def create_citation_tab(self, ample_dict): if self.citation_tab_id: return self.citation_tab_id = "citation_tab" pyrvapi.rvapi_insert_tab(self.citation_tab_id, "Citation", self.log_tab_id, False) refMgr = reference_manager.ReferenceManager(ample_dict) bibtex_file = refMgr.save_citations_to_file(ample_dict) if self.ccp4i2: # The horror of ccp4i2 means that this all gets dumped into xml so we can't use any markup tags tdata = refMgr.citations_as_text else: tdata = refMgr.methods_as_html tdata += refMgr.citations_as_html tdata += '<hr><p>A bibtex file with the relevant citations has been saved to: {}</p>'.format( bibtex_file) pyrvapi.rvapi_add_text(tdata, self.citation_tab_id, 0, 0, 1, 1) if not self.ccp4i2: pyrvapi.rvapi_add_data( "bibtex_file", "Citations as BIBTEX", self.fix_path(bibtex_file), "text", self.citation_tab_id, 2, 0, 1, 1, True, ) return self.citation_tab_id
def create_ensembles_section(self, ample_dict): self.rm_pending_section() ensembles_data = ample_dict['ensembles_data'] self.summary_tab_ensemble_sec_id = "ensembles" pyrvapi.rvapi_add_section(self.summary_tab_ensemble_sec_id, "Ensembles", self.summary_tab_id, 0, 0, 1, 1, True) if ample_dict['import_ensembles']: rstr = 'Imported {0} ensembles.'.format(len(ensembles_data)) pyrvapi.rvapi_add_text(rstr, self.summary_tab_ensemble_sec_id, 0, 0, 1, 1) else: # Get the ensembling data d = ensembler.collate_cluster_data(ensembles_data) clusters = d['clusters'] rstr = "" rstr += "Ensemble Results<br/>" rstr += "----------------<br/><br/>" rstr += "Cluster method: {0}<br/>".format(d['cluster_method']) rstr += "Cluster score type: {0}<br/>".format(d['cluster_score_type']) rstr += "Truncation method: {0}<br/>".format(d['truncation_method']) rstr += "Percent truncation: {0}<br/>".format(d['percent_truncation']) rstr += "Side-chain treatments: {0}<br/>".format(d['side_chain_treatments']) rstr += "Number of clusters: {0}<br/><br/>".format(len(clusters.keys())) rstr += "Generated {0} ensembles<br/><br/>".format(len(ensembles_data)) pyrvapi.rvapi_add_text(rstr, self.summary_tab_ensemble_sec_id, 0, 0, 1, 1) ensemble_table = "ensemble_table" pyrvapi.rvapi_add_table1(self.summary_tab_ensemble_sec_id + "/" + ensemble_table, "Ensembling Results", 1, 0, 1, 1, True) tdata = [] for i, cluster_num in enumerate(sorted(d['clusters'].keys())): header = True if i == 0 else False tdata += ensembler.cluster_table_data(clusters, cluster_num, d['side_chain_treatments'], header=header) self.fill_table(ensemble_table, tdata, tooltips=self._ensemble_tooltips) return
def display_citation_tab(self): """Function to display citations for programs used within SIMBAD Returns ------- object Section containing the relevant citations """ self._create_citation_tab() args = self.get_arguments_from_log(self.logfile) refMgr = reference_manager.ReferenceManager(args) bibtex_file = refMgr.save_citations_to_file(self.work_dir) if self.ccp4i2: # The horror of ccp4i2 means that this all gets dumped into xml so we can't use any markup tags tdata = refMgr.citations_as_text else: tdata = refMgr.methods_as_html tdata += refMgr.citations_as_html tdata += '<hr><p>A bibtex file with the relevant citations has been saved to: {}</p>'.format(bibtex_file) pyrvapi.rvapi_add_text(tdata, self.citation_tab_id, 0, 0, 1, 1) if not self.ccp4i2: pyrvapi.rvapi_add_data("bibtex_file", "Citations as BIBTEX", self.fix_path(bibtex_file), "text", self.citation_tab_id, 2, 0, 1, 1, True)
