xTc @ sddlmZddlmZddlmZddlZddlZddlZddl m Z ddl m Z ddl mZddlmZddlZ ddlZddlZddlZddlZd ejed Zeeeeeeeejd Zeeeeejd Zejjd deZejeedZ dZ!dej"fdYZ#dZ$e%dkreej&dndS(i(tdivision(tiotbx_option_parser(tcrystal_symmetry_from_anyN(tflex(tcrystal(t runtime_utils(tSorrysphenix.cif_as_mtzc C sVt|dkrdg}nywtdd|dd|jjdddd d td d d djdddd d dd dd djdddd d dd dd djdddd d dd d d djddddd djddddd djddddd djddddd djd ddd d!jd"ddd d#jd$ddd d%jd&ddd d'jd(|}Wn@tk r}t|d)krt|GHnt j dnX|j }t|j d*kr%|d+t|j I|j IJt d,n|j d}tjj|sWt d-|n|jj}|dtjkstjd.|rt d/d0d1|ntd2|d3|d4|jjd5|jjd6|jjd7|jjd8|jjd9|jjd:|jjd;|jjd<|jjd=|d>|jj d?|jj!d@|} |rR| SdS(ANis--helptusages"%s [reflection_cif_file] [options]t descriptions.Example: %s r1o9ksf.ent --symmetry=pdb1o9k.ents--output_file_nametactiontstoretdefaultttypetstringthelpsOutput mtz file name.s--wavelength_idtints*Extract data set with given wavelength_id.s --crystal_ids'Extract data set with given crystal_id.s--output_r_free_labels R-free-flagss@MTZ column label to use for R-free flags (default: R-free-flags)s--merget store_trues$Merge non-unique data where present.s --incompatible_flags_to_work_setsLWhen merging place reflections with incompatible flags into the working set.s--remove_systematic_absencess%Remove systematic absent reflections.s --map_to_asusMap to asymmetric unit.s--show_details_if_errors"Show data details for some errors.s --show_logsShow some output.s--ignore_bad_sigmassKSet sigmas to None instead of raising an error when bad sigmas are present.s--extend_flagss:Extend R-free flags to cover all reflections if necessary.targst0is-%d arguments are given from the command line:s'Please specify one reflection cif file.sFile is not found: %ss[^a-zA-Z0-9_\-]s8%s is not a suitable column label. 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Please make sEsure that the file contains reflection data, rather than the refined smodel.c sd}x|jjD]}d|krn|jr=d}n-|jrRd}n|jdrjd}nPqd|kr|jrd}nE|jrd}n0|jd rd}n|jd rd }nPq|jr|jrd }n|jrd }nPqd|ks*d|kr4}Pq|jrId}q|jr|jdrnd}Pq|jdrd}Pqq|j rd|krd}Pq|jdrd}PqqqW|S(Nt_meastFOBStIOBSs .phase_meastPHIMt_calctFCtICALCs.F_calcs .phase_calctPHICtFtItstatust_freetHLtDELFWTtFWTtpdbx_anom_differencetDANOs.fomtFOM( R%tinfotlabelstis_xray_amplitude_arraytis_xray_intensity_arrayR?tanomalous_flagtis_hendrickson_lattman_arraytis_complex_arrayt is_real_array(t miller_arraytlabeltl(R(sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/cif_as_mtz.pyt get_labels\                        tother_symmetrytforce(tStringIOs6Space group is incompatible with unit cell parameters.tfs %ssBCrystal symmetry is not defined. Please use the --symmetry option.ttitlesphenix.cif_as_mtztspace_group_infot unit_cell(t$cif_status_flags_as_int_r_free_flags(tmake_joined_setRs/Can't determine output label for %s - skipping.ttest_flag_valuetdataRt=s%itnames crystal_%it project_nametprojectRitdatasett wavelengths,Warning: bad sigmas, setting sigmas to None.s{Bad sigmas: all sigmas are equal to zero. Add --ignore_bad_sigmas to command arguments to leave out sigmas from mtz file.s Warning: merging non-unique datatincompatible_flags_replacementsiWarning: %i reflections were placed in the working set because of incompatible flags between equivalents.s%merge_equivalents_exact: incompatibles for %ss sjAdd --incompatible_flags_to_work_set to command line arguments to place incompatible flags to working set.s*Miller indices not unique under symmetry: s (%d redundant indices out of %d)s7Add --merge to command arguments to force merging data.tprefixs tother(t r_free_utilst r_free_flagst array_labelt complete_settpreserve_input_valuestallow_uniform_flagsR!s/%d reflections do not have R-free flags in the sarray '%s' - this may s=cause problems if you try to use the MTZ file for refinement s<or map calculation. We recommend that you extend the flags s>to cover all reflections (--extend-flags on the command line).tindicestnegateRUtPHItPRWtDQtDs-%itcolumn_root_labeltlabel_decoratort column_types(iii((iii(Tt iotbx.ciftcctbxRCt array_infotciftreadertbuild_miller_arraysR"RtsettTruet iteritemstvaluest join_symmetryRtAssertionErrorR)t cStringIORgt show_summarytgetvalueRkR%Rjtmtztobjectt set_titletset_space_group_infot set_hkl_basetiotbx.reflection_file_utilsRlRmtappendt enumeratetcustomized_copytset_infoRYRZt label_stringt startswitht isinstanceRoRtdoubletiroundt as_doubletall_eqR[R\Rtsplitt add_crystalRut add_datasettsigmastcountR&t set_sigmastis_unique_set_under_symmetrytmerge_equivalentstn_incompatible_flagstarrayRtsizetunique_under_symmetry_selectiontbooltshow_comprehensive_summaryRtsortt show_arrayRtlone_setRyR R*tstdouttlibtbxtwarntselect_indicest miller_indextccp4_label_decoratorR`taddtadd_miller_array(<RRRRRRRRRRRR