ó ‘™xTc@ sddlmZddlZddlmZddlZddlZddlZej j dƒZ dddd„Z d„ZdS(iÿÿÿÿ(tdivisionN(tSorrys9 import_data .short_caption = Import data and add/extend R-free flags .caption = This utility is used to combine new data with an existing set of R-free flags, or create new flags if necessary. All arrays in the data file will be included to the output. The reflection file editor offers additional options for file manipulation. .style = box auto_align caption_img:icons/custom/phenix.reflection_file_editor.png { data_file = None .type = path .short_caption = Data file .style = bold file_type:hkl input_file flags_file = None .type = path .short_caption = File with R-free flags .style = file_type:hkl input_file output_file = None .type = path .style = bold file_type:hkl new_file fraction_free = 0.05 .type = float .short_caption = Fraction to flag for R-free .help = Typically between 0.05 and 0.1. This option is ignored if an existing set of flags is being extended. ignore_shells = False .type = bool .short_caption = Disable check for test sets in thin shells .style = noauto } c# C s‘|dkrtj}nt|ƒddlm}ddlm}ddlm}|j|j j ddƒ}|j dƒ|j j }g}ddd g} g} t} xú|D]ò} |j| | jƒƒrt} |j jdk rtd |j j ƒ‚qn| jƒrPd | kr4| jd d ddgƒqf| jd dddgƒn| j| jƒjƒ| jƒ} | jƒs“| jƒjƒ} n|j| ƒq®W|j|ƒjƒ} | s~|j jdk r~|j|j jddƒ}|j dƒ|j jd|jdddddtdddtƒ}t |ƒdkrZtd|j jƒ‚n3t |ƒdkrtddd|j jƒ‚n|d\}}| j|jƒjƒ|jƒjƒjƒ}|j!d|j"ƒ|kƒ}| j#|ƒ}|j$ƒj%ƒ}|j"ƒj&tƒ|j"ƒj%ƒ}|dkre|j'd |dtƒ\}}}}t(|j$ƒj%ƒd!ƒ}||d"ks£|d!ks£||krõ|j j)sètd#d$d%d&d'd(d)d*d+|j jƒ‚qõ|d,IJn|d-kr2dd.l*m+}|jd|j,|tƒƒ}n|j-d/|d0dd1tƒ}|j.d2|ƒ}n|}|j|ƒq~n|dj/d3d4ƒ}xCt0|dƒD]1\}} |j1d | d3d5t2j3|dƒq¥W|j4ƒ}x1t0|j5ƒƒD]\}} | j6| |ƒqùW|j j7dkr]t8j9j:|j j ƒ\}!}"|!d6|j _7n|j;d|j j7ƒ|d7|j j7IJ|j j7S(8Niÿÿÿÿ(treflection_file_editor(treflection_file_utils(t file_readert force_typethkltHtKtLs1The data file (%s) already contains R-free flags.sF(+)sF_rec(+)s SIGF_rec(+)sF_rec(-)s SIGF_rec(-)sSIGF(+)sF(-)sSIGF(-)t file_nametlabelttest_flag_valuetdisable_suitability_testtparameter_scopetreturn_all_valid_arraysis*No R-free flags were found in the file %s.is6Multiple valid sets of R-free flags were found in the s<file %s. Please use the reflection file editor to select a ssingle set of flags.tdatat miller_arrayg{®Gázt?ids+The R-free flags in %s appear to have been s9assigned in thin resolution shells. PHENIX is unable to s6properly extend flags created in this manner. If you s?prefer to ignore this check and want to create new flags using s=random assignment, or if you think this message is in error, s0you can use the reflection file editor instead. s5(To view the distribution of R-free flags, click the s8toolbar button "Other tools" and select "Inspect R-free sflags".)sWARNING: ignoring thin shellsi(tflext fraction_freetmax_freetuse_lattice_symmetrytothertcolumn_root_labeltAs%ss _flags.mtzsData and flags written to %s(<tNonetsyststdouttvalidate_paramstiotbxRRRtany_filet import_datat data_filetcheck_file_typet file_servert miller_arraystFalsetis_rfree_arraytinfotTruet flags_fileRt%is_xray_reconstructed_amplitude_arraytextendtlabelst map_to_asutis_unique_set_under_symmetrytmerge_equivalentstarraytappendtmake_joined_sett complete_settget_r_free_flagsR tlentcustomized_copyRtlone_settindicestsizetcounttget_r_free_statstintt ignore_shellstscitbx.array_familyRtbooltgenerate_r_free_flagst concatenatetas_mtz_datasett enumeratetadd_miller_arraytstringt uppercaset mtz_objecttcolumnst set_labelt output_filetostpathtsplitexttwrite(#targstparamstoutRRRtdata_inR#t new_arraysR+twarningst have_r_freeR/R2tflags_intflags_and_valuest old_flagsR t missing_sett n_missingRtn_binstn_freetssetaccutmin_binsRt missing_flagst new_flagstmtz_outtitmtz_objtcolumntbasetext((sS/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/gui_tools/import_data_and_flags.pytrun.s¼                 %  (   !      cC sV|jjdkr!tdƒ‚n1tjj|jjƒsRtd|jjƒ‚ntS(NsPlease specify a data file.s%s is not a recognizable file.(RR RRRJRKtisfileR'(RO((sS/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/gui_tools/import_data_and_flags.pyR™s ((t __future__Rt libtbx.philtlibtbxt libtbx.utilsRRDRJRtphiltparset master_philRRgR(((sS/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/gui_tools/import_data_and_flags.pyts      k