def create_summary_tab(self, ample_dict): self._create_summary_tab() if self.do_create_ensembles_section(ample_dict): self.create_ensembles_section(ample_dict) if not self._got_mrbump_results(ample_dict): return self.summary_tab_id if not self.summary_tab_results_sec_id: self.rm_pending_section() # Only create the table once self.summary_tab_results_sec_id = "mrbump" pyrvapi.rvapi_add_section(self.summary_tab_results_sec_id, "MRBUMP", self.summary_tab_id, 0, 0, 1, 1, True) self.summary_tab_results_sec_table_id = "mrbump_table" pyrvapi.rvapi_add_table1(self.summary_tab_results_sec_id + "/" + self.summary_tab_results_sec_table_id, "MRBUMP Results", 1, 0, 1, 1, True) mrb_results = ample_dict.get('mrbump_results') if not mrb_results == self.old_mrbump_results: # We set old_mrbump_results when we create the results_tab self.fill_table(self.summary_tab_results_sec_table_id, mrbump_util.ResultsSummary().results_table(mrb_results), tooltips=self._mrbump_tooltips) if not self.summary_tab_survey_sec_id and not self.ccp4i2: # Only create the table once self.summary_tab_survey_sec_id = "survey" pyrvapi.rvapi_add_section(self.summary_tab_survey_sec_id, "Feedback", self.summary_tab_id, 0, 0, 1, 1, True) rstr = "<h2>How did we do?</h2><h3>Please follow this link and leave some feedback:</h3><a href='{0}' style='color: blue'>{0}</a>".format(reference_manager.survey_url) pyrvapi.rvapi_add_text(rstr, self.summary_tab_survey_sec_id, 0, 0, 1, 1) return self.summary_tab_id
def import_all(self): # ============================================================================ # start page construction: summary table pyrvapi.rvapi_add_table(self.import_summary_id(), "<font size='+1'>Import Summary</font>", self.report_page_id(), self.rvrow + 1, 0, 1, 1, 0) pyrvapi.rvapi_set_table_style(self.import_summary_id(), "table-blue", "text-align:left;") pyrvapi.rvapi_add_text(" ", self.report_page_id(), self.rvrow + 2, 0, 1, 1) self.rvrow += 3 pyrvapi.rvapi_put_horz_theader(self.import_summary_id(), "Imported file", "Name of imported file", 0) pyrvapi.rvapi_put_horz_theader(self.import_summary_id(), "Type", "Dataset type", 1) pyrvapi.rvapi_put_horz_theader(self.import_summary_id(), "Generated dataset(s)", "List of generated datasets", 2) # ============================================================================ # get list of uploaded files #self.files_all = [f for f in os.listdir(self.importDir()) if os.path.isfile(os.path.join(self.importDir(),f))] self.files_all = [] for dirName, subdirList, fileList in os.walk(self.importDir(), topdown=False): dName = dirName[len(self.importDir()) + 1:] for fname in fileList: self.files_all.append(os.path.join(dName, fname)) # ============================================================================ # do individual data type imports for importer in importers: importer.run(self) # ============================================================================ # finish import if len(self.files_all) > 0: self.file_stdout.write ( "\n\n" + "="*80 + \ "\n*** The following files are not recognised and will be ignored:\n" ) for f in self.files_all: self.file_stdout.write(" " + f + "\n") self.file_stdout.write("\n") for f in self.files_all: self.putSummaryLine_red(f, "UNKNOWN", "Failed to recognise, ignored")
