0xTc@ sddlmZddlmZddlmZddlmZddlmZddlmZddl Zddlm Z dd lm Z dd l m Z ddlZdd lmZdd lmZdd lmZddlZddlZddlZddlmZmZmZddlmZddlmZddl m!Z!ddl"m#Z#dd lm Z de$fdYZ%dej&fdYZ'de$fdYZ(de$fdYZ)dS(i(tdivision(text(tstructure_factors(tmiller(tcrystal(tsgtbxN(tadptbx(teltbx(tflex(tmatrix(tmath(tcount(t count_maxtSorrytKeep(t approx_equal(t group_args(t is_string(tneutron_news_1992_tabletscattering_type_registry_paramscB seZdddddZRS(cC s(||_||_||_||_dS(N(t custom_dicttd_minttablet'types_without_a_scattering_contribution(tselfRRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt__init__s   N(t__name__t __module__tNoneR(((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRst structurec B seZdZdddedddZdZdZdZdZ e e e e dZ dZ dZ dddd Zdddd Zd Zdd Zdd ZdZddZdZddddZddZddZddZddZddZddddedddZddZdZddZddZ dd Z!d!Z"d"Z#d#Z$d$Z%d%Z&ed&Z'dddedd'Z(dd(Z)d)Z*d*Z+d+Z,d,Z-d-Z.d.Z/d/Z0d0Z1d1Z2d2Z3d3Z4d4Z5d5Z6d6Z7d7Z8eeed8Z9d9d:d;d<geed=Z:d9d:d;d<geed>Z;d9d:d;d<d?geed@Z<d9d;d<geedAZ=dBZ>dCZ?dDZ@dEZAdeBdFZCdGZDddHZEddIZFdJdedKZGdLZHdMZIddddedNZJeBdOZKeBdPdQZLdRZMdSZNedTZOdUZPdddVZQdedWZRdXZSdYZTdZZUd[d\ZVdddeddddd]ZWdJd^ZXddJd_ZYded`ZZddddJdaZ[ddbZ\dce]j^dddedfZ_ddddgZ`ddhZadiZbdjZcdkZddlZedmZfdnZgdoZheedpZidqZjdrZkedsZldtduZmdvedwZndxZodyZpddzZqdd{Zrdd|Zsdd}Ztd~ZudZvedZwdZxdZydZzdZ{dZ|eddZ}eeeddZ~ddZdddddZdddddeeddZddddeddZdZdZdZddZdZdZdddZdddZdgedddZdZeeZddddZeeZddZdZdZRS(s!A class to describe and handle information related to a crystal structure. It offers various methods to modify the crystallographic information contained. Important members are: - .special_position_settings (base class) - .scatterers - .site_symmetry - .crystal_symmetry cC s||gjddks!t|dk s?|dks?t|dkr`tjd|}ntjj|||j||_||_|dk r|j d|d|d|jnd|_ d|_ dS(Nitcrystal_symmetryt scattererstsite_symmetry_tablet6non_unit_occupancy_implies_min_distance_sym_equiv_zero( R RtAssertionErrorRtspecial_position_settingst_copy_constructorterase_scattererst7_non_unit_occupancy_implies_min_distance_sym_equiv_zerot_scattering_type_registrytadd_scatterersRtinelastic_form_factors_source(RR#RR R!tscattering_type_registryR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR3s"!            cC s_tjj|t|j|_|j|_|j|_|j|_|j|_|j|_dS(N( RR#R$t _scattererst_site_symmetry_tableR&R't(_scattering_type_registry_is_out_of_dateR)(Rtother((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR$Ns       cC s"tjd|jd|jS(szGet crystal symmetry of the structure :returns: a new crystal symmetry object :rtype: cctbx.crystal.symmetry t unit_celltspace_group_info(RtsymmetryR/R0(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRZs  cC s4tj|_tj|_t|_d|_ dS(s=Remove all scatterers from structure :returns: none N( Rtxray_scattererR+RR R,tTrueR-RR)(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR%ds cC sFt|d|jd|j}|jj|_|jj|_|S(sCreate a deep copy of the structure with all scatterers :returns: a new cctbx.xray.structure object :rtype: cctbx.xray.structure R*R!(RR'R&R+t deep_copyR,(Rtcp((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytdeep_copy_scatterersns    c C s|tkr|}ntjj|d|d|}|tkrK|j}ntdtjd|d|jd|jd|j d|j d |d |j }|j |_ |S( NR/R0R#Rtmin_distance_sym_equivtu_star_tolerancetassert_min_distance_sym_equivRR!R*( RRR1tcustomized_copyR&RR#t_min_distance_sym_equivt_u_star_tolerancet_assert_min_distance_sym_equivR+R'R)(RRR/R0R!tstr((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR:|s&             cC s|jS(sGet all scatterers of the structure :returns: a reference to an array of cctbx.xray.scatterer :rtype: cctbx.xray.scatterer[] (R+(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRscC s|jS(N(R&(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR!scC s||gjddks!t|j}|dkrQtj|jt}n|j|jksot|dk r|jtj |j|||j n7|j|jkst|j|||j |S(sSet 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 iN( R RR"R+RtbooltsizeR3t set_u_isotdoubleR/(Rtvaluetvaluest selectionts((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRAs!   .cC s||gjddks!t|j}|dk rX|jdtj|d|nM|j|jksvt|}|tjd}|jd|d||S(sSet 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 iRCRERDN(R RR"R+RARtb_as_uR@(RRCRDRERFtb_isot u_iso_values((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt set_b_isos!  "c C s1|jj}t|ddkr5tj|tS|dksM|dkr\tdnd}d}t|dd}t |dd}xt d D]}x||kr(tj ||}|dk} t || j t|} t|| |krt|| }| }n|d 7}qWqW|S( NggMbP?g{Gz?gGz?s'fraction must be between 0.01 and 0.99.g8@g?g?ig-C6?(R+R@tabsRR?R3t RuntimeErrorRtmaxtmintxranget random_doubletfloatR ( Rtfractiontscatterers_sizettolREtltrtitarrtseltdeleted((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytrandom_remove_sites_selections&  cC s|dk r'|jj||}nt|d|jd|j}|jj}|j|||_|j j|_ |S(NR!R*( Rt sites_fract set_selectedRR&R'R+R4t set_sitesR,(Rt new_sitesRER5tnew_scatterers((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytreplace_sites_fracs      cC s(|jd|jjd|d|S(NR_t sites_cartRE(RaR/t fractionalize(RR_RE((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytreplace_sites_carts cC s|jjdS(N(R+t adjust_u_iso(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRescC s|dk rId|jjddkrItj|jj|}qIn|jj}||k}|j||}||k}|j||}|dkr|jj |n|jj ||dS(sqAdjust 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 s%ssarray_family_flex_ext.size_tiN( Rt __class__R RR?R+R@textract_occupanciesR]tset_occupancies(Rtocc_maxtocc_minREtoccRY((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytadjust_occupancys !   cC stj|jjtS(sGet a selector array for all scatterers of the structure. :returns: an array to select all scatterers of the structure :rtype: boolean[] (RR?R+R@R3(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt all_selectionsic C s|j}t|d|jd|j}|jj}|j|jjd|t j |j |||g||_|j j|_ |S(sgTranslates 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!R*Rb( RbRR&R'R+R4R^R/RcRt vec3_doubleR@R,(RtxtytzRbR5R`((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt translate%s    ) cC s|dkr*tj|jjt}n|jj|}|jj|}|j|jkr{tdntj ||j S(sCalculates 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[] sModels must be of equal size.N( RRR?R+R@R3RbtselectRLtsqrttdot(RR.REts1ts2((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt distances?s cC stj|jd|d|S(sCalculates the maximum pairwise distance 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: the maximum distance of two corresponding scatterers out of the selected scatterers :rtype: float R.RE(RRMRx(RR.RE((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt max_distanceSscC stj|jd|d|S(sCalculates the minimum pairwise distance 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: the minimum distance of two corresponding scatterers out of the selected scatterers :rtype: float R.RE(RRNRx(RR.RE((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt min_distancecscC stj|jd|d|S(sCalculates the arithmetic mean pairwise distance 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: the mean pairwise distance of the selected scatterers :rtype: float R.RE(RtmeanRx(RR.RE((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt mean_distancess cC s|dk r0|j|jjksKtntj|jjt}xt|j|D]\}}|r^|jj r^|jj r|j ||_ n|jj rg}x,t dD]}|j|j||qW||_qq^q^WdS(sScale the atomic displacement parameters of the selected scatterers of the structure with the specified factor. If no selection is given, all scatterers will be handled as if selected. :param factor: scale factor to apply to the adps of the selected scatterers :type factor: float :param selection: an array of bools to select the scatterers to have their adps scaled :type selection: boolean[] :returns: none iN(RR@R+R"RR?R3tziptflagstuset use_u_isotu_isot use_u_anisoROtappendtu_star(RtfactorREtscRYtresultRW((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt scale_adps $g$@g?g?cC s||gjddks!t||gjddkrQ|dksQtn||gjddkr|jj|j}|jdkrtjt j |} t | |}t t d| |}qn||kst|||| g|dk r4|j|j jksOtnt j|j jt}|jj} x2tt|j |D]\} } } | rw| jjrw| jjr||krt dtj||dtj}tj|| _n| jjr| rg}xGtdD]9}|j| j|| j|tj| |fqW| d| r|jj|}n|| _qqwqwWdS(Niigiiti_seq(ii( R RR"textract_u_iso_or_u_equivRsRR@Rtu_as_bRR{tintRMR+R?R3R tis_special_positionR}R~Rtrandomt randrangeRGRRRORRtchoicet space_grouptaverage_u_star(Rtb_maxtb_mintspreadt aniso_spreadtkeep_anisotropictrandom_u_cart_scaleREtu_isostb_meanRRRRYRVRRW((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt shake_adps6!