xTc@ sddlmZddlmZddlmZddlmZddlZ ddl m Z ddl m Z mZddlZ ddlmZddlZddlZddlZd e fd YZd e fd YZd ZdefdYZdZedZdZeedZdZ defdYZ!defdYZ"dZ#dZ$dZ%defdYZ&dZ'edZ(d d!Z)d"Z*eeed#Z+d$efd%YZ,d&Z-eed'Z.dS((i(tdivision(treflection_file_reader(tmiller(tflexN(t show_string(tSorrytnull_out(tcountt#Sorry_No_array_of_the_required_typecB seZeZdZRS(t exceptions(t__name__t __module__t__orig_module__(((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyR stSorry_Not_a_suitable_arraycB seZeZdZRS(R (R R R (((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyR scC s.x'|D]}|j|dkrtSqWtS(Ni(tfindtFalsetTrue(t search_labelst info_stringt search_label((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyt find_labelss t label_tablecB sPeZddZdddZdddddZddZddZRS(cC s||_|dkr$tj|_n ||_g|_g|_xttd|D]o\}}|j }|dk r|jj t |n|jj t ||jj t |ddqUWdS(Nitlabels( t miller_arraystNonetsyststderrterrt info_stringst info_labelstzipRtinfotappendtstrtgetattr(tselfRRtp_arrayt miller_arrayR((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyt__init__s     "  c C sd||gjddks!t|dkr9|g}nt|dksQtt|tdkru|g}ng}g|D]}|j^q}xt|j|jD]\}}t d|d|js|j dqt d|d|s |j dqd}|dk rKx*|D]} | |kr%|d7}q%q%Wn|j d|qW|S(NiitRRi( RRtAssertionErrortlenttypetlowerRRRRR ( R#tlabelRtresulttlblt labels_lowerRRtn_exact_matchest info_label((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytscores+s0!   "    cC s|dkr|j}n|dIJ|dkrUxf|jD]}|dI|IJq8WnBx?t|j|D]+\}}||krh|dI|IJqhqhW|J|dkrd}n d|}|d|IJ|JdS(NsPossible choices:t R's use %s to s>Please %sspecify an unambiguous substring of the target label.(RRRR(R#tfR2t minimum_scoretparameter_nameRtscorethint((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytshow_possible_choicesFs        cC s|dkr|j}n|dk s*t|jd|}d}xtt|ddD]}|j|dkr[|j|dkr|J|d||fIJ|J|jd|d|d|dS|j|j |Sq[W|J|d ||fIJ|J|jd|dS( NR,iiisAmbiguous %s=%sR4R2R5s Unknown %s=%s( RRR(R2txrangetmaxRR9Rtindex(R#R,tcommand_line_switchR4R2tselected_arrayt high_score((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytmatch_data_label[s(  cC s|dkr|j}nt|jdkrC|J|dIJ|JdSt|jdkrc|jdS|dkr|J|}|d|IJ|d|tt|jdjjddfIJ|J|jd|dS|j d |d |S( NisNo reflection arrays available.is+Please use %s to select a reflection array.sFor example: %s=%st:iR4R,R=( RRR)RRR!RtsplitR9R@(R#R,R=R4ts((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyt 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r|rc|jsw| r|j r| |7} q| |8} qnd} | dk st |j dk rt |j t jr|jr| dkr| d7} n|dk r3|jr3|r&| d7} q3| d8} n|j| q4W|S(Niiiiii(RHR RROtall_eqRKtanomalous_flagRJRIRFR(tsigmast isinstanceRtdoubletsigmas_are_sensible( Rtignore_all_zerostprefer_anomaloustprefer_amplitudestanomalous_bonustintensity_bonustamplitude_bonusR-R%R7((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytget_xray_data_scoressb                        cC st|tjstSt|jdkr/tS|jdj}x6dddddgD]}|j|dkrXtSqXWtS( Niitfreettesttcrosststatustflagi( RXRt array_infoRR)RR+RR(RgR,tword((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytlooks_like_r_free_flags_infostget_r_free_flags_scorecB seZdZRS(cC s|dk s||dkr(t|_nt|_||}d|_td|d|kol|dknrt|std|d|ko|dknrd |_qd |_ndS( Ng?iig{Gz?gffffff?ig{Gz?g?ii(RRtreversedRt flag_scoretminRi(R#ttest_flag_valuetntn_freetmiller_array_info((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyR&s    - - (R R 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R<R(R6RRt data_scoresRterror_message_no_arrayt"error_message_not_a_suitable_arrayt'error_message_multiple_equally_suitabletlbl_tabt label_scoresterrortcombined_scoresRot label_scoret data_scoreR((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyRDsZ            treflection_file_servercB seZd d d d dZdZd dZededZeddZdedd d dZ eddZ dedd Z RS( cC s||_||_|dkr-tj|_n ||_g|_|dk rx9|D].