def _create_summary_tab(self): if not self.summary_tab_id: self.summary_tab_id = "summary_tab" title = "Summary" pyrvapi.rvapi_insert_tab(self.summary_tab_id, title, self.citation_tab_id, False) # Create pending section until we have data to show self.summary_tab_pending_sec_id = 'summary_tab_pending' pyrvapi.rvapi_add_section(self.summary_tab_pending_sec_id, "Processing...", self.summary_tab_id, 0, 0, 1, 1, True) rstr = "<p>No results are currently available. Please check back later.</p>" pyrvapi.rvapi_add_text(rstr, self.summary_tab_pending_sec_id, 0, 0, 1, 1) return
def create_citation_tab(self, ample_dict): if self.citation_tab_id: return self.citation_tab_id = "citation_tab" pyrvapi.rvapi_insert_tab(self.citation_tab_id, "Citation", self.log_tab_id, False) refMgr = reference_manager.ReferenceManager(ample_dict) bibtex_file = refMgr.save_citations_to_file(ample_dict) if self.ccp4i2: # The horror of ccp4i2 means that this all gets dumped into xml so we can't use any markup tags tdata = refMgr.citations_as_text else: tdata = refMgr.methods_as_html tdata += refMgr.citations_as_html tdata += '<hr><p>A bibtex file with the relevant citations has been saved to: {}</p>'.format(bibtex_file) pyrvapi.rvapi_add_text(tdata, self.citation_tab_id, 0, 0, 1, 1) if not self.ccp4i2: pyrvapi.rvapi_add_data("bibtex_file", "Citations as BIBTEX", self.fix_path(bibtex_file), "text", self.citation_tab_id, 2, 0, 1, 1, True) return self.citation_tab_id
def _create_summary_tab(self): if not self.summary_tab_id: self.summary_tab_id = "summary_tab" title = "Summary" if self.ccp4i2: # Create summary tab pyrvapi.rvapi_add_tab( self.summary_tab_id, title, True) # Last arg is "open" - i.e. show or hide else: # Insert summary tab before log tab pyrvapi.rvapi_insert_tab( self.summary_tab_id, title, self.log_tab_id, False) # Last arg is "open" - i.e. show or hide # Create pending section until we have data to show self.summary_tab_pending_sec_id = 'summary_tab_pending' pyrvapi.rvapi_add_section(self.summary_tab_pending_sec_id, "Processing...", self.summary_tab_id, 0, 0, 1, 1, True) rstr = "<p>No results are currently available. Please check back later. when your structure will have been solved. Honest.</p>" pyrvapi.rvapi_add_text(rstr, self.summary_tab_pending_sec_id, 0, 0, 1, 1) return
def run( body, # body is reference to the main Import class sectionTitle="Reflection datasets created", sectionOpen=False, # to keep result section closed if several datasets freeRflag=True # will be run if necessary ): files_mtz = [] for f_orig in body.files_all: f_base, f_ext = os.path.splitext(f_orig) if f_ext.lower() in ('.hkl', '.mtz'): p_orig = os.path.join(body.importDir(), f_orig) f_fmt = mtz.hkl_format(p_orig, body.file_stdout) if f_fmt in ('xds_merged', 'mtz_merged'): files_mtz.append((f_orig, f_fmt)) if not files_mtz: return mtzSecId = body.getWidgetId("mtz_sec") + "_" k = 0 for f_orig, f_fmt in files_mtz: body.files_all.remove(f_orig) p_orig = os.path.join(body.importDir(), f_orig) p_mtzin = p_orig if not f_fmt.startswith('mtz_'): p_mtzin = os.path.splitext(f_orig)[0] + '.mtz' sp = subprocess.Popen('pointless', stdin=subprocess.PIPE, stdout=body.file_stdout, stderr=body.file_stderr) sp.stdin.write('XDSIN ' + p_orig + '\nHKLOUT ' + p_mtzin + '\nCOPY\n') sp.stdin.close() if sp.wait(): p_mtzin = None if p_mtzin: p_mtzout = p_mtzin rc = command.comrc() if freeRflag: p_mtzout = os.path.join(body.outputDir(), os.path.basename(f_orig)) if k == 0: scr_file = open(freerflag_script(), "w") scr_file.write("UNIQUE\n") scr_file.close() # run freerflag: generate FreeRFlag if it is absent, and expand # all reflections rc = command.call("freerflag", ["HKLIN", p_mtzin, "HKLOUT", p_mtzout], "./", freerflag_script(), body.file_stdout, body.file_stderr, log_parser=None) if rc.msg: msg = "\n\n Freerflag failed with message:\n\n" + \ rc.msg + \ "\n\n File " + f_orig + \ " cannot be processed.\n\n" body.file_stdout.write(msg) body.file_stderr.write(msg) body.putSummaryLine_red(f_orig, "MTZ", "Failed to process/import, ignored") else: mf = mtz.mtz_file(p_mtzout) body.summary_row_0 = -1 # to signal the beginning of summary row for ds in mf: if k == 0: body.file_stdout.write("\n" + "%" * 80 + "\n") body.file_stdout.write( "%%%%% IMPORT REFLECTION DATA\n") body.file_stdout.write("%" * 80 + "\n") # make HKL dataset annotation hkl = dtype_hkl.DType(body.job_id) hkl.importMTZDataset(ds) body.dataSerialNo += 1 hkl.makeDName(body.dataSerialNo) datasetName = "" if k == 0: if sectionTitle: pyrvapi.rvapi_add_section(mtzSecId, sectionTitle, body.report_page_id(), body.rvrow, 0, 1, 1, sectionOpen) else: pyrvapi.rvapi_add_section( mtzSecId, "Reflection dataset created: " + hkl.dname, body.report_page_id(), body.rvrow, 0, 1, 1, sectionOpen) subSecId = mtzSecId if len(files_mtz) > 1 or len(mf) > 1: subSecId = mtzSecId + str(k) pyrvapi.rvapi_add_section(subSecId, hkl.dname, mtzSecId, k, 0, 1, 1, False) #pyrvapi.rvapi_add_section ( subSecId, # f_orig + " / " + hkl.getDataSetName(), # mtzSecId,k,0,1,1,False ) # run crtruncate outFileName = os.path.join(body.outputDir(), hkl.dataId + ".mtz") outXmlName = os.path.join("ctruncate" + hkl.dataId + ".xml") cmd = ["-hklin", p_mtzout, "-hklout", outFileName] amplitudes = "" meanCols = hkl.getMeanColumns() if meanCols[2] != "X": cols = "/*/*/[" if meanCols[1] != None: cols = cols + meanCols[0] + "," + meanCols[1] else: cols = cols + meanCols[0] if meanCols[2] == "F": amplitudes = "-amplitudes" cmd += ["-colin", cols + "]"] anomCols = hkl.getAnomalousColumns() anomalous = False if anomCols[4] != "X": anomalous = True cols = "/*/*/[" for i in range(0, 4): if anomCols[i] != None: if i > 0: cols = cols + "," cols = cols + anomCols[i] if anomCols[4] == "F": amplitudes = "-amplitudes" cmd += ["-colano", cols + "]"] if amplitudes: cmd += [amplitudes] cmd += ["-xmlout", outXmlName] cmd += ["-freein"] pyrvapi.rvapi_add_text( " <p><h2>Data analysis (CTruncate)</h2>", subSecId, 1, 0, 1, 1) pyrvapi.rvapi_add_panel(mtzSecId + str(k), subSecId, 2, 0, 1, 1) """ log_parser = pyrvapi_ext.parsers.generic_parser ( mtzSecId+str(k), False,body.generic_parser_summary,False ) rc = command.call ( "ctruncate",cmd,"./",None, body.file_stdout,body.file_stderr,log_parser ) """ body.file_stdin = None # not clear why this is not None at # this point and needs to be forced, # or else runApp looks for input script body.setGenericLogParser(mtzSecId + str(k), False) body.runApp("ctruncate", cmd) body.file_stdout.flush() mtzTableId = body.getWidgetId("mtz") + "_" + str( k) + "_table" if rc.msg: msg = "\n\n CTruncate failed with message:\n\n" + \ rc.msg + \ "\n\n Dataset " + hkl.dname + \ " cannot be used.