ó ™xTc@ s°dZddlmZddlmZddlmZmZddlZddl Z d„Z ddde d„Z de ddd„Zddd „Zd efd „ƒYZdS( sd Utilities for re-refining (or otherwise working with) structures downloaded directly from the PDB. iÿÿÿÿ(tdivision(teasy_run(tnull_outtSorryNcC s²ddlm}t|ƒjƒ}d}}xd|D]\}|jdƒr3d|kr3|j|ƒ}|dk r|jdƒdjƒ}Pqq3q3W|dkr¨d}n||fS( Niÿÿÿÿ(tremark_3_interpretations REMARK 3tPROGRAMt:itPHENIXs PHENIX.REFINE( t iotbx.pdbRtopent readlinestNonet startswitht get_programtsplittstrip(tpdb_fileRtlinestprogramt program_fulltline((s?/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/wwpdb/utils.pyR s      c C s[ddlm}ddlm}|dkrJ|r>tj}qJtƒ}nd|}d|}d|} |jd|gd|ƒtj j |ƒs™t ‚|jdd |gd|ƒtj j d|ƒsÞt d |ƒ‚n|j d|d |d d | gƒtj j | ƒs9td| djtjƒfƒ‚ntj j|ƒtj j| ƒfS(sr Copy data from local repository if defined and available, or download it from the PDB, and run cif_as_mtz. iÿÿÿÿ(t fetch_pdb(t cif_as_mtzs%s.pdbs %s-sf.cifs%s.mtztargstlogs-xs+Structure factors are not available for %s.s --symmetry=%ss--merges--output_file_name=%ss!Missing %s! cif_as_mtz stderr: %ss N(tmmtbx.command_lineRRR tsyststdoutRtrun2tostpathtisfiletAssertionErrorRtrunt RuntimeErrortjoint import_outt stderr_linestabspath( tpdb_idtpdb_dirtsf_dirRtverboseRRRtcif_filetmtz_file((s?/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/wwpdb/utils.pytfetch_pdb_datas.        cC s}ddlm}ddlm}|dkr8tj}nd}}} } ||ddƒ} | j} | jdddddt d d d t d d dt dt ƒ} t | ƒdkrÆt d|ƒ‚n| d}|dk r(xc| D].}|j ƒjƒ}t|krã|}PqãqãWt d|ƒ‚n|d|j ƒjƒIJ| jdddddt d d d t d dƒ}t |ƒdkr‘|d}n| jdddddddt d d d t d dƒ}t |ƒdkrì|d\} } n|dk rO|jd|ƒ}| dk r+| jd|ƒ} n|dk rO|jd|ƒ}qOn|jd|d| d| d|d|d|ƒS(sŠ Guess an appropriate data array to use for refinement, plus optional Hendrickson-Lattman coefficients and R-free flags if present. iÿÿÿÿ(treflection_file_utils(tany_filet force_typethklt file_nametlabelstignore_all_zerostparameter_scopettreturn_all_valid_arrayst minimum_scoreitprefer_amplitudestprefer_anomalousisNo data arrays found in %s.sCan't find label string '%s'!sDefaulting to using %sitlabelttest_flag_valuetdisable_suitability_testtcrystal_symmetrytobst r_free_flagstphasesRtmerge_anomalousN(tiotbxR.tiotbx.file_readerR/R RRt file_servert get_xray_datatFalsetTruetlenRtinfot label_stringt array_labeltget_experimental_phasestget_r_free_flagstcustomized_copytprocess_raw_data(R,RRBtpreferred_labelsR>R.R/RAtdatatflagst flag_valuethkl_int hkl_servert data_arraystarrayt array_labelst hl_arraystflags_and_values((s?