xTc@ sddlmZddlZddlZddlZddlmZddlmZddlm Z ddl m Z ddl m Z ddl mZdd lmZmZmZdd lmZddlZddlZd ed ZdS( i(tdivisionN(treflection_file_reader(treflection_file_utils(t option_parser(tcrystal(tsgtbx(tflex(tSorryt date_and_timetplural_s(tStringIOs phenix.reflection_file_converterc C stdd|dd|jjdddddtd d jjdd dd d dd dddjdddddtd djdddd d dd dddjdddd d dd dddjdddddtd djdddddddtd djdddddd d d!jdd"dd dd#d d$d d%ddjdd&dd dd'd dd d(dd)jdd*d+ddd,d d/dd0jdd1dd d dd d2dd3ddjdd4dd d dd d5dd)jdd6dd d dd d7ddjdd8dddtd d9jdd:dddtd d;jdd<dd d dd d=dd>jdd?dddtd d@jddAdddtd dBjddCdddtd dDjddEdddtd dFjddGdd d d$d dHddjddIdd d d$d dJddjddKdd d dd dLddMjddNdd d dd dOddMjddPdd d dd dQddjddRdd d dd dSddMjddTdd d dd dUddMjdV|}|j}|j dk r9t j |j t j dW|j n|jrV|jrVHdXGHHdS|jsh|jr|jdkrHdYGHHdSn|jdk r|jdk rHdZGHHdSt|jd[kr|jjdStjd\|jd]dd^td_td`tdadb}|r|St|d[krEHdctt|jdbGHHdStjdd|}|jde|jdfd }|dkrdSd}d} |jdk rh|jde|jdfd}|dkrdSt |j!} |j"shtj#dd|gdg|j$j%d[} | dkrD|j$dkr5t&dhqDt&din|j'dj|j(| k}qhndkGHdlG|j!GHdmG|j)GHH| dk rdnGHdlG| GHHn|j'd]|j*do|j+dp|j, j-|j)} |dk r|j'd]| }ndqGHt.j+j/| drdsH| j0dkrJ|jjdtGHHdS| j1dkrs|jjduGHHdS|dk r|j'd]| }n|j2dk r| j3dv|j2dw|j4\} } |dk r|j5dx| }qn| j6s<dyGH| j7} | j/drdsH| j8} ~ | j9drdsHn|dk r|j6 rdzGH|j7} | j/drdsH| j8}~ |j9drdsHn|j:rd{GH|dk rt&d|n| j:} | j9drdsHn|j;dk r |dk r t&d}nt<j1d~|j;}dG|GHt.j+d| j0d|dt}|j0j=| j0s dGHdGHdGHdGHdGHdG| j0GHdG|j0GHn| j'd]|} H| j6s dGH| j7} | j/drdH| j8} ~ | j9drdHq n| j>rq |j?rq dGH| j@s@ | jA} qq | jB} | jA} | jC} | jDn|dk r |j>r |j?r dGH|jA}n|jE}|jF}|dk s |dk r1 |dk r d|GHn|dk r d|GHn| jGd|d|} dG| jHjIGHHn|jdk re d|jGH| jJd|j} Hn|jdk r d|jGH| jJd|j} Hn|jK|jLgjMtdkr t&dn|jKr@ | jNr1 dGH| jO| j(d[k} | jPdk r= | jO| jPd[k} q= q@ t&dn|jLr | jNr | j@r |jQdk r |jr dGHdGHdGHdGHH| jR} q t&dq t&dq t&dq t&dn|jSs |dkr g} q|j>| j>krA | j>r$ d}nd}t&d|dnd| g} |jHjT| jHs| jU} |jUjV| }| jHjI|jHjI}|d[kr t&d|q qn|dk r t&dndGH| jSd|jWd|jXd|jYd|jZ}t} |jZd-kr?d[} n|jZd.krWd} n|j'dj|j(| k}d|g} | j[dst\| j[d|jW| j[dt |jX| j[d|j(jMt| j[d|j(jMtt]}|j^drdsd||jZd-krU| j[dt j_|j(n,|jZd.krt| j[dn | j[ddj`| dd!GH| dGH|jaGHHd[}|jbdk r>|jSrt&dntjcd|j!jdgd|jbdddd}dG|GHtejfjgjhd|d| |db7}Hn|jQdk rtjcd|j!jdgd|jQdddd}dG|GHt ji}|j[t\|j[d||j[dtjjkjl|j!jd|j[dtjjkjmtjjkjn|j!jd|j[d|j!jo| }|jrj|jpsdGH|jB}|j[dqn9|jr|j@sdGH|jC}|j[dqn|j}|dkr|j!jqd[}n|jrd|}~|dk r-|jsd|d|jtx"| D]}|j[d|qWn|j[dtjjkjl||j[dtjjkjmtjjkjn||ju}|jv||jhd||db7}Hn|jwdk rEtjcd|j!jdgd|jwdddd,}dG|GH| jxdty|dd|ddt |j!g| d||db7}Hn|jzdk r|jSrlt&dntjcd|j!jdgd|jzdddd.}dG|GH| j{j|ty|d|db7}Hn|d[kr|jjdGdGHHdS| S(Ntusages %s [options] reflection_file ...t descriptionsExample: %s w1.sca --mtz .s--weak_symmetrytactiont store_truetdefaultthelps?symmetry on command line is weaker than symmetry found in filess--labeltstorettypetstrings,Substring of reflection data label or numbertmetavartSTRINGs--non_anomalouss6Averages Bijvoet mates to obtain a non-anomalous arrays--r_free_labels--r_free_test_flag_valuetints8Value in R-free array indicating assignment to free set.tFLOATs--generate_r_free_flagssGGenerates a new array of random R-free flags (MTZ and CNS output only).s0--use_lattice_symmetry_in_r_free_flag_generationtdestt.use_lattice_symmetry_in_r_free_flag_generations\group twin/pseudo symmetry related reflections together in r-free set (this is the default).s/--no_lattice_symmetry_in_r_free_flag_generationt store_falses<opposite of --use-lattice-symmetry-in-r-free-flag-generations--r_free_flags_fractiong?tfloats6Target fraction free/work reflections (default: 0.10).s--r_free_flags_max_freeis3Maximum number of free reflections (default: 2000).tINTs--r_free_flags_formattchoicestcnstccp4tshelxs&Convention for generating R-free flagsscns|ccp4s--output_r_free_labelsALabel for newly generated R-free flags (defaults to R-free-flags)s R-free-flagss --random_seedsFSeed for random number generator (affects generation of R-free