}|jj|jd|jd|jqRWni|_ xB|jD]7}|j j t j j |jjgj|qWdS(Ntcrystal_symmetrytforce_symmetry(RRRRRRRtextendtas_miller_arraystfile_name_miller_arrayst setdefaulttlibtbxtpathtcanonical_pathRtsourceR (R#RRtreflection_filesRtreflection_fileR%((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyR&s            cC s5|dkr|jStjj|}|jj|d}|dkrttjdrxK|jj D]7}tjj ||rh|j|}|j|t|t st |jj |kr>|Sq>WdS(N( RRRRRRRXR!Rt label_stringtlistR(R(R#RRRRR((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytget_miller_arrays    ic C s|jd|} td| d|} |dk rD|d|}n|rZt| | |Std|d|d| d| d|jd d d d d d} | | } |r| j} | dkrd}n | j}| jr'| j } |dk r| j | j d|d q| j d| q| j r| j } |dk rr| j | j d|d dgq| j d| qn| S(NRRRLt.R6RRRRsNo array of amplitudes found.Rs$Not a suitable array of amplitudes: Rs5Multiple equally suitable arrays of amplitudes found.iRtas_amplitude_array(RRMRRRDRRRRGt amplitudestset_infotcustomized_copyRKR(R#RRt"convert_to_amplitudes_if_necessarytparameter_scopeR6treturn_all_valid_arraysR5RLRRRR-RR((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytget_amplitudessD                  c C s9|dkst|jd|} td| } |dk rP|d|}n|rft| | |Std|d|d| d| d |jd d d d dd} | | } | j} | dkrd}n | j}|r| j rN| j dt } |dk r;t |dkr;| j | jd|dgq| j d| q5| jr5| jj dt } |dk r| j | jd|dgq| j d| q5n~| j r5|dkr5| jd| jdtj} |dk r"| j | jd|dgq5| j d| n| S(NtdegtradRRRR6RRRRsNo array of phases found.Rs Not a suitable array of phases: Rs1Multiple equally suitable arrays of phases found.iiRtconverted_to_centroid_phasesROitconverted_to_deg(NsdegR(RR(RRTRRDRRRRGtphasesRR)RRRNtphase_integralsROtmathtpi(R#RRtconvert_to_phases_if_necessarytoriginal_phase_unitsRR6RR5RRRR-RR((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytget_phases_deg@sR          #    # Rc C sV|jd|} td| d|d|d| } |rIt| | |S| } | } |dkr g} g} xt| | D]\}}|jjddgdd d d gd d gddddggkpt|jt j s}| j || j |q}q}Wnt d|d|d|d| d| d|j dddddd}| |S(NRRR[R\R]sF-obs-filteredsSIGF-obs-filteredsF-obs-filtered(+)sSIGF-obs-filtered(+)sF-obs-filtered(-)sSIGF-obs-filtered(-)sF-models PHIF-models F-model(+)s PHIF-model(+)s F-model(-)s PHIF-model(-)R6RRRRRs%No array of observed xray data found.Rs,Not a suitable array of observed xray data: Rs=Multiple equally suitable arrays of observed xray data found.(RRaRRRRRRXRORtcomplex_doubleR RDR(R#RRR[RR6RR5R\R]RRtnew_miller_arraystnew_data_scorestmatdsR((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyt get_xray_datazsB          cC sn|jd|}|r|dks0|dkrXtd|d|d|dfn|rqtddnd} d} ntd|d |} | j} |rh| j} g} x8t|D]*\} }| j|| | | | fqW| jd g}x]| D]U\}}}||kr |j rJt ||\}}n|j||fq q W|S|dkr}d}n |g}y`t d |dd |d|d | d|j dddd|d|d|dddd} Wn1t k r}t t|dd|nX|| }| dk r@| j| }n|j rdt ||\}}n||fS(NRs^%s=True: Suitability test for R-free flags can only be disabled if both %s and %s are defined.s.disable_suitability_tests.labels.test_flag_values7return_all_valid_arrays=True: Suitability test can not sbe disabled in this mode.RRncS s|d|dS(Ni((RR((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyRsR6RRRRs!No array of R-free flags found. sFor manual selection define: s %s.label s %s.test_flag_value s" %s.disable_suitability_test=TrueRs&Not a suitable array of R-free flags: Rs7Multiple equally suitable arrays of R-free flags found.s) To override the suitability test define:s! %s.disable_suitability_test=True(RRRRrR2Rtt enumerateR R}Rt$cif_status_flags_as_int_r_free_flagsRDRR R!