xTc@ sddlmZmZddlZddlmZddlmZmZmZddlm Z ddlm Z ddl m Z ddl Z ddlmZmZdd lmZdd lmZdd lmZmZmZmZdd lmZdd lmZddlm Z ddl!Z!ddl"Z"ddl#Z#ej$ddddddddgZ%ddgZ&e'e(dZ)e(e'ddZ*dZ+dZ,de-fdYZ.d e-fd!YZ/d"e-fd#YZ0d$Z1e#j2e'e'd%Z3dS(&i(tprint_functiontdivisionN(tpickle_support(t master_paramst phaser_stylet match_modes(t phaser_result(t callbacks(t file_reader(tcrystaltsgtbx(tflex(tobject_oriented_patterns(tSorrytimport_python_objectt multi_outtnull_out(t interface(tStringIO(t easy_pickletMR_AUTOtMR_FRFtMR_FTFtMR_LLGtMR_PAKtMR_RNPtMR_BRFtMR_BTFtEP_AUTOtEP_SADcC sd}|rd}n|dk r.d|}ng|jdD]}|d ^q>}|djg|D]}|j^qd7}|jr|jdr|jdd}n|S(Ntsettadds%s_t_i(tNonetsplittjointuppert as_multiplet startswithtreplace(tnametstyletprefixtmultiplet method_nametstfields((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyttranslate_keywords   &,icC s|}x|j|D]}|jdkr/qnt|} | jrJqqt|| j|r|jr|} | dkrtd|j d| d|j } n|j rd| d} n| j s| j rg} xi|jD]^} | j st | j} | dkr+|jtd| jn| j| qWt|| }| j rtd| d jg| D]}t|^qjfd ||| qtd | d jg| D]}t|^qfd ||| q| jr?i}g}x|jD]} | j st | j} | dkrV|jtd| jn| || j corrupted input file; please inspect your data and convert to s!amplitudes manually if necessary.s%s is not X-ray data.is %s_data.mtztcolumn_root_labeltFsF,SIGF(/tphaserthklinReRtany_filetcheck_file_typeRit file_objecttas_miller_arraystsigmasR!R tFalsetcustomized_copyRORwRmRnRQRttis_xray_intensity_arraytcctbxRxtfrench_wilson_scaletanomalous_flagtaverage_bijvoet_matestis_xray_amplitude_arrayRhtis_unique_set_under_symmetrytmerge_equivalentsR>tcounttselecttkeywordstgeneraltroott test_modetostpathtabspatht map_to_asutas_mtz_datasett mtz_objecttwritet d_max_mintd_maxtd_min(tselftparamstsymmetrytoutRqthkl_filet input_arrayt is_changedRxt bad_sigmasR~t mtz_datasetRtlabout((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyt__init__s                             (RKt __module__tsyststdoutR(((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyRustprocess_ep_crystalcB seZejdZRS(c C s|jjjj|_|jjjj|_|jjj|_|jjj |_ |jdk rfd}ni|_ i}x|jj D]}|j }x|jD]}d|j|j|jgkrqn|j} |j|kr tj|j} | jd| ||j}|j} d|| f}|j)|dk rntdd|| fn<t*|dkrtdd|| t*|dfn|j || f}| j+d|} | j,\}}|jdks|j|kr ||_n|jdks)|j|kr5||_n| j-rrddl.m/}|j0d| d td!|} n| j1std"| n| j2} | j3s| j4j5} n| jd#k}| j6|} |j"dkr| |_"n|dkr| j7d$|}n|j8d| d$|d%t9|gd&}||_||_qWqW|j:}|j;d|~||_dS('NRvs%s:%sRdReRfs0Anomalous data required in mode '%s' (offending s data: %s).s!Experimental sigmas are required.RmRnRoRpRqs.Couldn't determine automatic crystal symmetry s:information from the provided reflection file(s). Please s&specify the space group and unit cell.RQt%raise_sorry_if_incompatible_unit_cells[^a-zA-Z0-9_\-]{1,}s %s_data.mtzsF_%s_%ss0The crystal ID and dataset ID must only contain s<alphanumeric characters or underscores (current: '%s','%s').is3The crystal ID and dataset ID combined must not be s4more than 21 characters (current: '%s'+'%s' = %dc.).iRwi(RxRgRyRzs%s is not X-ray data.iR{s%s(+),SIG%s(+),%s(-),SIG%s(-)i(<R}Rt