flags).s--change_of_basisswChange-of-basis operator: h,k,l or x,y,z or to_reference_setting, to_primitive_setting, to_niggli_cell, to_inverse_hands--eliminate_invalid_indicessBRemove indices which are invalid given the change of basis desireds--expand_to_p1sGenerates all symmetrically equivalent reflections. The space group symmetry is reset to P1. May be used in combination with --change_to_space_group to lower the symmetry.s--change_to_space_groupsFChanges the space group and merges equivalent reflections if necessarys SYMBOL|NUMBERs--write_mtz_amplitudessWConverts intensities to amplitudes before writing MTZ format; requires --mtz_root_labels--write_mtz_intensitiessWConverts amplitudes to intensities before writing MTZ format; requires --mtz_root_labels--remove_negativess;Remove negative intensities or amplitudes from the data sets--massage_intensitiess'Treat' negative intensities to get a positive amplitude. |Fnew| = sqrt((Io+sqrt(Io**2 +2sigma**2))/2.0). Requires intensities as input and the flags --mtz, --write_mtz_amplitudes and --mtz_root_label.s --scale_maxs=Scales data such that the maximum is equal to the given values--scale_factors%Multiplies data with the given factors--scasBwrite data to Scalepack FILE ('--sca .' copies name of input file)tFILEs--mtzs<write data to MTZ FILE ('--mtz .' copies name of input file)s--mtz_root_labels#Root label for MTZ file (e.g. Fobs)s--cnss<write data to CNS FILE ('--cns .' copies name of input file)s--shelxs@write data to SHELX FILE ('--shelx .' copies name of input file)targstvaluesJ--write_mtz_amplitudes and --write_mtz_intensities are mutually exclusive.sL--write_mtz_amplitudes and --write_mtz_intensities require --mtz_root_label.s6--scale_max and --scale_factor are mutually exclusive.it file_namestcrystal_symmetrytforce_symmetrytmerge_equivalentstdiscard_arraystverboseis)No reflection data found in input file%s.t miller_arraystlabeltcommand_line_switchttest_flag_valuesnCannot automatically determine r_free_test_flag_value. Please use --r_free_test_flag_value to specify a value.s!Invalid --r_free_test_flag_value.tdatasSelected data:t s Observation type:s R-free flags:tother_symmetrytforcesInput crystal symmetry:tprefixs sCUnit cell parameters unknown. Please use --symmetry or --unit_cell.s<Space group unknown. Please use --symmetry or --space_group.tchange_of_basisteliminate_invalid_indicestcb_ops#Merging symmetry-equivalent values:s)Merging symmetry-equivalent R-free flags:s3Expanding symmetry and resetting space group to P1:s8--expand_to_p1 not supported for arrays of R-free flags.sA--change_to_space_group not supported for arrays of R-free flags.tsymbolsChange to space group:t unit_celltspace_group_infotassert_is_compatible_unit_cells *************s W A R N I N Gs> Unit cell parameters adapted to new space group symmetry ares: significantly different from input unit cell parameters:s! Input unit cell parameters:s! Adapted unit cell parameters:s8 Merging values symmetry-equivalent under new symmetry:s s6Converting data array from anomalous to non-anomalous.s8Converting R-free flags from anomalous to non-anomalous.s*Applying low resolution cutoff: d_max=%.6gs+Applying high resolution cutoff: d_min=%.6gtd_maxtd_minsNumber of reflections:s1Scaling data such that the maximum value is: %.6gt target_maxs&Multiplying data with the factor: %.6gtfactorisXIt is not possible to use --remove_negatives and --massage_intensities at the same time.sRemoving negatives itemss9--remove_negatives not applicable to complex data arrays.s1The supplied intensities will be used to estimates# amplitudes in the following way: s8 Fobs = Sqrt[ (Iobs + Sqrt(Iobs**2 + 2sigmaIobs**2))/2 ]s* Sigmas are estimated in a similar manner.sK--write_mtz_amplitudes has to be specified when using --massage_intensitiess5--mtz has to be used when