(R#RR,Rntdisable_suitability_testRRR5Rt flag_scoresRRtRRRtvalid_arrays_and_flagst flag_valueR7RteR%((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytget_r_free_flagssl     "      "    c C s|jd|}td|d|} |r=t|| |Std|d|d|d|d| d|jd d d d d d} || S(NRRR[R6RRRRRs&No array of experimental phases found.Rs-Not a suitable array of experimental phases: Rs>Multiple equally suitable arrays of experimental phases found.(RRRRDR( R#RRR[RR6RR5RRR((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytget_experimental_phasess    N( R R RR&RRRRRRRR(((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyRs*    1 7 / FcC s|dkst|jr|jdk|jdkB}|j}|j|}tj|jd}|j|jdkd|j d|}|j |d}n||fS(NR4toiiRO( R(RRORtselectRtintRPt set_selectedRR(R%Rnt selectionRRO((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyRs "   cC s#td|gd|}|jdS(NRRni(RrRt(R%RnR((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytguess_r_free_flag_values  RcC s|dkrJt|dkr1td|ntjj|d}n|jj|sp|||7}ntjdkrtjj |r||dkr|||7}qn<tjj |rtjj ||dr|||7}n|S(NRis=Ambiguous name for output %s file (more than one input file).itwin32( R)RRRtbasenameR+tendswithRtplatformtisfileR(tinput_file_namestuser_file_nametfile_type_labeltfile_extensiontextension_seperator((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytconstruct_output_file_name#s   cC sddlm}|jd|djd|djdt}|djj}xU|dD]I}|j}|j||jd}|j |}|j |qcW|jd|djd|dt}|j j S(Ni(RRitindicesRVi( tcctbxRtsetRRRt deep_copyt match_indicestsinglesRRt map_to_asutunique_under_symmetry(RRt master_settmaster_indicesRtcurrent_indicest missing_iseltmissing_indices((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytmake_joined_set:s"      c  s|dkrtj}ndks*td}tjd|j}fd}|dIJg}g}xb|D]Z} |d| rt|dI| jjIJ|j | |j | jjqtqtWt |dkrt d nt |d kr|d}nt |d krd } |dkrEt | qx]|D]R} |d| rL| jj|krL|d I| jjIJ| }qLqLWn|dkrd } t | n|S(NtcomplextrealRc s:dkr|jp9dkr0|jp9dkS(NRR(RGRHR(R(R*(sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytget_flagSss Available suitable arrays:Rs isNo suitable arrays.isMultiple choices available.s Selected:s No map coefficients array selected. See choices listed above and use 'label=' to select one. Example: label="2FOFCWT,PH2FOFCWT" (scomplexsrealN( RRtstdoutR(RRRRRR R)R( RR,R*tlogR-RRtsuitable_arraystsuitable_labelsRRStmsg((R*sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytextract_miller_array_from_fileMs>         ' tprocess_raw_datacB seZdZdddddgZddddeejedZ dZ dZ d Z d Z d Zd Zd ZdZddedZRS(s  Automation wrapper - prepares single-wavelength experimental data (and optional R-free flags and experimental phases) for any future step in the structure determination process. Used in Phenix for ligand pipeline and automated re-refinement of PDB entries. tf_obst r_free_flagsRnRt _generate_newc  C s1| dk r|dk st|dkrUddlm} tjj| j}n|j} d} }|j }|j j j }|j d| }|jd|d|}|jrddlm}| r| }n t}|jd|ddd|}n|dk s t|j}|jd kre| d d |j|jfIJn|rz|j}n|dk r|j} d }|d krd}n|dkrd}n|jr|j}nt}|jj}|jj}|jj|jjkr4t}n|rs|j j j }|j d| }|d kr|jd|jd|j |k}t}n|j!}|jr|j}n|j"d|}|j#j$}|j#j$}|dks+|j j%|j d r>| dIJd}n||kr7|j&d|}|j#j$}|d kr7| d||fIJ|dkr|d kr|j dt'j(|t}q|j dt'j)|d}n7|j*d|j j+||dddtd|}|j,d|}q7n|dk r|j#j$|j#j$ksptqq | dt-|j dj.g|j/j0D]}d|^qt-|j dj.g|j/j0D]}d|^qfIJn | dIJt|_1|dkrp|j*d|j2d|j3d|j4d|j5d |j6dd}d }t|_1n|jr|j}n|dk r|j}|j jd|d|}n|j7st|j8| |_9|j8| |_:||_;d|_<|dk r-|j8||_<ndS(!Ni(tgenerate_r_free_params_strRtd_mintd_max(t french_wilsonR%tparamsg?s WARNING: data are incomplete (%.1f%% of possible reflections measured to %.2fA). This may cause problems if you plan to use the maps for building and/or ligand fitting! idtcnsitccp4tshelxRROtothers} WARNING: uniform R-free flags detected; a new test set will be generated, but this will bias the refinement statistics. s WARNING: R-free flags are incomplete relative to