\n\n" body.file_stdout.write(msg) body.file_stderr.write(msg) makeHKLTable(body, mtzTableId, subSecId, hkl, hkl, -1, msg, 0) datasetName = hkl.dname elif not os.path.exists(outFileName): body.file_stdout.write ( "\n\n +++ Dataset " + hkl.dname + \ "\n was not truncated and will be used as is\n\n" ) hkl.makeUniqueFNames(body.outputDir()) body.outputDataBox.add_data(hkl) makeHKLTable(body, mtzTableId, subSecId, hkl, hkl, 0, "", 0) datasetName = hkl.dname srf.putSRFDiagram(body, hkl, body.outputDir(), body.reportDir(), subSecId, 3, 0, 1, 1, body.file_stdout, body.file_stderr, None) pyrvapi.rvapi_set_text ( " <br><hr/><h3>Created Reflection Data Set (merged)</h3>" + \ "<b>Assigned name:</b> " + datasetName + "<br> ", subSecId,4,0,1,1 ) pyrvapi.rvapi_add_data( "hkl_data_" + str(body.dataSerialNo), "Merged reflections", # always relative to job_dir from job_dir/html os.path.join("..", body.outputDir(), hkl.files[0]), "hkl:hkl", subSecId, 5, 0, 1, 1, -1) else: body.file_stdout.write ( "\n\n ... Dataset " + hkl.dname + \ "\n was truncated and will substitute the " + \ "original one\n\n" ) mtzf = mtz.mtz_file(outFileName) # ctruncate should create a single dataset here for dset in mtzf: dset.MTZ = os.path.basename(outFileName) hkl_data = dtype_hkl.DType(body.job_id) hkl_data.importMTZDataset(dset) hkl_data.dname = hkl.dname hkl_data.dataId = hkl.dataId hkl_data.makeUniqueFNames(body.outputDir()) body.outputDataBox.add_data(hkl_data) makeHKLTable(body, mtzTableId, subSecId, hkl, hkl_data, 1, "", 0) datasetName = hkl_data.dname srf.putSRFDiagram(body, hkl_data, body.outputDir(), body.reportDir(), subSecId, 3, 0, 1, 1, body.file_stdout, body.file_stderr, None) pyrvapi.rvapi_set_text ( " <br><hr/><h3>Created Reflection Data Set (merged)</h3>" + \ "<b>Assigned name:</b> " + datasetName + "<br> ", subSecId,4,0,1,1 ) pyrvapi.rvapi_add_data( "hkl_data_" + str(body.dataSerialNo), "Merged reflections", # always relative to job_dir from job_dir/html os.path.join("..", body.outputDir(), hkl_data.files[0]), "hkl:hkl", subSecId, 5, 0, 1, 1, -1) if body.summary_row_0 < 0: body.putSummaryLine(f_orig, "HKL", datasetName) else: body.addSummaryLine("HKL", datasetName) k += 1 pyrvapi.rvapi_flush() if len(mf) <= 0: body.putSummaryLine_red(f_orig, "UNKNOWN", "-- ignored") body.file_stdout.write("... processed: " + f_orig + "\n ") body.rvrow += 1 pyrvapi.rvapi_flush() return
def results_section(self, results_tab_id, mrb_results, ensemble_results, section_title): """Results Tab""" if not mrb_results: return # Create unique identifier for this section by using the id # All ids will have this appended to avoid clashes uid = str(uuid.uuid4()) section_id = section_title.replace(" ", "_") + uid self.results_tab_sections.append( section_id) # Add to list so we can remove if we update pyrvapi.rvapi_add_panel(section_id, results_tab_id, 0, 0, 1, 1) pyrvapi.rvapi_add_text("<h3>{0}</h3>".format(section_title), section_id, 0, 0, 1, 1) results_tree = "results_tree" + section_id pyrvapi.rvapi_add_tree_widget(results_tree, section_title, section_id, 0, 0, 1, 1) for r in mrb_results: ensemble_name = r['ensemble_name'] container_id = "sec_{0}".format(ensemble_name) + uid pyrvapi.rvapi_add_panel(container_id, results_tree, 0, 0, 1, 1) header = "<h3>Results for ensemble: {0}</h3>".format(ensemble_name) pyrvapi.rvapi_add_text(header, container_id, 0, 0, 1, 