יxTc@ s|ddlmZddlmZddlmZddlmZddlmZddlZddl Zddl m Z ddl m Z dd l m Z dd lmZdd lmZdd lmZmZdd lmZddlZddlZdefdYZddZddZdZddddddedZ ej!j"ddeZ#dZ$ddZ%dS(i(tdivision(t xmanip_tasks(treflection_file_reader(treflection_file_utils(tcrystal_symmetry_from_anyN(tcrystal(tsgtbx(tadptbx(tflex(tmatrix(tSorryt multi_out(tStringIOt quick_rt_mxc B sieZddlmZdddddddddg d dZdZdZdZd dZ RS( i(R iicC s(tj||_tj||_dS(N(R tsqrtrmRtdoublettv(tselftrtt((s:/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip.pyt__init__scC s|jS(N(R(R((s:/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip.pyRscC s|jS(N(R(R((s:/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip.pyRscC sCtd|jjd|jd |jd |jd f}|S(NRRiii(R RtinverseR(Rttmp((s:/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip.pyRs?cC s|dkrtj}n|J|dIJ||jjdtddIJ|dIJx"|jD]}|d|Iq_W|J|JdS(NsR :tone_row_per_linetformats%6.3fsT :(tNonetsyststdoutRtmathematica_formtTrueR(Rtouttitem((s:/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip.pytshow s   " (iiiN( t__name__t __module__tscitbxR RRRRRR!(((s:/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip.pyR s    c C sh|dkrtj}ng}dddddg}dddd d d d g}xt||D]\}}|dkrd }nt|d}x5|D]-} |j| r|t| d }PqqWx5|D]-} |j| r|t| d}PqqWt|dkr|d}n|t|ddkrO|t|d }n|j||q^W|S(NtFtItSIGtHLAtHLs(+)s(-)tPLUStMINUSt+t-tMINUtiit_( RRRtziptstrtendswithtlent startswithtappend( tlabelstlabel_appendixRtnew_label_roottstandard_prefixtstandard_postfixtlabeltappttmp_roottposttpre((s:/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip.pytconstruct_output_labels,s.       cC s|dkrtj}ntjj|s=td|ntjd|}|j d|}t j |}|j d|ddd|S(NsNo such file: >%s> out, "hello world" } } manipulate_pdb{ task = apply_operator *set_b apply_operator{ operator = "x,y,z" invert=False concatenate_model=False chain_id_increment=1 } set_b{ b_iso = 30 } } } output { logfile = "xmanip.log" hklout = "xmanip.mtz" xyzout = "xmanip.pdb" } } #phil __END__ Further details can be found in the documentation. ((t command_name((s:/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip.pyt print_helpsfs phenix.xmanipcB C syt|dks6d|ks6d|ks6d|krFtd|n/t}d|krw|jddd tjnt}t}|jdd d |g}tjd d }|d IJ|dIJ|dIJ|dIJ|dIJ|Jx1|D])}d}t } t j j |r}y;tjjd|}|dk rR|j|t} nWqtk riqtk ryqXn_y8|jd|}|dk r|j|t} nWn$tk rntk rnX| s|dIJ|dI|IJ|dIJ|Jtd|qqWtjd|} | j} g} d} xE| jjjD]4}|jdk r[| jtjd|jq[q[W| jjjjdk rtjd| jjjj} nt j!d| jjj"d| jjj#}t j$d|| g| }|dk rV|j"| jj_"t%j&d|j#| jj_#n|dIJtj'd| }|j(d||dIJ| jjj"dkrtdn| jjj#dkrtdng}g}g}g}i}t| jjjdkrt j!d| jjj"d| jjj#}t)j*d |d!td"g}d}x8| jjjD]'}|jdk rkd}t+|j|j,|}|J|d#IJ|d$IJ|dkrtd%n|j-d&||J|j||j|j.j,|j|j/d't0|}|j1dk rC|j1}n|j2|ratd(n|j3i||6|d)7}|j|j4qkqkWt5||}xt6t|D]}d}xt6|d)t|D]n}x>t7||||D]%\}} || kr|d)7}qqW|d*kr|d+t0||IJqqWqWxt6t|D]{}xrt6|d)t|D]W}||||kr||r||r|d,IJ||IJtd-qqqqWqgWnd}!d}"| jjjjdk rktj8jd| jjjj}!