$ $(( cC st}|jjtdkr|j}tjtj|}tjtj |}tjtj |}t |||krt |||kr|j t}qn|S(Ni( tFalseRR R3RRRRRMRNR{RKR(Rtb_iso_tolerancet performedRRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytshake_adp_if_all_equals   cC s|jjd|j}tj}x^t|jD]M\}}|jjsa|jjr7|j t t j ||q7q7Wtj |S(NR/( R+textract_u_cart_plus_u_isoR/RRBt enumerateR~RRRRNRt eigenvalues(Rtu_cartsRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytmin_u_cart_eigenvalues  'cC sp|j}tj|jd}|dkr>|j|n.|j|jks\t|j||dS(Ng@(R+RRPR@RRhR"(RRERFtq_new((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytshake_occupanciess   cC s|dk r<t|tjr<tj|jj|}n|j}t|dr|}|dk r|j|jkstqntj |j|}|dkr|j |n.|j|jkst|j |||S(NR@( Rt isinstanceRtsize_tR?R+R@thasattrR"RBRh(RRCRERFRD((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRhs  $ cC s&|dks-|j|jjks-t|j}|jj|jjks]tidd6dd6dd6|jj d6}|dkr|dc|jj7(RRttgtstypetgaussiantaatabR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytscattering_dictionary_as_strings     <c C sg}|j}|j}tj||jjkrHtdn|j|j}|j|j}xT|j j D]@\}}|j t d|d||d||d||qW|S(Ns%scattering_type_registry out of date.tscattering_typeR t occupancy_sumtunit_cell_occupancy_sum( R*t unique_countsRtsumR+R@RLtoccupancy_sumstunit_cell_occupancy_sumsttype_index_pairs_as_dictRRR(RRtregRRRRt unique_index((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt*scattering_types_counts_and_occupancy_sums%s     cC slddlm}tg|jD]%}|j|jj|j^q }|jj }d||S(sGet the value of the diffraction-determined density for the crystal, suitable for the CIF item _exptl_crystal_density_diffrn Density values are calculated from the crystal cell and contents. The units are megagrams per cubic metre (=grams per cubic centimetre). Equivalent to: 1.66042 * _chemical_formula_weight * _cell_formula_units_Z / _cell_volume :returns: chemical density in megagrams per cubic metre (=grams per cm^3) :rtype: float i(ttiny_pseg7ُ?( t cctbx.eltbxRRRRRtweightRR/tvolume(RRteltt numeratort denominator((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytcrystal_density5s 8c C s:d}|j}|j}tj||jjkrHtdn|j|j}|jd}x6|j j D]"\}}|||||7}q|W|s|Sd} d} xh|j D]Z} | j r| | j | j | j7} n| jr| | j| j | j7} qqWtt|| | S(sGet the effective number of electrons in the crystal unit cell contributing to F(000), suitable for the CIF item _exptl_crystal_F_000. 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 is%scattering_type_registry out of date.(R*RRRR+R@RLRt unique_form_factors_at_d_star_sqRRRtfpt occupancyt multiplicitytfdpRKtcomplex( Rtinclude_inelastic_partt elastic_partRRRtunique_form_factors_at_originRRtinelastic_part_realtinelastic_part_imagR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytf_000Is(    ! %cC s||gjddks!t|dk rH|dks?t|}n|dksZt|}|dkrpdS|jjdkst|j}|jj|jjkst|dk r|j|jjkst|jt}|dkrtdnd} n|jj}d} t j } x^|j D]P} |j | j jdkrI|dks|| r| j| qqIqIW|| j8}|dkr|rtStd| n||jjkrd}n|j} |jj} |jj}|dkr3t j}nxNtdd D]=} t j|d |jjd d d d}|dk r|j|dn|j| dxw|j D]i} tj| | j}|j | j|tj| || }|tj|||| =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 iiNsNo scatterers selected.s selectedRs0All%s scatterers are fixed on special positions.tassert_less_thani R@iRig?gư>(iii(iii(!R RR"R+R@R,RR3RLRRRRRRRRR/Rct orthogonalizeRPR RnR]R tcoltsitet special_opRRuRttset_sites_fracR\(Rtrms_differenceR|REtallow_all_fixedRPttarget_differenceR t n_variabletalltselection_fixedRWRtfractortht shifts_carttsite_frac_origt site_fract difference((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytshake_sites_in_placelst!    ' !          # !  "  c  sldkrdSj}|jjjjks@tjjjjdkrt j ddnt j xt jD]\}j |j| jj}|dkrqn|dkr# fd}|q|dkr3g}xdddgD]}xxdddgD]g} tj } | dc|7<| dc| 7<|jj|  q[WqEWt|d kstdd} xtd D]z} || } xgt| dd D]R}||}| j|}|j}dksb|| kr||} qqWqWdk st| dkstd}d}xA|D]9 j}|dks||kr }|}qqW|dk st f d }|q f d }|qWdS( s1Shifts 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 iNtseedic s}x|dkrxktdD]]}j|}|}jd|}|jr"|_dSq"W|d9}q WdS(Nii Rg?(ROtrandom_double_point_on_spheret site_symmetrytis_point_group_1R(tslti_trialt shift_fractsite_modtss_mod(RRtmersenne_twisterRRt shift_lengthR(sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytfind_3s   iiii ic s}x|dkrxtddD]}jdjdtj}| j|}|}jd|}|jjkr%|_dSq%W|d9}q WdS(NiRi tangleiRg?( R t$axis_and_angle_as_r3_rotation_matrixRPR tpit normalizeRRR(RRRVRRR( taxisRRRRRRRtsstv(sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytfind_2s    c s$}x|dkrjdkr6ddg}n ddg}x|D]}tj}|dc|7<j|}|jdkst|j}|}jd|}|j jkrI|_ dSqIW|d9}q WdS(Nig?iiR( RPtlisttindependent_paramst all_paramstlengthR"RRRR(RtustutindepR RRR( RtconstrRRRRRRRR (sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytfind_1s"  %  (R,RR@R+R"R/RcRRRRR RRRRRRR R RRRROtcrossR(RRRtsstti_sctnpRt plane_vectorsts0RvRt axis_lengthRWtvitjtvjRRtv_maxtl_maxRUR R(( RRRRRRRRRRR R sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytshift_sites_in_placesl  '      !   (      * *cC sV|jjtjd}tj|}tj|}tj|}|||fS(sGet 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 i(R+t extract_u_isoRRGRRNRMR{(Rtb_isosRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytb_iso_min_max_mean,s cC s t|_dS(N(R3R-(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt discard_scattering_type_registry9scC stj|jS(N(Rtn_undefined_multiplicitiesR+(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR&<scC s |jjS(N(R+t extract_sites(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR\?scC s |jjS(N(R+textract_use_u_iso(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRBscC s |jjS(N(R+textract_use_u_aniso(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyREscC s5|j|jjks!t|jj|dS(sSet 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(R@R+R"R^(RR\((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRHs !cC s|jjd|jS(sGet 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 R\(R/RR\(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRbTscC s#|j|jjd|dS(sSet 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 RbN(RR/Rc(RRb((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytset_sites_cart\s cC sCtj}x0|jjD]}|j|jjqW|S(N(Rt std_stringR+textract_scattering_typesRtstriptupper(RRtsct((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytscattering_typesgs cC s|jjd|jS(NR/(R+RR/(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRms cC s|jjd|jS(NR/(R+RR/(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRqs cC s|jj|S(N(R+t scale_adps(Rt scale_factor((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR1uscC s|jddjS(NRtneutron(R*R(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt'switch_to_neutron_scattering_dictionaryxscC s_|jj}tj}x=|D]5}|jdkrJ|jtq"|jtq"W|S(sGet 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[] tHtD(R5R6(R+R,RR?R-RR3R(RR0RR/((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt hd_selection~s  c C s|r|rtdn|jj}|j}tj}x9t|D]+\}}|r||jdd!dkr|jt qOqn|r||jdd!dkr|jt qOqn|rKx{ddddd d d d d dddddddddddgD]$} ||jdd!| krPqqW|jt qOn|j dkrm|jt qO|jt qOW|S(s_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[] s/Mutually exclusive alternative location optionsi i t tALAtCYStASPtGLUtPHEtGLYtHIStILEtLYStLEUtMETtASNtPROtGLNtARGtSERtTHRtVALtTRPtTYRi R5R6(R5R6( R R+R,RRR?RtlabelRRR-R3( Rt+ignore_atoms_with_alternative_conformationst1include_only_atoms_with_alternative_conformationst only_proteinR0RRRWR/tresname((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytheavy_selectionsZ        tCtOtCAtNcC sE|r|rtdn|jj}tj}x|jD]}|jjddkrt|jt qCn|r|jdd!dkr|jt qCqn|r|jdd!dkr|jt qCqnxb|D]M}|jdd!jd|dkr|j |d kr|jt PqqW|jt qCW|S( scGet a selector array for scatterers of the structure by "atom" names. :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[] s/Mutually