RR!tiotbxRCRFtall_miller_arrayst column_labelsRdt data_namet miller_arraystmaReR9tstr_eRgtsRBRkt mtz_crystalsRlRmt all_arraysR|tmiller_array_listtiRZRbt_tdata_inttcrys_idRcRtdatasetstw_idRuRttmergingtn_allt sel_uniquetsel_dupt n_duplicatetn_uustmsgt n_missingRytdecRt label_base((RsK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/cif_as_mtz.pyR=s       0           %   !'0  $     $      3      %             s input .caption = This program will convert CIF-formatted structure factors (used by the PDB) to an MTZ file. Other CIF types (restraints, etc.) will be ignored. Because the data in the PDB often contains mistakes or lacks symmetry, an optional model file is strongly recommended. If you want the program to generate an MTZ file for a specific PDB ID, you may specify that instead of input files, and the CIF and PDB will be fetched from www.rcsb.org. .style = caption_img:icons/custom/phenix.reflection_file_editor.png { pdb_id = None .type = str .short_caption = PDB ID to retrieve .input_size = 80 .style = bold noauto cif_file = None .type = path .short_caption = CIF data file .style = bold noauto OnChange:extract_symm_for_cif pdb_file = None .type = path .short_caption = Model file .style = bold noauto file_type:pdb OnChange:extract_symm_for_cif wavelength_id = None .type = str .short_caption = Wavelength ID .help = Not required when only one wavelength is present .input_size = 120 .style = noauto crystal_id = None .type = str .short_caption = Crystal ID .help = Not required when only one crystal is present .input_size = 120 .style = noauto } crystal_symmetry { space_group = None .type = space_group .style = bold unit_cell = None .type = unit_cell .style = bold } output_file_name = None .type = path .style = new_file bold include scope libtbx.phil.interface.tracking_params options { merge = False .type = bool .short_caption = Merge non-unique data map_to_asu = True .type = bool .short_caption = Map HKL indices to ASU eliminate_sys_absent = False .type = bool .short_caption = Remove systematic absences show_details_if_error = True .type = bool .short_caption = Show data details for some errors incompatible_flags_to_work_set = False .type = bool .short_caption = Move incompatible flags to work set ignore_bad_sigmas = False .type = bool extend_flags = False .type = bool .short_caption = Extend incomplete R-free flags show_log = True .type = bool } tprocess_includescC sddl}tjjtjtjdd}d}d}g}x |D]} t j j | rt j j| rt j j| } qb| jds| jdrt j j| }qbyt jjd| } Wntk rd| GHqbX|j| qJ| jdr"| d d } ny#|jd | } |j| WqJtk rad | GHqJXqJW|dkrtjd |j}nd} |jjdk rJ|jjjd|jjgd||j_|jjjdd|jjgd||j_t j!|jj} | j"|j#_$| j%|j#_%d|j_n|r]t&|n|j'dkrt j j(|jj\} }t j j)t j*| d|_'n| dkrt+|j#j$j,dkst-t.j/d|j#j$d|j#j%} nt0d|jjd| d|j'd|jj1d|jj2d|j3j4ddd|j3j5d|j3j6d|j3j7d|j3j8d|j3j9d |j3j: }|j'|fS(!Nit home_scopets.cifs.cif.txtRs!Unrecognizable file format for %ss--is=TruetargsUnrecognizable parameter %stsourcesRR!s-xs.mtzRjRkRRRRRRt FreeR_flagRRRRRR (;tmmtbx.command_line.fetch_pdbRt call_backtset_warning_logR*tstderrt master_philt!command_line_argument_interpreterR%R-R.R/Rtpdbt is_pdb_filetabspathR?tphiltparset RuntimeErrorRRR'tfetchR=tinputtpdb_idR8t fetch_pdbtrun2tpdb_filetcif_fileRt extract_fromRjRt space_groupRktvalidate_paramsRtsplitexttjointgetcwdR t__name__RRR,R4RRR0RR5Rteliminate_sys_absentRRR (RR!t check_paramstparamstmmtbxtparameter_interpreterRRRRt pdb_filest user_philtsymmtbasetexttn_refl((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/cif_as_mtz.pyRs         %             cC sA|jjdkr3|jjdkr3tdn|jjdk r|jjdk rftdnddl}y|jjj|jjWqt k r}tt |qXn3|j j dks|j j dkrtdn|jdk r=tjj|j}tjj|s=tdd|q=ntS(NsNo CIF file provided!s7Please specify either a PDB ID or a CIF file, not both.is'Crystal symmetry missing or incomplete.s3The output directory %s does not exist or is not a s directory.(RRR%RRtiotbx.pdb.fetchRRtvalidate_pdb_idRR)RRRkRR-R.tdirnametisdirR(RRR9t output_dir((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/cif_as_mtz.pyRgs&$ tlaunchercB seZdZRS(cC s/tj|jtdt|jdtjS(NRR!(R-tchdirR RtlistRR*R(tself((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/cif_as_mtz.pyR;~s(Rt __module__R;(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/cif_as_mtz.pyR }scC se|\}}|dkr!d}n|dk r[tjj|r[d|fgd|fgfSggfS(NisMTZ filesNumber of reflections(R%R-R.R/(tresultstmtz_fileR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/cif_as_mtz.pyt finish_jobs    t__main__i('t __future__Rtiotbx.option_parserRRRt iotbx.philt iotbx.mtzt iotbx.pdbtcctbx.array_familyRRRRRt libtbx.utilsRtlibtbx.callbacksR R2R-R*RR&R;R4R=RRRRR%RRttarget_with_save_resultR RRtargv(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/cif_as_mtz.pytsP          c' I G