resolutionthighRtlowRRwRmRnR!RdR txtal_idtdatasettwave_idR~ReRRRRiRRRR R4RRQRtRROtretcompiletdataRRRRRRtsearchtlenRRRRRxRRRRRR>RRtadd_miller_arrayttupleRR(RRRRRrt input_filestxtalRRRRRqRtarray_sgtarray_uct not_alnumRR~R{t input_arryRRRxRtlabelsR((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyR1s                                         (RKRRRR(((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyR0stphaser_parameter_interpretercB sAeZejdZdZeedZejedZ RS(c2 C s|jj}||_|jj}t}||_d|_t dd||j drt dd|tj }tj }nC|j drt dd|tj }tj}n d}d}tj} | j||dk r|js|jr|jtqntjd} |jjjjdkrItdn0| j|jjjjdk rytd nd} |jjjdk r|jjjdk rtj d |jjjd |jjjd t} nd} t!||j"d r|jj#dkrtd|n%|jj$dkrDtd|nt%d|d| d|} t d|jj#d||j&|jj#|jj$j'd} t(| dkst)t d| d| dfd||j*| d| dnt!||j"drt(|jjdkr9td|n't(|jjdkr`tdn|jjd}t(|j+dkrtdnt,d|d| d|} t d| j#d||j&| j#| j-|_x|jjD]}|j.}d|j/|j0gkr)tddnx|j+D]}|j1}|j$j'd} t(| dkrtd d!d"d#d$|j$nt d%||| d| d| d| d&fd||j2||| d| d| d| d&q3WqWnt!||j"d'r8|jjjdkr]| jdk rJ| j|jj_q]td(d)nt3|jjj}t d*|d||j4||jjjdkr| jdk r| j|jj_qtd+d)n|jjjj5}t d,d-j6g|D]}d.|^qd||j7|n| dk r|jjj8j9dkrt| j:|jjj8_9n|jjj8j;dkr| j<|jjj8_;qnt=d/d0|d1d2d3d2d4d2j>}t d5|d||}||_?|dk r t d6|j@d|||| }tA|d7t d8d|t d9d||j7|jB|jC|jD|jEjFr|jEjGdkr|jH||jE_Gqn|j d:r|dxkrt d<d||jI|jJ|jK|jLn|j d=r t d>d||jM|jJx|jjD]}|j.}x|j+D]}|j1}t d?||fd|t d@||fd|t dA||fd|t dB||fd|t dC||fd|t dD||fd||jN||}|jO||}|jP||}|jQ||}|jR||}|jS||}t dEdF||fd||jT|||||||||jU|jVgjWddkr tdGdHq^|jUdk r" t dI|jUd||jX|jUq^|jVdk r^|jVdJ}t dI|d||jX|q^q^W|j/dk r t dK||j/fd||jY||j/qE|j0dk rEt dL||j0fd||jZ||j0qEqEWn~~nt[} }!t!||j"dMr t(|jj\dkr t(|jj]dksR t)t(|jj^j_dkss t)t(|jjdks t)|jj`dk r |jj`dks t)|jjadk r |jjadks t)|jjbdk rc t(|jj\t(|jjbks! t)xtc|jj\|jjbD]\}"}#|jddN|"|#q= WnX|jjedk r xCtc|jj\|jjeD]#\}"}$|jfdN|"|$dOq Wn|jjgdk r |jjhdPkr |ji|jjg|jj`q |jj|jjg|jj`nb|jjkdk r |jjhdPkr` |jl|jjk|jj`q |jm|jjk|jj`n|jndN|jjat} }!q nt!||j"dQrx0to|jj]D]\}%}&|&jp}'|'dkrtdR|%dnt(|&jqdkr|&jrdk rCtdSdT|'nx]to|&jqD]L\}(})|)jsdkrtdUdV|'|(dfn|)jtsl|)ju|)jvgjWddkrtdWdX|)jsq|)judk r't dY|'|)jst3|)jufd||jd|'|)js|)juqt dZ|'|)jst3|)jvfd||jf|'|)js|)jvqSt d[|'|)jsfd||jw|'|)jstqSW|&jxr|jy|'tn|&jzrh|j{|'tqhn|&jrdk rh|&}*|*j|dkrtd\|'n|*j}dks]t(|*j}d&ks]|*j~dks]t(|*j~d&krxtd]d^d_|'nd|*j|*jgks|*jdkr|*jdkrtd`da|'n|*j|j'd\}+},t dbdc|'|*jr|+|,t3|*j}|*jt3|*j~|*j|*jf d||j|'|*jr|+|,|*j}|*j|*j~|*j|*j n|&jdk rt dd|&jp|&jfd||j|&jp|&jt} n|&jr t de|&jpd||j|&jpq q Wnt!||j"dfr |! r6t(|jjdkr6tdgnxto|jjD]\}%}-|-jdkr{tdh|%dqIt(|-jdkrt di|-jdt3|-jfd||jn|-jd|-jqIt djt3|-jt3|-jfd||j|-j|-jqIWnt!||j"dkrQ| sQ|j|qQn|jjdk rftjj|jjst)tj|jj}.t|.dlr|.j}.nt|.j@dmkr|.j}/n |.j}/t(|/dkrtdnn|dykr3|/jsVtdqdrqVn#|/jrVtdsdtdun|j|/n|jj}0|jdv}1t||1|||j|||_t dw|d||j|_||_?||_dS(zNs import phaserR0tMR_sdata = phaser.InputMR_DAT()tEP_sdata = phaser.InputEP_DAT()s[^a-zA-Z0-9_\-\.]