exclusive alternative location optionstHOHii i R8is%s i( R R+R,RR?RRMtfindRRRR3(Rt atom_namesRNROR0RRtname((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytatom_names_selections0       # cC s|jd|d|d|S(sGet a selector array for scatterers of the backbone of the structure. (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[] RYRNRO(R[(RRYRNRO((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytbackbone_selections tCBcC s|jd|d|d|S(sGet a selector array for scatterers of the main chain of the structure. (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[] RYRNRO(R[(RRYRNRO((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytmain_chain_selections cC s|jd|d|d|S(sGet a selector array for peptide dihedral scatterers of the structure. (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[] RYRNRO(R[(RRYRNRO((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytpeptide_dihedral_selection+s cG s8tjg|jD]}|jj|k^qS(s1Get 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[] (RR?Rtelement_symbolR-(RtelementsR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytelement_selectionCs cG s/tjg|jD]}|j|k^qS(s'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[] (RR?RRM(RtlabelsR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytlabel_selectionOs cC sbt|r*ddl}|j|}ntjg|jD]}|j|jdk ^q=S(sCGet 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[] iN( RtretcompileRR?RtsearchRMR(Rt label_regexReR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytlabel_regex_selectionZs   cC s`tj|jjt}y|jtj|tWn!tk r[t ddnX|S(srGet 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[] s3Tried to select a scatterer by index with index => s#of scatterers for this structuture.( RR?R+R@RR]RR3RLt IndexError(Rtselected_scatterersR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytby_index_selectionjs  cC s|dkr0tj|jjtj}n|jd|jd|j d|d|d|d|j d|j }|j d|j |r|j }|j|jd|ndS( NRbR\trotttransRER/tatomic_weightsR(RRR?R+R@R3t iselectiontapply_rigid_body_shift_objRbR\R/RoRRR%R((RRmRnREtrecompute_site_symmetriestrbs_objR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytapply_rigid_body_shift}s $      cC s4tjd|d|d|d|d|d|d|S(NRbR\RmRnRoR/RE(RRt(RRbR\RmRnRER/Ro((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRqscC sK|dkr(|jjd|jn|jjd|jd|dS(NR/RE(RR+tconvert_to_isotropicR/(RRE((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRus cC sK|dkr(|jjd|jn|jjd|jd|dS(NR/RE(RR+tconvert_to_anisotropicR/(RRE((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRvs Rc C sb|dkrtj}n|jj}|rBtj|t}n |j}dt j d}|j j |}|j j |}||B} |jt} |jt} |jj |} | jt} | jt}|j|j |j | }|jj|j |j |}|jdkrN|}nd|}d}dt||}||d||IJdt|d}|d | | | |fIJ|d tj|tj|tj|fddIJ|d tj|tj|tj|fddIJ|d dddIJ|dIJ|dIJtjd|dd}|j}tjd|dd}|j}xtt|jt|jD]\\}}\}}|j|j|d}|j|j|d}|d||||||fIJ|}|}qW|ddddIJdS(Niiis|-s-|iOt-t|sK| iso = %-5d aniso = %-5d pos. def. = %-5d non-pos. def. = %-5d |sL| Total B(isotropic equivalent): min = %-6.2f max = %-6.2f mean = %-6.2fR8sL| Isotropic B only: min = %-6.2f max = %-6.2f mean = %-6.2fs| s- i&sO| Distribution of isotropic B-factors: |sO| Isotropic | Total |tdatatn_slotsi is5| %9.3f -%9.3f:%8d | %9.3f -%9.3f:%8d |iMs s (RtsyststdoutR+R@RR?R3R7R RRRsRR tis_positive_definite_uRRRR"RRNRMR{t histogramtdata_minR}Rtslotst slot_width(Rttexttoutt use_hydrogensR@R7tepisRRtsel_usedt n_anisotropict n_isotropictipdtnpdtnnpdtbeqtbisostpart1tpart2tnt histogram_1t low_cutoff_1t histogram_2t low_cutoff_2ti_1tn_1ti_2tn_2t high_cutoff_1t high_cutoff_2((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytshow_u_statisticss\   #)  66    + cC s|jS(N(R,(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR scC s |jjS(N(R,R(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRsc C si|dkst|dkr?|dks?