ó ±™xTc@ sddlmZddlmZddlZddlZddlmZddlm Z ddl Zddl m Z m Z ddlZddlZejjddeƒZeZd „Zejed „Zd „Zd e jfd „ƒYZd„ZedkreejdƒndS(iÿÿÿÿ(tdivision(tutilsN(t file_reader(t runtime_utils(tSorrytUsages mtz_file = None .type = path .short_caption = MTZ file .style = bold file_type:hkl OnChange:extract_map_coeffs_for_fft .help = MTZ file containing map coefficients pdb_file = None .type = path .short_caption = Model file .help = Model file around which to draw the map. If not supplied, the map will fill the unit cell. labels = None .type = strings .multiple = True .help = Map column labels. Common examples are "2FOFCWT,PH2FOFCWT" and "FP,SIGFP" "PHIM" "FOMM". If left blank, all maps present in the input file will be used. buffer = 5.0 .type = float .short_caption = Region padding .help = Extra padding (in Angstroms) around the selected region (or unit cell) selection = None .type = str .input_size = 400 .short_caption = Atom selection .help = Atom selection around which to draw map (plus buffer). If left blank, the entire model file will be used. d_min = None .type = float .help = High-resolution cutoff d_max = None .type = float .help = Low-resolution cutoff grid_resolution_factor = 0.25 .type = float .help = Grid spacing (multiplied by the high-resolution limit) scale = *sigma volume .type = choice(multi=False) .expert_level = 1 .short_caption = Map scaling .help = Scaling method for map values output { directory = None .type = path .short_caption = Output directory .help = Output directory (defaults to current) .style = output_dir bold prefix = None .type = str .input_size = 400 .short_caption = Output file prefix .help = Output file prefix (defaults to the MTZ file name base) include scope libtbx.phil.interface.tracking_params format = xplor *ccp4 dsn6 .type = choice .caption = XPLOR CCP4 DSN6 extension = *Auto ccp4 xplor map dsn6 .type = choice } r_free_flags { remove = False .type = bool .short_caption = Remove R-free set from map file_name = None .type = path .short_caption = R-free flags .style = OnChange:extract_r_free_flags_for_fft label = None .type = str .input_size = 120 .short_caption = R-free label .style = renderer:draw_rfree_label_widget test_flag_value = None .type = int } include_fmodel = False .type = bool .short_caption = Include F(model) if present show_maps = False .type = bool tprocess_includescC s1x*|D]"}|jƒjƒ|kr|SqWdS(N(tinfot label_stringtNone(t miller_arraystlabelstarray((sH/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/mtz2map.pyt find_arrayes c,C sr ddl}d}d}g}t|ƒdkrc|dIJtjd|ddƒtddƒ‚ntjd d ƒ}x·|D]¯}tjj |ƒrÆt j |ƒ} | j d krÿ|dk rÍt d ƒ‚n|j|jjd tjj|ƒƒƒ| }q+| j dkry|jdƒs,t dƒ‚n|dk rGt dƒ‚n|j|jjdtjj|ƒƒƒ| }q+y|jjd|ƒ} Wn!tk rµt d|ƒ‚q+X|j| ƒq||jdƒræ|dd}ny|jd|ƒ} Wntk r|d|IJq|X|j| ƒq|Wtjd|ƒ} | jƒ} |dkrw| jdkrwt dƒ‚n|s| jjdkr¤tjƒ| j_ntjj| jjƒsÒtj| jjƒn1tjj| jjƒst d| jjƒ‚n| jj}n tjƒ}| jjdkr^tjj tjj!