{1,}s+Please define a root filename for this run.s8The root filename must be alphanumeric (underscores OK).RnRQRs phaser.hklins/You must specify a reflections file in mode %s.s3You must specify reflection data labels in mode %s.RRRsdata.setHKLI('%s')t,isdata.setLABI('%s','%s')iisphaser.crystals"Crystal data required for mode %s.s(Only one crystal supported at this time.s+Only one wavelength supported at this time.s5For each crystal, you may supply heavy-atom sites as s-EITHER a PDB file OR 'ha' file, but not both.is2The data labels %s do not appear to correspond to s@the appropriate data type. For experimental phasing, data must s>be merged, anomalous amplitudes in MTZ format. The graphical s>reflection file editor (phenix.reflection_file_editor) can be s$used to convert the data as neeeded.s:data.addCRYS_ANOM_LABI('%s', '%s', '%s', '%s', '%s', '%s')isphaser.crystal_symmetrys4Couldn't determine space group information - please s#supply crystal symmetry parameters.sdata.setSPAC_NAME('%s')s2Couldn't determine unit cell information - please sdata.setCELL6([%s])s, s%.3ft import_pathsphaser.Input%st error_prefixtttarget_must_bet where_strsinput = phaser.Input%s()sr = phaser.%s(data)ssetting up data inputssinput.setCELL6(r.getUnitCell())s)input.setSPAC_HALL(r.getSpaceGroupHall())tMRRs7input.setREFL(r.getMiller(),r.getFobs(),r.getSigFobs())tEPs#input.setCRYS_MILLER(r.getMiller())sFpos = r.getFpos('%s', '%s')sSpos = r.getSIGFpos('%s', '%s')sPpos = r.getPpos('%s', '%s')sFneg = r.getFneg('%s', '%s')sSneg = r.getSIGFneg('%s', '%s')sPneg = r.getPneg('%s', '%s')s6input.addCRYS_ANOM_DATA('%s','%s',Fpos,Spos,Ppos,Fneg,s Sneg,Pneg)s-Please enter EITHER a wavelength (Angstroms) sOR energy (eV), but not both.sinput.setWAVE(%.5f)g7@sinput.setATOM_PDB('%s','%s')sinput.setATOM_HA('%s','%s')s phaser.modeltense_1g{Gz?tproteinsphaser.ensembles"Missing model ID for ensemble #%d.s/Please specify either PDB files or an MTZ file sfor ensemble %s, but not both.s0Missing PDB file for ensemble %s coordinate set s%d.s,Please specify EITHER an RMSD OR fractional sidentity for PDB file %s.s#input.addENSE_PDB_RMS('%s','%s',%s)s"input.addENSE_PDB_ID('%s','%s',%s)s(input.addENSE_PDB_CARD('%s', '%s', True)s,You must specify labels for map data for %s.s2You must specify the extent and center of the map s<used for ensemble %s; this must both take the form of three s%decimal numbers between zero and one.s2Please specify protein and/or nucleic acid masses sfor ensemble %s.s8input.addENSE_MAP('%s', '%s', '%s', '%s', %s, %.3f, %s, s %.1f, %.1fsinput.setENSE_FRAC('%s',%s)sinput.addSOLU_ORIG_ENSE('%s')s phaser.searchsNo search procedure defined.s.No model IDs supplied for search component %d.sinput.addSEAR_ENSE_NUM('%s',%s)s%input.addSEAR_ENSE_OR_ENSE_NUM(%s,%s)sphaser.compositiontget_phaser_objectt ResultMR_RFs/The specified previous solutions file is empty.RRs6Input solutions for the translation functions must be s$the output from a rotation function.s0The specified solutions file is from a rotation s:function; both rotation and translation are