|dks?tn|dkrl|dksl|dksltn|dkr|dks|dkstn|js|dk s|dk s|dk s|dk r(td |d |d |d||_itjjdd6}i}d}|jdk r|jj}|jj } |jj } x;| j D]-\} } | | dk rd| | || s     tcustomcC sx|jD]x}|j|jd}|dkrRd|_d|_t|_q |d|_|d|_|r |jj t q q W||_ dS(s Expects a dictionary of tuples like 'C' : (fp, fdp). If an element is not in the dictionary, the fp and fdp are reset to 0 and the use_fp_fdp is set to false. iiN( RRRRRRRt use_fp_fdpR~RR3R)(RRRtsourceRtfp_fdp((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt!set_custom_inelastic_form_factorsHs      cC s&|j}|j|jjS(N(R*t0sum_of_scattering_factors_at_diffraction_angle_0R/R(RRV((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytmean_scattering_density[s  c C st|tjkst|jdk s3ttjd|jj d|}t d|d|jj |d|j j |d|j S(Nt array_sizet python_sliceR#RR R*(ttypettypest SliceTypeR"RRRt slice_indicesR+R@RRsR,R'(Rt slice_objectRY((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt __getitem__`s  c C sb|jdk st|r(|}ntd|d|jj|d|jj|d|jS(NR#RR R*(RRR"RR+RsR,R'(RREtnegate((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRsls cC sO|jdk st|jj||_|jj||_t|_dS(N(RRR"R+RsR,R3R-(RRE((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytselect_inplaceusc C s|dkr|jj}n|jj|||dkr|j|jd|jd|jd|jd|jd|j }n#|j|jd|d|j|j j d|d|t |_ dS(NR/RR7R8R9tsite_symmetry_opstinsert_at_index(RR+R@tinserttapply_symmetryR/RR7R8R9R,RR3R-(Rt scattererRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt add_scatterer{s          cC s|dkrtj}n1|jj|jks?t| sLt|jj|tj d|j d|j d|jd|j d|d|j d|jd|jd | t|_dS( NR/RRR tsite_symmetry_table_for_newR7R8R9R!(RRR RR@R"R+textendRtadd_scatterers_extR/RR,R7R8R9R3R-(RRR R!((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR(s  $         cC s,|j}|jd|jd|j|S(NRR (R6R(R+R,(RR.R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt concatenates     c C s|jj}|jj}x?t|j|jD]"\}}xt|j|jD]\}}||krh|d}|d} t} xAt|j| jD]$\} } t| | st} qqWxAt|j | j D]$\} }t| |st} qqWt|j | j sFt} n| r^t dq^qhqhWq@W|j d|j d|j|j}|j}|jd|jd|jd|jd|j|jd|jd|jd|jd|jdS( Nis*Cannot concatenate: conflicting scatterersRR RRRR(R*RR}tkeysRRRRR3RRRLR(R+R,RRRRR(RR.td1td2tkey1titem1tkey2titem2ti1ti2t problem_flagta1ta2tb1tb2tstrp1tstrp2((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytconcatenate_inplaces@((   ( (              cC sj|dkst|jdk s*ttjd|jjd|d|jd|jd|S(Nit asu_mappingstbuffer_thicknessRbtdistance_cutofftprimary_selection(R"R#RRtneighbors_fast_pair_generatorRRbt neighbors_of(RtradiusRE((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytselection_withins  texistingcC su|dkr|j}n|dk rQ|jj|jjksQtn|j|jd|d|dS(NRRR (R,RRR@RR"R%R((RRR ((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytreplace_scattererss   -  c C s|dkr6|jjdkr-t}qjt}n4|sj|jjdkrjtddqjntj|||} tj d|d|d|d|d|d |d |d |d | d |S(s Calculate structure factors for the current scatterers using either direct summation or FFT method; by default the appropriate method will be guessed automatically. :param anomalous_flag: toggles whether the returned structure factors are anomalous or not :type anomalous_flag: bool :param d_min: resolution cutoff (required) :type d_min: float :param algorithm: specifies 'direct' or 'fft', or if None (default), the algorithm will be chosen automatically :type algorithm: str or None :param cos_sin_table: if True, uses interpolation of values from a pre-calculated lookup table for trigonometric function calls in the structure factor calculations in preference to calling the system libraries :type cos_sin_table: bool :param quality_factor: determines accuracy of sampled density in fft method :type quality_factor: float :param u_base: additional smearing B-factor for scatterers which have too small Bs so they fall between the grid nodes :type u_base: float :param b_base: same as u_base (but 8*pi^2 larger) :type b_base: float :param wing_cutoff: is how far away from atomic center you sample density around atom :type wing_cutoff: float :returns: a custom Python object (exact type depends on method used), from which f_calc() may be called :rtype: derived from cctbx.xray.structure_factors.manager.managed_calculation_base is(xray.structure with anomalous