experimental data (%d vs. %d reflections). The flags will be extended to complete the set, but we recommend supplying flags that are already generated to the maximum expected resolution. iitfractiontmax_freetuse_lattice_symmetrytformats NOTE: incompatible symmetry between the data and the R-free flags: Data : %s %s Flags : %s %s A new test set will be generated. R3s%gsx WARNING: R-free flags not supplied. This may bias the refinement if the structures are very nearly isomorphous! tuse_dataman_shellstn_shells(=RR(tcctbx.r_free_utilsRRtphiltparsetextractRtspace_group_infoRtmerge_equivalentsRteliminate_sys_absenttresolution_filterRKRR Rtfrench_wilson_scaletaverage_bijvoet_matest completenessRRVRt space_grouptbuild_derived_point_groupR*tnumberRRRRORt common_setRRPRUtlone_setRRvRtgenerate_r_free_flagsRt concatenateR!Rt unit_cellt parametersRRRRRRRJRRRRnR(R#tobsRRnRRRtr_free_flags_paramstmerge_anomalousRtverboseRtobs_infotr_free_flags_infot phases_infotsgR tfw_outt merged_obsRtis_compatible_symmetrytobs_pgtflags_pgtobs_tmptn_r_freetn_obst missing_sett n_missingt missing_flagsR((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyR&s            #       $             !   0/9             !   cC sc|jjrdS|jjrB|jjdk r;dSdSn|jjdk r[dSdSdS(NsF,SIGF,DANO,SIGDANO,ISYMsF(+),SIGF(+),F(-),SIGF(-)s F(+),F(-)sF,SIGFtF(RRIRVRWR(R#((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyt data_labelsscC sdS(Nt FreeR_flag((R#((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytr_free_flags_labelscC sV|jjd|jj|jk}|jjrR|j rR|j}n|S(NRO(RRRORnRRVtgenerate_bijvoet_mates(R#tflags((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytr_free_flags_as_boolean_array s  cC s|jjd|jS(NR(Rt common_setsRB(R#((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytdata_and_flags'scC s|jdk rdSdS(NsHLA,HLB,HLC,HLD(RR(R#((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyt phase_labels*scC s|jjjS(N(RRORP(R#((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyR8/scC s,|jjj|j|jjjS(N(RRORRnRP(R#((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyt fraction_free2scC s|jS(N(R(R#((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyt flags_are_new6scC s|jjddd|}|jjrS| rS|jd|jjddn|jdk r{|j|jddn|j|jdd|jj |dS(Ntcolumn_root_labelR<t wavelengthR%tHLR>( Rtas_mtz_datasetRVtadd_miller_arrayRRRRt mtz_objecttwrite(R#RttitleRItsingle_datasettmtz_data((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytwrite_mtz_file9s     N(R R t__doc__t __slots__RRRRRR&R=R?RBRDRER8RFRGRR(((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pyRqs0        cC sStj|}|jdks't|j}|j|}|j|dS(sA Update the space group in an MTZ file, writing it in place. tccp4_mtzN(RRRR(t file_contenttset_space_group_infoRN(RRtmtz_inRMtmtz_new((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytchange_space_groupKs  c C s;tj|}|jdks'ttdddtd|gdtj}d}}}|j d|ddd dd t d d \}}|j } |dk st|j d |j |k}d} } xq|jD]f} | j j} | jr!| jr!| }|j } q| dkr| }| j } qqW|dkrm|dk rm|j}n|j}|jd|}|jd|}d||gkst|dk r|r|j}|j}|jd|j| }|jd|j| }||fS|j| |j| fS(s\ Automation wrapper for reading in MTZ files generated by the process_raw_data class. RURRRRRR,R>RnRRR'ROsF,SIGFRN(RRRR(RRRRRRRRRRORRRJRVRRR#R@R(RRVRRXt file_serverRt f_obs_anomtr_freeRnt r_free_infot f_obs_infotf_obs_anom_infoRR,((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytload_f_obs_and_r_freeUsN          (/t __future__RtiotbxRRRtcctbx.array_familyRt libtbx.pathRtlibtbx.str_utilsRt libtbx.utilsRRt libtbx.philt itertoolsRRRRRR RtobjectRRFRRMRTRRaRiRjRrRRRDRRRRRRRRZRa(((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_utils.pytsD    k   < m   9B  $