|!j9d |}"|d.IJ|d/IJ|"j-d&||Jnt }#t }$g}%d}&| jj:j;d0krt}#t<j=|||"| jj:j=|}'|j|'| jj:j=j>}(|(dkrd1}(n|j|(|jtn| jj:j;d2kr t}#|j-|j?})|j@}*|jA}+|jB},d}-| jj:jCjDd3kr|)}-n| jj:jCjDd4kr|*}-n| jj:jCjDd5kr|+}-n| jj:jCjDd6kr t%jE| jj:jCjF}-n| jj:jCjDd7kr( |,}-n|-dkrC td8n|d9IJ|d:IJ|d;I|-jGIJ|d<I|-jHIJ|d=I|-jIIJx?|D]7}d}.|dk r |jJ|-}.|%j|.q q W|!dk r t}$|"jJ|-}&q n|#r t|%dkr# |}%n|J|d>IJ|d?IJ|J|d@IJd}/t|%dkr d}0xAt6t|D]-}1||1rz |1}0|%|0dk r Pq qz qz W|%|0dk r |%|0jK}2|2jLdA||0}/q n|/dk r xTt7|%|0d)||0d)D]3\}}3|dk r |/jMdB|dA|3}/q q W|dC| jjNjOIJ|/jPjQd| jjNjOn|&dk r tR| jjNjSdD}4|dE| jjNjSIJtTdF|!dG|&d|4dHddIdJ||4jUn||&gjVdd*kr |dKIJq n| jj:j;dLkr| jj:jWjXdMkrDd}5| jj:jWjYjZdNkr t%j[| jj:jWjYj\dOde}5|dRI|5jHIJn| jj:jWjYjZdSkr| jj:jWjYj]}6d}7d}8dT|6j^kr |6j^j_dT}7n|6j^j_dU}7dT|6j^kr@ |6j`j_dT}8n|6j`j_dU}8g}9g}:x!|7D]}1|9jta|1qe Wt|9dVkr tdW|6j^nx!|8D]}1|:jta|1q Wt|:dXkr tdY|6j`n|:}:tb|9|:}5|dZIJ|5j(tcjd|"j"je};|;jf|5j^|;}7|;jftcjgth|5j`}8|J|d[IJtbd\|7jid]th|8}5|5j(d||Jn| jj:jWjYjjr|5jf}5|J|d^IJ|Jn|"jk}<tljm}=xb|<D]Z}>|5j^tcjg|>}?tljn|?tljn|5j`jo}?|=jtp|?qW|"jq}&|&jr|=tR| jjNjSdD}4|dE| jjNjSIJ| jj:jWjYjsrtTdF|!dG|"d|4dHddIdd_tntTdF|!dG|&d|4dH| jj:jWjYjtdIdd_t |4jUn| jj:jWjXd`kr| jj:jWjur| jj:jWjv}@|"jwda|@}&|J|db|@IJ|dc| jjNjSIJ|JntR| jjNjSdD}4tTdF|!dG|&d|4dHddIdd_t|4jUqntR| jjNjxdD}A|dd| jjNjxIJ|A|jydt|jyd)!IJ|AjUdS(fNis--helps--hs-hRs--quietR<Rt file_objectt log_buffert home_scopet map_coefss #phil __OFF__s==========================s XMANIP sreindexing and other tasksRBtargs2##----------------------------------------------##s## Unknown file or keyword:sUnknown file or keyword: %stsourcest unit_cellR~tgroups #phil __ON__t python_objectRs #phil __END__sunit cell not specifiedsspace group not specifiedRCtforce_symmetrytreflection_filessSummary info of observed datas=============================s%Failed to read data. see errors aboveREtCOL_s7Non unique dataset name. Please change the input scriptiisU ***** You are trying to import the data with label(s) %s more then one time. ***** sOutput label roots:s+Output labels are not unique. Modify input.sAtomic model summarys====================tmanipulate_millert UNSPECIFIEDtreindextnigglitreference_settingtinvertt user_suppliedtprimitive_settings)No change of basis operation is supplied.sSupplied reindexing law:s========================shkl notation: sxyz notation: sabc notation: s'The data has been reindexed/manipulateds&--------------------------------------sWriting