using --massage_intensitiessHIntensities must be supplied when using the option --massage_intensitiess<--massage_intensities not applicable to complex data arrays.ts nots9The data array is%s anomalous but the R-free array is%s. s Please try --non_anomalous.sR-free flags source: saR-free flags not compatible with data array: missing flag for %d reflections selected for output.sB--r_free_label and --generate_r_free_flags are mutually exclusive.s'Generating a new array of R-free flags:tfractiontmax_freetuse_lattice_symmetrytformatisR-free flags generated by %s:s fraction: %.6gs max_free: %ss size of work set: %ds size of free set: %dtouts& convention: CCP4 (test=0, work=1-%d)s& convention: SHELXL (test=-1, work=1)s) convention: CNS/X-PLOR (test=1, work=0)s is,Cannot write R-free flags to Scalepack file.tinput_file_namestuser_file_nametfile_type_labelt Scalepacktfile_extensiontscasWriting Scalepack file:t file_namet miller_arraytMTZtmtzsWriting MTZ file:s > program: %ss> input file name: %ss> input directory: %ss> input labels: %ss' Converting intensities to amplitudes.s&> Intensities converted to amplitudes.s' Converting amplitudes to intensities.s&> Amplitudes converted to intensities.tcolumn_root_labels> s> output file name: %ss> output directory: %stCNSsWriting CNS file:t file_objecttwtinfossource of data: t r_free_flagss(Cannot write R-free flags to SHELX file.tSHELXsWriting SHELX file:s/Please specify at least one output file format,se.g. --mtz, --sca, etc.(scnsRsshelx(R>s not(s notR>(}Rtenable_symmetry_comprehensivetoptiontNonetFalsetenable_resolutionstTruetprocesstoptionst random_seedtrandomtseedRtset_random_seedtwrite_mtz_amplitudestwrite_mtz_intensitiestmtz_root_labelt scale_maxt scale_factortlenR"tparsert show_helpRtcollect_arraysR Rt label_tablet select_arrayR+t r_free_labeltmatch_data_labeltstrRRt is_bool_arraytget_r_free_flags_scorestr_free_test_flag_valuettest_flag_valuesRtcustomized_copyR.tobservation_typet join_symmetrytsymmetryt weak_symmetrytset_observation_typeRt show_summaryR7R8R3tapply_change_of_basisR4t change_basistis_unique_set_under_symmetryR'tarraytshow_comprehensive_summaryt expand_to_p1tchange_to_space_groupRt is_similar_totanomalous_flagt non_anomaloustis_xray_intensity_arraytaverage_bijvoet_matest f_sq_as_ft f_as_f_sqt#set_observation_type_xray_intensitytlow_resolutiont resolutiontresolution_filtertindicestsizet apply_scalingtremove_negativestmassage_intensitiestcountt is_real_arraytselecttsigmasRMtenforce_positive_amplitudestgenerate_r_free_flagstall_eqt map_to_asut common_settr_free_flags_fractiontr_free_flags_max_freeRtr_free_flags_formattappendRR tshow_r_free_flags_infotmaxtjointgetvalueRItconstruct_output_file_nametsourcetiotbxt scalepacktmergetwritet std_stringtostpathtbasenametdirnametabspatht label_stringtis_xray_amplitude_arraytlabelstas_mtz_datasettadd_miller_arraytoutput_r_free_labelt mtz_objectt add_historyRtexport_as_cns_hkltopenR tas_amplitude_arraytexport_as_shelx_hklf(R"t command_nametsimply_return_all_miller_arrayst command_linetcotall_miller_arraysRjtselected_arrayRSt r_free_infoR-tprocessed_arrayR5tmergedtnew_space_group_infotnew_crystal_symmetryR:R;tis_nottn_missing_r_free_flagstr_free_as_booltr_free_info_strtn_output_filesRJtmtz_history_buffertmtz_output_arrayRNt mtz_datasettlineR((sM/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_converter.pytruns                                                                                                                                            !                                                 )                                    (t __future__Rt iotbx.mtzRtiotbx.cns.miller_arraytiotbx.scalepack.mergeRRtiotbx.option_parserRtcctbxRRtcctbx.array_familyRt libtbx.utilsRRR t cStringIOR R^RRXR(((sM/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_converter.pyts