/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/wwpdb/utils.pytfind_data_arrays<sv                 cC s:ddlm}ddlm}|dkr8tj}n|jd|ƒ}|jƒ}d}xZ|D]R} | j dƒrc| j ƒj ƒj ƒ} | d}t |ƒdksµt‚qcqcW|dk r6|g} g} xÓ|D]Ë} | j ƒ|j ƒkrÿqÛntjj|| ƒ}tjj|ƒs5tjƒ}ntjj|d| ƒ}tjj|ƒsv|jd | gƒntjj|ƒsŒPn| j|ƒ| j| ƒqÛWt | ƒdkr2tjj|d |ƒ}|d |d j|ƒfIJtjd d j| ƒ|fƒtj|ƒtj||ƒn| SdS(sÁ Assembles complete structures from split PDB files (e.g. ribosomes), preserving the original file name. Return value is a list of IDs which were added to the current model (or None). iÿÿÿÿ(R(tpdbR2tSPLITiis%s.pdbRs %s_new.pdbs#Joining multi-part structure: %s %st s%iotbx.pdb.join_fragment_files %s > %sN(RRRCR]R RRtinputt title_sectionR RtlowerRRIR RRR#tisdirtgetcwdRRtappendRtcalltremovetrename(RR'tbase_dirRRR]tpdb_inttitlet other_idsRtfieldst pdb_filest combined_idstother_idt dest_dir_2t pdb_file_2tpdb_all((s?/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/wwpdb/utils.pytcombine_split_structuresL            tfilter_pdb_filecB s&eZdZddeeed„ZRS(s Processing of PDB files to remove common pathologies and enable automatic refinement behavior. In particular, delete unknown atoms and ligands, reduce the occupancy of Se atoms from 1 to trigger occupancy refinement, and optionally remove zero-occupancy atoms. cC suddlm}ddl}|dkr4tƒ}n||ddƒ} | jdƒ| jj} t| j ƒƒdkr†t dƒ‚nd} | j ƒ} | j ƒ} | j dƒ}| j d ƒ}| jƒdk}|jtƒ|_|jtƒ|_|jtƒ|_|}t}|jdksO|jdkr:|sO|jdkrm|rmt}|dkrm|}qmn|jdkrÇ| rÇ|d |jIJx0|jƒD]}|d | |jƒIJq¢Wn|jdkrBd }|röd }||M}n|sB|||jIJx/|jƒD]}|d | |jƒIJqWqBn| j|ƒ}|jdkrß|rßxv|j ƒD]e}|jdkrs|jƒjdkrs|jdkrØ|sÉ|d|jƒIJnd|_qØqsqsWn|rqt|dƒ}|dj| jjjƒƒIJ|dj| jjj ƒƒIJ||j!j"d| jj#ƒƒIJ||j$ƒIJ|j%ƒndS(Niÿÿÿÿ(R/R0R]is(Multi-MODEL PDB files are not supported.is-not (element X or resname UNX or resname UNL)selement SE and resname MSEs-Warning: %d unknown atoms or ligands removed:s %ss;Warning: %d atoms with zero occupancy present in structure:s.Warning: %d atoms with zero occupancy removed:tSEtMSEgð?sSet occupancy of %s to 0.99g®Gáz®ï?tws R>(&RDR/RR Rtassert_file_typet file_objectt hierarchyRItmodelsRtatomstatom_selection_cachet selectiont extract_occtcountRGt n_unknownRHtn_semett n_zero_occt iselectiontid_strtselecttelementt fetch_labelstresnametoccR R#R`Ratremark_sectionR]tformat_cryst1_recordR>t as_pdb_stringtclose(tselfRt output_fileRtquiett set_se_occt remove_atoms_with_zero_occupancyR/RCRjR{R‚t all_atomstcachet known_selt semet_selt zero_occ_seltkeep_seltmodifiedti_seqtmsgthierarchy_filteredtatomtf((s?/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/wwpdb/utils.pyt__init__¸sp          "$N(t__name__t __module__t__doc__R RGRHR¡(((s?/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/wwpdb/utils.pyRu±s (R¤t __future__RtlibtbxRt libtbx.utilsRRRRR R RGR-R\RttobjectRu(((s?/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/wwpdb/utils.pyts    G ,