scattererss# but miller.array is non-anomalous.RRt cos_sin_tabletquality_factortu_basetb_baset wing_cutofftxray_structuret miller_sett algorithmN( RRtcount_anomalousR3RRLRt build_setRtfrom_scatterers( Rtanomalous_flagRRRRRRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRs*(     c C sd|||jjd|d|f}g}xOt|jD];\}}|j|d|jd|ddd|qEW|dj|dS( seval(self.as_py_code()) is similar (but sometimes not identical) to self and meant to enable quick formatting of self as Python code for unit tests. sP%sxray.structure( %s crystal_symmetry=%s, %s scatterers=flex.xray_scatterer([ tindents s tcomments #%ds, s]))(Rt as_py_codeRRRtjoin(RR tr0tr1RWR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR #s -cC sx|dkrtj}n||dI|jjIJ||dI|jjIJtjj|d|d||S(NsNumber of scatterers:sAt special positions:tftprefix( RR{R|RR@RRR1t show_summary(RRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR6s cC s}|dkrtj}n|dIJ|j}|rL|j|j}nx*|D]"}|jd|d|jqSW|S(NsLLabel, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as UisoRR/(RR{R|RRsRtshowR/(RRtspecial_positions_onlyRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytshow_scatterers?s     cC sS|jjd|d|jjd|d|d|jjd|d|dS(NR#t site_labelstsites_frac_originaltsites_cart_originaltsites_frac_exactRR(R,tshow_special_position_shiftsRtextract_labelsR'(RRRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRJs cC sT|dkr+tjd|jd|jStjd|jd|jd|SdS(NRR/tu_cart_tolerance(RRR}R+R/(RR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR}Xs       gư>gR?@g?c C sP||ksttjd|jd|jd|jd|d|d|dS(s Clean up atomic displacements so they fall within a sensible range (this is especially important when writing out PDB format). RR/R tu_mintu_maxtanisotropy_minN(R"Rttidy_usR+R/R,(RRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR cs    c C s||gjddks!t|dkr?tj|}n|dkrstjd|jd|jd|n+tjd|jd|jd|d|dS(NiRR/tu_shiftRE( R RR"RRGRtshift_usR+R/(RR!tb_shiftRE((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR"rs!       cC sK|dk r.tjd|jd|d|ntjd|jd|dS(NRtq_shiftRE(RRtshift_occupanciesR+(RR$RE((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR%s   cC s tjd|jd|jdS(NR R(Rtapply_symmetry_sitesR,R+(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR&s  cC s,tjd|jd|jd|jdS(NR RR8(Rtapply_symmetry_u_starsR,R+R8(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR's   cC s3|j|jd|jj|d|jdS(NRR8(R+RR,RR8(Rt i_scatterer((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytre_apply_symmetryscC slxe|jD]W}|jj|j}tj|jj}tj|||j ||Rtchange_of_basis_opRRR#t change_basisRR+R,R'(RR3((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR5scC s%|jjj}|j|S(N(R0Rtchange_of_hand_opR5(Rtch_op((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt change_handscC stdtjtjj|dtjd|jd|jd|j d|j d|d|j }|r~|j }n|S(s4Get 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#RR/RR tappend_number_to_labelsR*( RRR#R1R0Rt expand_to_p1R/RR+R,R'tsites_mod_positive(RR9R;R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR:s       cC s(td|d|jjd|jS(sGet 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#RR*(RRR;R'(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR;scC s(td|d|jjd|jS(sGet the current structure converted into a structure with short coordinates vectors of all scatterers :returns: the same instance of the structure with only short coordinates vectors of its scatterers :rtype: cctbx.xray.structure R#RR*(RRtsites_mod_shortR'(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyR<sc C sc|jj}|j|j||r8d}n |j}td|d|d|d|jS(NR#RR R*(RR4R^R'RR,RR'(RtshiftRrtshifted_scatterersR ((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt apply_shifts  g?cC sStjtj|jjddd|}|j|jjd|S(NiiiRb(RRnRPRR@R?R/Rc(Rtmax_shift_carttshifts((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytrandom_shift_sitess.Rc C s|dkst|ttfks*ttjd|jjd|}td|d|jj |d|j j |d|j S( NRRytreverseR#RR R*(s occupancy( R"RR3Rtsort_permutationRRgRR+RsR,R'(Rtby_valueRCtp((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytsorts  cC s\ddlm}g}x3|jD]%}|j|j|j|jq#W|j||S(Ni(teuclidean_model_matching(tcctbxRHRRtpositionRMRtmodel(Rtemmat positionsR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt as_emma_models #cC sddlm}tj}xv|jD]h}tjjd|jdt dt }|dkrut d|jn|j |j |jq)W|S(Ni(RRMRRsUnknown atomic weight: (RRRRBRRRRRR3RRLRRR(RRRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRos    cC s1|dkr|j}n|jjd|S(Ntweights(RRoRbt mean_weighted(RRo((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytcenter_of_mass%s cC s:|dkr|j}ntjjd|jd|S(NtpointsRO(RRotscitbxR tprincipal_axes_of_inertiaRb(RRo((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRT*s    cC sx|jj|jks!t|dk rU|jjd|jd|d|n|jjd|jd|dS(NR/tu_cartRE(R+R@R"Rt set_u_cartR/(RRURE((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRV1s!  cC sy|dkrtj}nd}d}d}d}d}d}d}d} d} d} d} x.|jD] } | j}|jr|d7}n|j|j}}|r|r|d7}n0|r|d7}n|r|d7}n |d7}|jr |d7}n|j r#|d7}n|j r<| d7} n|j rU| d7} n|j rn| d7} n|j rg| d7} qgqgW|dI|IJ|dkr|dI|IJn|dkr|dI|IJn|dI|IJ|dI|IJ|dI|IJ|d I|IJ|d I| IJ|d I| IJ|d I| IJ|d I| IJ|dI|jjIJdS(Niisn_use = sn_use_u_none = sn_use_u_both = sn_use_u_iso = sn_use_u_aniso = sn_grad_site = sn_grad_u_iso = sn_grad_u_aniso = sn_grad_occupancy = sn_grad_fp = sn_grad_fdp = stotal number of scatterers = (RR{R|RR~RRRt grad_sitet grad_u_isot grad_u_anisotgrad_occupancytgrad_fptgrad_fdpR@(RRtn_uset n_use_u_botht n_use_u_isot n_use_u_anisot n_use_u_nonet n_grad_sitet n_grad_u_isotn_grad_u_anisotn_grad_occupancyt n_grad_fpt n_grad_fdpRR~RWta((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytshow_scatterer_flags_summary;sf               cC stj|jS(N(Rtshared_scatterer_flagsR(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytscatterer_flagsfscC s|j|jdS(N(t assign_toR(RRk((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytset_scatterer_flagsiscC sd}|r|j}nd}xZt|jD]F\}}|j}|dkr^d}n$|j|}|jrd}n|jr|dkr|d7}q||jj 7}n|j r|j r|d7}n|j r/|j r/|dkr|d7}q/||jj 7}n|jrH|d7}n|jra|d7}n|jr4|d7}q4q4W|S(Niiii(R RRRR~RRRWRRRXRRYRtadp_constraintsRZR[R\(Rt%considering_site_symmetry_constraintsRtsstabRRR~R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt n_parametersls<                 cC s|jjS(N(RRc(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRcscC s|jjS(N(RRd(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRdscC stjj|jS(N(RIRt parameter_mapR(R((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRrscC s4|j}|j}|j}x|jD]}|g||jD]}td|^qD|_|jdkrtjtdtj |j|_ntd|j |_ |j dkr+gtj ||j D]}t |d^q}tj|g|D]}t|d^q|_ q+q+WdS(Ns%8.3fgs%6.2fs%5.2fii'(iiiiii(R/RcRRRRQRRRGRRRtu_star_as_u_cartRtu_cart_as_u_star(RtuctfratortRRWtu_pdb((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyt truncate_at_pdb_format_precisions   5+2cC sXtjd|jd|jd|jd|jd|jd|d|d|S( NR/RRR*R tmiller_indicestda_dbt daa_dbb_dab(Rt:structure_factors_curvatures_simple_grads_and_curvs_targetR/RRR*R (RRzR{R|((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytgrads_and_curvs_target_simples      c C s[|rd}n |j}|jd|d|jjd|d|jd|jS(NRRR R\R/(RR RRRR\R/(Rtpair_sym_tabletis_full_connectivityRR ((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytpair_sym_table_shows    cC sX|jd|jd|jd|jjd|jd|d|d|d|S( NR/R RR\tshow_cartesiantskip_j_seq_less_than_i_seqtskip_sym_equivR(tshow_distancesR/R RRR\(RRRRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pytpair_sym_table_show_distancess    cC sDtjj|d|d|}tjd|d|jd|j|S(NRtasu_is_inside_epsilonRRR (RR1RRtasu_mappings_processR+R,(RRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRs    icC s|dk s|dk st|dkr3|}n|jd|d|}tjd|}|dk r|jd|d|n|S(NRRRRtmin_cubicle_edge(RR"RRtpair_asu_tablet add_all_pairs(RRtasu_mappings_buffer_thicknessRRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRs        c C s||gjddks!t|dkrT|jd|d|d|d|}n|jd|jjd|jd|d |d |S( NiRRRRRR\Rtkeep_pair_asu_tableR(R RR"RRRRR\( RRRRRRRRR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/xray/structure.pyRs ! 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