required when s,supplying an existing solution in this mode.sphaser.keywordssresult = phaser.run%s(input)(R(RR(t working_philR@RR}R4Rt _script_outR!t input_dataRER&t InputMR_DATt runMR_DATt InputEP_DATt runEP_DATtOutputtsetPackagePhenixtdry_runt show_scripttsetMUTERORRRRRR RRwRnRmR RRtget_phaser_modesR~ReRutsetHKLIR"RR?tsetLABIRRRRtpdb_filetha_fileRtaddCRYS_ANOM_LABIRFt setSPAC_NAMEt parametersR#tsetCELL6RRRRRRtobjectR2RKthandle_runtime_errort getUnitCellt setSPAC_HALLtgetSpaceGroupHalltdensity_modificationtdmtsolvent_fractiontget_solvent_contenttsetREFLt getMillertgetFobst getSigFobstsetCRYS_MILLERtgetFpost getSIGFpostgetPpostgetFnegt getSIGFnegtgetPnegtaddCRYS_ANOM_DATAt wavelengthtenergyRtsetWAVEt setATOM_PDBt setATOM_HARtmodeltensemblet compositiontchaintcomponent_copiest search_copiest model_rmsdtziptaddENSE_PDB_RMStmodel_identitytaddENSE_PDB_IDtseq_filet chain_typetaddCOMP_PROT_SEQ_NUMtaddCOMP_NUCL_SEQ_NUMt mol_weighttaddCOMP_PROT_MW_NUMtaddCOMP_NUCL_MW_NUMtaddSEAR_ENSE_NUMt enumeratetmodel_idt coordinatest map_hklintpdbtread_variance_from_pdb_remarkstrmsdtidentitytaddENSE_PDB_CARDt disable_checktsetENSE_DISA_CHECt use_hetatmt setENSE_HETAt map_labelst map_extentt map_centretmap_protein_mwtmap_nucleic_mwtmap_rmst addENSE_MAPtfractional_comptaddCOMP_ENSE_FRACtsolution_at_origintaddSOLU_ORIG_ENSEt ensemblestcopiestaddSEAR_ENSE_OR_ENSE_NUMtset_compositiontsolutionRRtisfileRtloadthasattrRRJt getDotRlistt getDotSoltis_rlisttsetSOLUtget_scope_by_nameRNtupdate_from_pythontgetvaluetscript(2Rtindext working_dirRRR4R-Rtrun_data_classt phaser_outRRt process_dataRRtxtalidRtwaveidRmRntxt input_classR2trtwavetFpostSpostPpostFnegtSnegtPnegRthave_compositiont have_searchRRRtiRRtjtcoordstenstf_labelt phi_labelt componentt old_resultR/RR3((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyRsZ            !    "      0   .       (  "!   !*   !        $$    &         cC s|j}|jjjdk r+|jjjStj}|j|j|j|j |j |dt |j t tj|}|jstddddn|j}dd|SdS(NR5s8Could not determine solvent fraction automatically. If sByou want to use density modification, we recommend you explicitly s@set the solvent fraction (available under "Density modification"sin the Settings menu).g?gGz?(RR}RtsolventR!tInputCCARRRRR.RRROtrunCCAtSuccessR t getBestVM(Rt data_resultRR2RDtvm((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyRs        cC sw|j}|dkr!|j}n|}|dkr?|j}n|jjjdk rt|jjjdkrt ddnt dd||j nt|jjjdkrt dd||j xt |jjjD]\}}ddd d g}g|D]}t||^q} | jdd kr^t d d d|dn|jdkrt d|dn|jdkrd} nd} |jdk r| d7} |j} n]|jdk r| d7} |j} n8|jdk r| d7} |j} n| d7} |j} t|| } t| trOd| } n t| } t d| | t|jfd|| | |jqWnt dd||jxt |jjjD]\}}|jdks|jdkr t dd|dnt d|j|jfd|y|j|j|jWqtk rn}t t|qXqWdS(Nis4Please specify EITHER fractional solvent content OR s$individual components, but not both.sinput.setCOMP_SOLV()R0sinput.setCOMP_ASU()t sequence_filetsequencetnrestmwis2Please specify ONE source of mass information for s=chain #%d: sequence file, sequence string, # of residues, or smolecular weight (Da).is4Please specify a number of copies for component #%d.Rt addCOMP_PROT_t addCOMP_NUCL_tSEQ_NUMtSTR_NUMtNRES_NUMtMW_NUMs'%s'sinput.