| jƒƒd| j_n|dkr‹t j | jdddt"ƒ}ng}| j#s¯t| j$ƒdkr¹t%j&|j'dt(d | j) d!t"ƒ}| j)st%j&|j'dt(d t(d!t"ƒ}n|}t|ƒdkr|d"IJx}|D]f}t*|t+ƒrQ|g}n|}||krld#}nd }| j$j|ƒ|d$||fIJq0Wn t d%ƒ‚| j#r¹t(Sn|dkrü| j,dk rüt j | j,dd ƒ}|j-d ƒn|j.j/ƒ}d}| j0j1rÂ| j0j2dk rMt j | j0j2ddƒ}n|}|j'j3d|j2d&| j0j4d'| j0j5d(t(d)d*ƒ\}}|j6d+|j7ƒ|kƒj8ƒj9ƒ}nd}|dk rU|j.j:}|j;ƒj<ƒ}| j=dk r_|j>ƒ}|j=| j=ƒ}|j?|ƒ}t|ƒdkrRt d,ƒ‚qRq_n |d-IJg}g}xt@| j$ƒD]ï\}}d} t|ƒd.krŒtA||dƒ} | dkrJt%j&|j'd!t"dt(d | j) ƒ}g}!t|ƒdkrnxC|D];}t*|t+ƒr&|g}n|!jdd/jB|ƒƒqWt d0d1|dd2jB|!ƒfƒ‚q‰t d3d4|dƒ‚qJn¾t|ƒdkr®|jdƒnt%jCd5|d6|dd7|d.d8|dƒ\}"}#}$|"jDƒsùtE‚|#jFƒs tE‚|$dks)|$jFƒs)tE‚|jGjHd9|"d:|#d;|$ƒ} |d<d/jB|ƒIJ| jIƒsstE‚| j8ƒj9ƒ} | jJd=| jKd>| jLƒ} |dk rý| jMd?|ƒ\} }%|d@|%j7ƒjNt"ƒIJ| j?|%j7ƒƒ} n| jOdA| jPƒ}&| jQdBkr8 |dCIJ|&jRƒn&| jQdDkr^ |dEIJ|&jSƒnd}'|dFdGdHgkr‚ d }'n|djdIƒrº |djdJƒr± dK}'q™ dL}'nß|djdMƒrÖ dN}'nÃ|ddOkrï dL}'nª|ddPkr dN}'n‘|djdQƒr$ dR}'nu|djdSƒr@ dT}'nY|djdUƒsf |djdVƒro dW}'n*|djdXƒr‹ dY}'ndZ|d.}'d[|dkr¶ |'d[7}'nd\|dkrÓ |'d]7}'n|'|kr |j|'ƒ|jN|'ƒ}(|'dZ|(7}'n |j|'ƒ| jjT})| jjUd^krj |)d_krL d_}*qÌ |)d`kra da}*qÌ db}*nb| jjU}*|)dbkr¡ |*dokr¡ t dd|*ƒ‚n+|)d_krÌ |*dpkrÌ t de|*ƒ‚ntjjB|| jj|'df|*ƒ}+|)dbkrX t%jVdg|dh| jWƒdi|&jXƒdj|&jYƒd|+dk| jZƒ|j|+dlfƒn|)d`krØ |dk rÅ ddl[}|jGj\dg|dh| jWƒdi|&jXƒdj|&jYƒd|+dk| jZƒq\ |&j]d|+ƒn„|dk r9 ddl[}|jGj^dg|dh| jWƒdi|&jXƒdj|&jYƒd|+dk| jZƒn|&j_d|+ƒ|j|+dmfƒ|dn|+IJq{W|S(qNiÿÿÿÿisParameter syntax:touttprefixs s2phenix.mtz2map [mtz_file] [pdb_file] [param_file] s [--show_maps]t home_scopettpdbs&A model file has already been defined.s pdb_file=%sthkls.mtzs3Only MTZ files are supported for reflections input.s%An MTZ file has already been defined.s mtz_file=%st file_names-The file %s was not in a recognizable format.s--is=TruetargsUnknown argument '%s'.tsourcess7Please specify an MTZ file containing map coefficients.s2The specified output path '%s' is not a directory!t force_typetraise_sorry_if_errorstexclude_anomaloustexclude_fmodeltkeep_array_labelss,Available map coefficients in this MTZ file:s/ (skipping, add include_fmodel=True to include)s %s%ss+No map coefficients found in this MTZ file.tlabelttest_flag_valuetdisable_suitability_testtparameter_scopet r_free_flagstdatas0No atoms found matching the specified selection.s1No model input - will output map(s) in unit cell.it s4No map coefficients found with labels %s. Possible schoices are: %ss s4No map coefficients found with labels %s; this file s6does not appear to contain any other map coefficients!R tf_labtphi_labtfom_labtftphitfomsProcessing map: %std_mintd_maxtothers( removing %d R-free flagged