiftÈs z structure.apply_rigid_body_shiftc Cstj|||||||dS)N)rkrermrnror:rP)rrs)rrkrermrnrPr:ror r r!rqÚsz$structure.apply_rigid_body_shift_objcCs4|dkr|jj| ¡dn|jj| ¡|ddS)N)r:)r:rP)r6Úconvert_to_isotropicr:)rrPr r r!rtês zstructure.convert_to_isotropiccCs4|dkr|jj| ¡dn|jj| ¡|ddS)N)r:)r:rP)r6Úconvert_to_anisotropicr:)rrPr r r!ruòs z structure.convert_to_anisotropicrÊc CsŠ|dkrtj}|j ¡}|r*t |d¡}n| ¡}dtjd}|  ¡  |¡}|  ¡  |¡}||B} |  d¡} |  d¡} |  ¡  |¡} |   d¡} |   d¡}| ¡|  |¡  | ¡}| ¡ ¡|  |¡  |¡}| ¡dkrè|}d|}d}dt||ƒ}t|d |||d dt|d ƒ}td | | | |f|d td t |¡t |¡t |¡fdd |d tdt |¡t |¡t |¡fdd |d td|d td|d td|d tj|dd}| ¡}tj|dd}| ¡}x„tt| ¡ƒt| ¡ƒƒD]f\\}}\}}| ¡| ¡|d}| ¡| ¡|d}td||||||f|d |}|}qWtd|d dS)NTrr“Frz|-z-|éOú-)Úfileú|zK| iso = %-5d aniso = %-5d pos. def. = %-5d non-pos. def. = %-5d |zL| Total B(isotropic equivalent): min = %-6.2f max = %-6.2f mean = %-6.2fz zL| Isotropic B only: min = %-6.2f max = %-6.2f mean = %-6.2fzO| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |zO| Distribution of isotropic B-factors: |zO| Isotropic | Total |rë)ÚdataZn_slotsr'z5| %9.3f -%9.3f:%8d | %9.3f -%9.3f:%8d |zO|-----------------------------------------------------------------------------|)ÚsysÚstdoutr6rLr rKr8r r r‰rzr‡rÚis_positive_definite_ur•r)r#rÀÚprintrYrXr‚Ú histogramÚdata_minrr¥ÚslotsÚ slot_width)rÚtextÚoutZ use_hydrogensrLr8Zepisr‰r‡Zsel_usedZ n_anisotropicZ n_isotropicZipdZnpdZnnpdZbeqZbisosZpart1Zpart2ÚnÚ histogram_1Z low_cutoff_1Ú histogram_2Z low_cutoff_2Zi_1Zn_1Zi_2Zn_2Z high_cutoff_1Z high_cutoff_2r r r!Úshow_u_statisticsùs`      ..  zstructure.show_u_statisticscCs|jS)N)r7)rr r r!r*,szstructure.site_symmetry_tablecCs |j ¡S)N)r7rº)rr r r!rº/sz"structure.special_position_indicescCsò|dks t‚|dkr(|dks(|dks(t‚|dkrD|dksD|dksDt‚|dkr`|dks`|dks`t‚|jsˆ|dk sˆ|dk sˆ|dk sˆ|dk rÄt||||d|_d tj d ¡i}i}d}|jdk r(|j ¡}|j ¡} |j  ¡} x,|   ¡D] \} } | | dk ræ| | || <qæW|dkr(|dkr(|  |¡|dk rRx|D]} tj d ¡|| <q8W|dk rf|  |¡|dkrtd }t   ¡|_|j |j¡x.|j ¡D]} | | d¡}|dkrŠtjj| d d d }|dk rŠ|dkrâ|}n|}|dkrtj |d ¡ ¡}n†|dkr"tj |d ¡ ¡}nh|dkrFd dlm}||d d}nD|dkrrt|d ƒ}| ¡}tj |j¡}ntj ||d ¡ ¡}d}|dk rš|j | |¡|dk rš|j |¡qšWd|_|sì| ¡rìd}|| ¡7}t |ƒ‚|jS)N)NÚ n_gaussianÚit1992Úwk1995ÚxrayÚelectronr4rŠ)rNgÐ?r‹gUUUUUUµ?r)rrrrÚconstr'rT)rOÚexactÚoptional)Ú.ito_vol_c_2011_table_4_3_2_2_entry_as_gaussian)rOrr4r‰Fz)Mixed xray and neutron scattering table! )!r,r8rr Úxray_scatteringrÐr1Ú last_tabler¿rÚrÍÚupdaterr5Úprocessr6Úunassigned_typesr»Úget_standard_labelrŠÚfetchr‹Zcctbx.eltbx.e_scatteringr‘rÚbound_coh_scatt_lengthÚrealÚn_gaussian_table_entryÚassignÚset_last_tablerÉrÓrW)rrrrrZexplicitly_allow_mixingZnew_dictZold_dictZlast_used_scattering_tableÚugsZtipÚtr`Zt_undefÚvalÚstd_lblr¬Úscattering_infoÚbÚerrmsgr r r!r52s                              z"structure.scattering_type_registrycCsF|dkrtj}n|dkr tj}n td|ƒ‚||_|| ¡||ƒdS)NÚsasakiÚhenkez(Unknown inelastic form factors table: %s)rÚ&set_inelastic_form_factors_from_sasakiÚ%set_inelastic_form_factors_from_henkerWr3r))rZphotonrÚset_use_fp_fdpZset_inelastic_ffr r r!Úset_inelastic_form_factors‡s z$structure.set_inelastic_form_factorsÚcustomcCsjx^| ¡D]R}| |jd¡}|dkr8d|_d|_d|_q |d|_|d|_|r |j d¡q W||_dS)z¬ Expects a dictionary of tuples like 'C' : (fp, fdp). 