%s(%s,%s)sinput.setCOMP_AVER()s.Please specify an element and number of atoms sfor heavy atom %d.s input.addCOMP_ATOM_NUM('%s', %d)(RR!RR2R}RRVRRR REt setCOMP_SOLVt setCOMP_ASURRDRtnumR R]R^R_R`RHRFt setCOMP_AVERtatomtelementtaddCOMP_ATOM_NUMt ValueError(RR2R5RR-RNRt mass_attrR(tmassesR,t mass_valueRYt out_valueRkR]((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyR.st        ""            "c C sQtdd|jddddddj}tj}|rLtj}n tj}t }t |j jj j jdd}|jd ||jd ||j||r|j|nz6||j|}|jt|d ||_Wd|jX|j jjrMd d lm} g} |j jjjdrf|j jj j jdg} nM|j jjjdr|j jj j jd|j jj j jdg} n|jddddxh| D]`} tjj| r|jdddd| | j d| d|j!d|j jd|qqW|jddddndS(NRs phaser.run%sRRRRs.logtwsPrimary output streamsPhaser logfilesrunning main functioni(RRs.1.mtzRs .1.hand.mtztmessaget phaser_startRtMODEsdensity modification with %st phases_filetf_obsRRzt phaser_end("RR4RR}RRtmanagertooptnullRtopenRRRRtregisterRtsetPhenixCallbackR2t flush_summaryRtresulttcloseRRtphaser.phenix_interfaceR&t call_backR!RRR0trun_density_modificationR( RRt use_callbackt run_classR>tcallbackt out_wrappertlog_fileRDRt mtz_filesRf((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pytrunPsP    "          ( RKRRRRRR!R.ROR(((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyRs W AcC s8|js4td||j|jfndS(NsERROR %s (%s): %s(RYR t ErrorNamet ErrorMessage(Rt procedure((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyR|s c C syddlm}Wntk r3tj}nXddl}|jg}|dk r~|jj |}|j |n|dk r|j |nt }|jj d|d|ddddd d } | j }tj||d |jj } | j} | jr |jd |tS| jjdk rm| jjdkrm| jjj rmdd lm} | j| jjdd} | jdd}}x| jjD]}|jj }|dkr|}Pq|j!r|j"d r|dkr|}q|j#r|dkr|}qqW|dk rB|| j_n|dk r]|| j_n| j$| n|}| j%st&}nt'| t(j)d |}| j*r|j+|j,tS| j-rt.|j/_-| j$|j/| j0jd |tS| j%r!| j0jd |n|j1d ||j/} |j2ddd|jd |ddt3d|j4d| dt(j)}|S(Ni(t citationsRVt master_philt pdb_file_defs phaser.modeltreflection_file_defs phaser.hklint seq_file_defsphaser.seq_filetparseR(Rt force_typeRvsF,SIGFs FOBS,SIGFOBSsF(+),SIGF(+),F(-),SIGF(-)tFCR}tsourcetPhasert phaser_objectRtrun_dir(sF,SIGFs FOBS,SIGFOBSsF(+),SIGF(+),F(-),SIGF(-)(5tphenix.utilitiesRt ImportErrorR{R|t iotbx.philtclear_citationsR!tphilRRCRtprocess_command_line_with_filestworktphil_interfaceR;tget_python_objectt show_defaultsRAROR}R~Ret run_controltgui_runtiotbxRRRt file_serverRdRbRcRR&RR8tverboseRRRtgetcwdRRR:RRRtget_diffRt add_citationRR(RVRtphil_strRRRtsourcest input_philRtcmdlineR;RRR~RRti_labelR>tlabelttmp_outt run_phaserR((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyRs           $                (4t __future__RRR}RRRRRRRRRRRR R tscitbx.array_familyR tlibtbxR R{t libtbx.utilsR RRRt libtbx.philRRtlibtbx.str_utilsRRRRRtenabletmr_modestep_modesR!RR/RNRiRtRRuRRRRR(((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/phenix_interface/driver.pyts@  "       Ns