output files....tcolumn_root_labelt miller_arraysWriting mtz file with name %stwsWring pdb file to: %sRRRRsGenerated by %ss7No input reflection of coordinate files have been giventmanipulate_pdbtapply_operatortuser_supplied_operatortt_deni isApplied operator : t'user_supplied_cartesian_rotation_matrixt,t i s/Invalid rotation matrix. Please check input: %sis4Invalid translational vector. Please check input: %ss+User supplied cartesian matrix and vector: s$Operator in fractional coordinates: RRs Taking inverse of given operatorRRtvalues#All B-values have been set to %5.3fsWriting PDB file %ssWriting log file with name %s i`(zR4RR tregisterRRR t master_paramst!command_line_argument_interpreterRtFalseRFRGRHtiotbxtphiltparseR6RtKeyboardInterruptt ExceptiontprocessR tfetchtextracttxmaniptinputt xray_dataRBRt extract_fromtmodelRtsymmetryRt space_grouptselect_crystal_symmetryRR~RR!Rtreflection_file_serverRQR7t show_summarytinfoR8R2tnamethas_keytupdatet write_outRAtrangeR1tpdbtxray_structure_simplet parameterstactionRRtoutput_label_roott!change_of_basis_op_to_niggli_cellt'change_of_basis_op_to_reference_settingt"change_of_basis_op_to_inverse_handt'change_of_basis_op_to_primitive_settingRt standard_lawstchange_of_basis_optuser_supplied_lawtas_hkltas_xyztas_abct change_basist map_to_asutas_mtz_datasettadd_miller_arraytoutputthkloutt mtz_objecttwritetopentxyzoutRtclosetcountRttaskRtstandard_operatorstrt_mxRRRtsplitRtfloatR R Rtorthogonalization_matrixRtcoltlisttas_floatRt sites_fracRt vec3_doubleRt as_doublettupletdeep_copy_scattererstset_sites_fractconcatenate_modelRRtb_isot set_b_isotlogfiletgetvalue(BtargsRRNt string_buffertstring_buffer_plotst phil_objectstargument_interpreterRtcommand_line_paramstarg_is_processedteffective_paramstparamsthkl_xstpdb_xsRtphil_xst combined_xst new_paramsRPR7R8twrite_ittnamestxray_data_serverRRt this_nameRtiittesttjjt lab_name1t lab_name2t pdb_modelRtwrite_miller_arraytwrite_pdb_filetnew_miller_arrayst new_modelt new_millerR>t to_nigglit to_referencet to_inverset to_primitivetcb_optnew_miller_arrayt mtz_datasettfirstR Rtnew_roottpdb_fileRtrtttmp_rttmp_tt tmp_tmp_rt tmp_tmp_ttotsitest new_sitestsitetnew_siteRtlogger((s:/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip.pytrunas|6                            $              $  #                                                 % !     (       '(&t __future__RtmmtbxRRRRRt iotbx.philt iotbx.pdbtcctbxRRRtcctbx.array_familyRt scitbx.mathR t libtbx.utilsR R t cStringIOR RRFtobjectR RRARQRzRRRRRRR3(((s:/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip.pyts:   "    o h