reflectionstresolution_factortsigmas applying sigma-scalingtvolumes applying volume-scalingsFP,SIGFPtPHIMtFOMMt2FOFCWTtno_fills_2mFo-DFc_no_fills _2mFo-DFctFOFCWTs_mFo-DFcsFWT,PHWTsDELFWT,PHDELWTtANOMt_anomtLLGt_llgtFMODELsF-modelt_fmodeltFCt_fcalcs_%dt_no_fillt_fillt_filledtAutotccp4tdsn6tomaptxplortmaps2%s is not an appropriate extension for Xplor maps.s1%s is not an appropriate extension for CCP4 maps.t.t sites_cartt unit_celltmap_datatn_realtbuffers XPLOR mapsCCP4 maps wrote %s(RCsmap(R@smap(`t iotbx.philR tlent master_philtshowRt!command_line_argument_interpretertostpathtisfileRtany_filet file_typeRtappendtphiltparsetabspathtendswitht RuntimeErrort startswithtprocesstfetchtextracttmtz_filetoutputt directorytgetcwdtexiststmakedirstisdirRtsplitexttbasenametTruet show_mapsR Rtget_map_coeff_labelst file_servertFalsetinclude_fmodelt isinstancetstrtpdb_filetassert_file_typet file_objecttas_miller_arraysR tremoveRtget_r_free_flagsRRR R!t map_to_asutaverage_bijvoet_matest hierarchytatomst extract_xyzt selectiontatom_selection_cachetselectt enumerateR tjointextract_map_coeffstis_xray_amplitude_arraytAssertionErrort is_real_arrayt map_toolstcombine_f_phi_and_fomtis_complex_arraytresolution_filterR)R*t common_setstcounttfft_maptgrid_resolution_factortscaletapply_sigma_scalingtapply_volume_scalingtformatt extensiontwrite_xplor_mapRGtreal_mapRIRJtiotbx.map_toolstwrite_dsn6_mapt as_dsn6_maptwrite_ccp4_mapt as_ccp4_map(,targstlogt run_in_current_working_directorytiotbxRpR_t input_philtparameter_interpreterRt input_filet file_philtarg_philt working_philtparamst output_dirt all_labelst map_labelsR t labels_listtextraR R t rfree_filet raw_arrayt flag_valueRFt pdb_hierarchytselection_cacheR{t file_infotsuffixestit map_coeffst labels_outR&R'R(tflagsRDtsuffixtnRRt map_file_name((sH/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/mtz2map.pytrunksì               %                    $        $  !                                                    cC s |gfS(N((tresult((sH/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/mtz2map.pyt finish_jobxstlaunchercB seZd„ZRS(cC sEtj|jƒtj|jƒtdt|jƒdtjdt ƒS(NR˜R™Rš( RPRdR£tchdirR¶tlistR˜tsyststdoutRh(tself((sH/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/mtz2map.pyR¶|s  (t__name__t __module__R¶(((sH/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/mtz2map.pyR¹{scC s"|jdkrtdƒ‚ndS(NsNo MTZ file was provided.(R_R R(R¢((sH/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/mtz2map.pytvalidate_paramsƒst__main__i(t __future__Rt mmtbx.mapsRR“R›RKRtlibtbxRt libtbx.philt libtbx.utilsRRR¼RPRVRWRhRMt master_paramsR R½RlR¶R¸ttarget_with_save_resultR¹RÁR¿targv(((sH/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/mtz2map.pyts&    Q ÿ