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Can be endlessly fortified as needed. FTr'r)r)rLr(Úis_similar_symmetryrrer•rpr,r5r¿rÚ parametersrÚsetrÀ)rr9ÚepsÚf1Úf2Úf3Úf4Zf5Zsr1Zsr2Zf6r}r~rër r r!Ú is_similar£s"     zstructure.is_similarcCs6|dkrtj|j| ¡dStj|j| ¡|dSdS)N)r)r:)r)r:Úu_cart_tolerance)rr}r6r:)rrr r r!r}¸s z structure.is_positive_definite_ugR¸…ë?@gÐ?cCs.||ks t‚tj|j| ¡|j|||ddS)zŒ Clean up atomic displacements so they fall within a sensible range (this is especially important when writing out PDB format). )r)r:r*Úu_minÚu_maxÚanisotropy_minN)r,rÚtidy_usr6r:r7)rrrrr r r!rÃs zstructure.tidy_uscCsd||g d¡dkst‚|dkr(t |¡}|dkrHtj|j| ¡|dntj|j| ¡||ddS)Nr')r)r:Úu_shift)r)r:rrP)rr,r rRrÚshift_usr6r:)rrZb_shiftrPr r r!rÒs  zstructure.shift_uscCs0|dk rtj|j||dntj|j|ddS)N)r)Úq_shiftrP)r)r)rÚshift_occupanciesr6)rrrPr r r!rás  zstructure.shift_occupanciescCstj|j|jddS)N)r*r))rÚapply_symmetry_sitesr7r6)rr r r!r êszstructure.apply_symmetry_sitescCstj|j|j| ¡ddS)N)r*r)rD)rÚapply_symmetry_u_starsr7r6rD)rr r r!r ïsz structure.apply_symmetry_u_starscCs$|j|j|j |¡| ¡ddS)N)r¸rD)r6r»r7r»rD)rZ i_scattererr r r!Úre_apply_symmetryõs  zstructure.re_apply_symmetrycCsPxJ| ¡D]>}|j |¡ ¡}t | ¡ ¡¡}t ||¡|j ||<q WdS)N) rºr7r»rðr Úsqrr_Ú as_doubleÚrowÚelems)rZd_target_d_siter`rðr_r r r!Ú*apply_special_position_ops_d_target_d_siteúsz4structure.apply_special_position_ops_d_target_d_sitecCs@tt tj |¡¡|j|jd}| ¡ ¡|_ |  ¡ ¡|_ |S)N)r5r4) r&rr-r<Úcell_equivalent_p1r1r4r)r@r6r*r7)rZ new_structurer r r!Úasymmetric_unit_in_p1s  zstructure.asymmetric_unit_in_p1cCsJt|tƒrt |¡}ttj ||¡tj|j |d|j j|d|j |j dS)N)r)Úcb_op)r)r-r)r*r5r4) rµrJr Úchange_of_basis_opr&rr-Ú change_basisrr6r7r1r4)rrr r r!r s    zstructure.change_basiscCs| ¡ ¡ ¡}| |¡S)N)r;r±Úchange_of_hand_opr)rZch_opr r r!Ú change_handszstructure.change_handc CsNtt tj |¡¡tj| ¡| ¡|j |j |d|j |j d}|rJ|  ¡}|S)a4Get the current structure expanded into spacegroup P1. This turns all symmetry induced scatterers into independent individual scatterers. The expanded structure may have sites with negative or > 1.0 coordinates. Use '.sites_mod_positive()' or '.sites_mod_short()' on the result, or alternatively set sites_mod_positive to 'True' in case you want to change this behaviour. :param append_number_to_labels: If set to 'True' scatterers generated from symmetry will be labelled with a numerical suffix :type append_number_to_labels: boolean :param sites_mod_positive: If set to 'True' xyz coordinates of the scatterers will be kept inside [0,1[ :type sites_mod_positive: boolean :returns: a new instance of the structure expanded into P1 :rtype: cctbx.xray.structure )r:rœr)r*Úappend_number_to_labels)r-r)r5r4)r&rr-r<rrÚ expand_to_p1r:rœr6r7r1r4Úsites_mod_positive)rrrrŽr r r!rs  zstructure.expand_to_p1cCst|| ¡ ¡|j|jdS)zöGet the current structure converted into a structure with x,y,z of all scatterers in the interval [0,1[ :returns: the same instance of the structure with only posive coordinates of its scatterers :rtype: cctbx.xray.structure )r-r)r5r4)r&r)rr1r4)rr r r!r=s  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