1) sec_table = "sec_table_{0}".format(ensemble_name) + uid title = "Results table: {0}".format(ensemble_name) title = "Summary" pyrvapi.rvapi_add_section(sec_table, title, container_id, 0, 0, 1, 1, True) table_id = "table_{0}".format(ensemble_name) + uid pyrvapi.rvapi_add_table(table_id, "", sec_table, 1, 0, 1, 1, False) tdata = mrbump_util.ResultsSummary().results_table([r]) self.fill_table(table_id, tdata, tooltips=self._mrbump_tooltips) # Ensemble if ensemble_results: epdb = self.ensemble_pdb(r, ensemble_results) if epdb: sec_ensemble = "sec_ensemble_{0}".format( ensemble_name) + uid pyrvapi.rvapi_add_section(sec_ensemble, "Ensemble Search Model", container_id, 0, 0, 1, 1, False) data_ensemble = "data_ensemble_{0}".format( ensemble_name) + uid pyrvapi.rvapi_add_data(data_ensemble, "Ensemble PDB", self.fix_path(epdb), "XYZOUT", sec_ensemble, 2, 0, 1, 1, True) # PHASER self.add_results_section( result_dict=r, ensemble_name=ensemble_name, program_name='PHASER', logfile_key='PHASER_logfile', pdb_key='PHASER_pdbout', mtz_key='PHASER_mtzout', uid=uid, container_id=container_id, ) # REFMAC self.add_results_section( result_dict=r, ensemble_name=ensemble_name, program_name='Refmac', logfile_key='REFMAC_logfile', pdb_key='REFMAC_pdbout', mtz_key='REFMAC_mtzout', uid=uid, container_id=container_id, ) # Buccaner self.add_results_section( result_dict=r, ensemble_name=ensemble_name, program_name='BUCCANEER', logfile_key='BUCC_logfile', pdb_key='BUCC_pdbout', mtz_key='BUCC_mtzout', uid=uid, container_id=container_id, ) # Arpwarp self.add_results_section( result_dict=r, ensemble_name=ensemble_name, program_name='ArpWarp', logfile_key='ARP_logfile', pdb_key='ARP_pdbout', mtz_key='ARP_mtzout', uid=uid, container_id=container_id, ) # SHELXE self.add_results_section( result_dict=r, ensemble_name=ensemble_name, program_name='SHELXE', logfile_key='SHELXE_logfile', pdb_key='SHELXE_pdbout', mtz_key='SHELXE_mtzout', uid=uid, container_id=container_id, ) # Buccaner Rebuild self.add_results_section( result_dict=r, ensemble_name=ensemble_name, program_name='BUCCANEER SHELXE Trace Rebuild', logfile_key='SXRBUCC_logfile', pdb_key='SXRBUCC_pdbout', mtz_key='SXRBUCC_mtzout', uid=uid, container_id=container_id, ) # Arpwarp Rebuild self.add_results_section( result_dict=r, ensemble_name=ensemble_name, program_name='ARPWARP SHELXE Trace Rebuild', logfile_key='SXRARP_logfile', pdb_key='SXRARP_pdbout', mtz_key='SXRARP_mtzout', uid=uid, container_id=container_id, ) pyrvapi.rvapi_set_tree_node(results_tree, container_id, "{0}".format(ensemble_name), "auto", "") return
def run(self): # Prepare gesamt job # Just in case (of repeated run) remove the output xyz file. When gesamt # succeeds, this file is created. if os.path.isfile(self.gesamt_xyz()): os.remove(self.gesamt_xyz()) if os.path.isfile(self.gesamt_json()): os.remove(self.gesamt_json()) # Prepare gesamt input # fetch input data xyz = self.input_data.data.xyz nXYZ = len(xyz) # make command-line parameters cmd = [] for i in range(nXYZ): cmd += [ os.path.join(self.inputDir(), xyz[i].files[0]), "-s", xyz[i].chainSel ] if nXYZ < 2: if not "GESAMT_ARCHIVE" in os.environ: self.fail ( "<b> *** Error: jsCofe is not configured to work " + \ "with GESAMT Archive</b><br>" + \ "<i> Please look for support</i><br>", "No GESAMT Archive configured" ) cmd += [ "-archive", os.environ["GESAMT_ARCHIVE"], "-nthreads=auto", "-min1=" + self.getParameter(self.task.parameters.sec1.contains.MIN1), "-min2=" + self.getParameter(self.task.parameters.sec1.contains.MIN2), "-trim-size=1", "-trim-Q=" + self.getParameter(self.task.parameters.sec1.contains.QSCORE), "--json", self.gesamt_json() ] self.rvrow += 1 pyrvapi.rvapi_add_grid(self.progress_grid_id(), False, self.report_page_id(), self.rvrow, 0, 1, 1) pyrvapi.rvapi_add_progress_bar(self.progress_bar_id(), self.progress_grid_id(), 0, 0, 1, 1) pyrvapi.rvapi_add_text(" ETR: ", self.progress_grid_id(), 0, 1, 1, 1) pyrvapi.rvapi_add_label(self.etr_label_id(), self.progress_grid_id(), "--:--:--", 0, 2, 1, 1) self.storeReportDocument(self.progress_bar_id() + ";" + self.etr_label_id()) else: cmd += [ "-o", self.gesamt_xyz(), "-o-cs", self.task.parameters.sec1.contains.MODE.value ] if nXYZ == 2: cmd += ["-domains"] self.putPanel(self.gesamt_report_id()) self.storeReportDocument( self.gesamt_report_id()) # self.job_id.zfill(4) ) r0 = self.getParameter(self.task.parameters.sec1.contains.R0) if r0: cmd += ["-r0=" + r0] sigma = self.getParameter(self.task.parameters.sec1.contains.SIGMA) if sigma: cmd += ["-sigma=" + sigma] cmd += ["--rvapi-rdoc", self.reportDocumentName()] # run gesamt self.runApp("gesamt", cmd) if nXYZ < 2: # PDB scan pyrvapi.rvapi_remove_widget(self.progress_grid_id()) pyrvapi.rvapi_reset_task() pyrvapi.rvapi_flush() if os.path.isfile(self.gesamt_json()): hitlist = jsonut.readjObject(self.gesamt_json()) pyrvapi.rvapi_add_table(self.query_table_id(), "Query structure", self.report_page_id(), self.rvrow, 0, 1, 1, 0) pyrvapi.rvapi_put_horz_theader(self.query_table_id(), "Name", "Structure name", 0) pyrvapi.rvapi_put_horz_theader( self.query_table_id(), "Size", "Structure size in number of residues", 1) pyrvapi.rvapi_put_table_string( self.query_table_id(), hitlist.query.file + " (" + hitlist.query.selection + ")", 0, 0) pyrvapi.rvapi_put_table_string(self.query_table_id(), hitlist.query.size, 0, 1) self.rvrow += 1 self.putMessage(" ") querySize = float(hitlist.query.size) nColumns = len(hitlist.columns) if nColumns < 1 or not hasattr(hitlist.columns[0], "value"): nHits = 0 elif type(hitlist.columns[0].value) is list: nHits = min( len(hitlist.columns[0].value), self.task.parameters.sec1.contains.MAXHITS.value) else: nHits = 1 if nHits < 1: self.putTitle("No PDB matches found") self.putMessage( "<i>Hint:</i> try to reduce report thresholds " + "(ultimately down to 0) in order to see any hits;<br>" + "doing so will increase computation time and report " + "lower-quality (less relevant) matches.") else: self.putSection(self.hits_table_sec_id(), "PDB Hits Table", False) pyrvapi.rvapi_add_table(self.hits_table_id(), "PDB hits found", self.hits_table_sec_id(), 0, 0, 1, 1, 100) pyrvapi.rvapi_set_table_type(self.hits_table_id(), True, True) pyrvapi.rvapi_set_table_style(self.hits_table_id(), "", "text-align:center;") for j in range(nHits): pyrvapi.rvapi_put_vert_theader(self.hits_table_id(), str(j + 1), "Hit number", j) pyrvapi.rvapi_shape_vert_theader( self.hits_table_id(), j, "text-align:right;", "", 1, 1) for i in range(nColumns): column = hitlist.columns[i] pyrvapi.rvapi_put_horz_theader(self.hits_table_id(), column.title, column.tooltip, i) if i == 0: td_css = "font-family:courier;" elif i == nColumns - 1: td_css = "text-align:left;font-size:80%;" pyrvapi.rvapi_shape_horz_theader( self.hits_table_id(), i, td_css, "", 1, 1) else: td_css = "" for j in range(nHits): if nHits == 1: pyrvapi.rvapi_put_table_string( self.hits_table_id(), column.value, j, i) else: pyrvapi.rvapi_put_table_string( self.hits_table_id(), column.value[j], j, i) if td_css: pyrvapi.rvapi_shape_table_cell( self.hits_table_id(), j, i, "", td_css, "", 1, 1) pyrvapi.rvapi_add_button( "hits_dnl_btn", "Export hit list", "{function}", "window.parent.downloadJobFile(" + self.job_id + ",'hits.txt')", False, self.hits_table_sec_id(), 1, 0, 1, 1) if nHits > 1: self.putSection(self.hits_graph_sec_id(), "Score Plots", False) pyrvapi.rvapi_add_text("<h3>Alignment scores</h3>", self.hits_graph_sec_id(), 0, 0, 1, 1) pyrvapi.rvapi_add_graph(self.hits_graph_id(), self.hits_graph_sec_id(), 1, 0, 1, 1) pyrvapi.rvapi_set_graph_size(self.hits_graph_id(), 700, 400) pyrvapi.rvapi_add_text(" <p><hr/>", self.hits_graph_sec_id(), 2, 0, 1, 1) pyrvapi.rvapi_add_text("<h3>Correlation plots</h3>", self.hits_graph_sec_id(), 3, 0, 1, 1) pyrvapi.rvapi_add_loggraph(self.corr_graph_id(), self.hits_graph_sec_id(), 4, 0, 1, 1) pyrvapi.rvapi_add_graph_data("data", self.hits_graph_id(), "Scores") pyrvapi.rvapi_add_graph_data("data", self.corr_graph_id(), "Score correlations") def addDatasets(ref, name): pyrvapi.rvapi_add_graph_dataset( ref, "data", self.hits_graph_id(), name, name) pyrvapi.rvapi_add_graph_dataset( ref, "data", self.corr_graph_id(), name, name) return addDatasets("hno", "Hit number") addDatasets("qscore", "Q-score") addDatasets("rmsd", "R.m.s.d.") addDatasets("nalign", "Nalign/n0") addDatasets("seqid", "Seq. Id.") def addData(ref, value): pyrvapi.rvapi_add_graph_real( ref, "data", self.hits_graph_id(), value, "%g") pyrvapi.rvapi_add_graph_real( ref, "data", self.corr_graph_id(), value, "%g") return for j in range(nHits): pyrvapi.rvapi_add_graph_int( "hno", "data", self.hits_graph_id(), j) addData("qscore", float(hitlist.columns[2].value[j])) addData("rmsd", float(hitlist.columns[3].value[j])) addData( "nalign", float(hitlist.columns[4].value[j]) / querySize) addData("seqid", float(hitlist.columns[5].value[j])) pyrvapi.rvapi_add_graph_plot("plot", self.hits_graph_id(), "Score profiles", "Hit number", "Scores") def addLine(xset, yset, color): pyrvapi.rvapi_add_plot_line( "plot", "data", self.hits_graph_id(), xset, yset) pyrvapi.rvapi_set_line_options( yset, "plot", "data", self.hits_graph_id(), color, "solid", "off", 2.5, True) return addLine("hno", "qscore", "#00008B") addLine("hno", "rmsd", "#8B0000") addLine("hno", "nalign", "#8B8B00") addLine("hno", "seqid", "#008B00") pyrvapi.rvapi_set_plot_legend("plot", self.hits_graph_id(), "e", "") def addPlot(plotId, name, xname, yname, xset, yset, color): pyrvapi.rvapi_add_graph_plot( plotId, self.corr_graph_id(), name, xname, yname) pyrvapi.rvapi_add_plot_line( plotId, "data", self.corr_graph_id(), xset, yset) pyrvapi.rvapi_set_line_options( yset, plotId, "data", self.corr_graph_id(), color, "off", "filledCircle", 2.5, True) return addPlot("p1", "R.m.s.d. vs Seq. Id", "Seq. Id", "R.m.s.d.", "seqid", "rmsd", "#8B0000") addPlot("p2", "R.m.s.d. vs Q-score", "Q-score", "R.m.s.d.", "qscore", "rmsd", "#8B0000") addPlot("p3", "R.m.s.d. vs Nalign", "Normalised alignment length", "R.m.s.d.", "nalign", "rmsd", "#8B0000") addPlot("p4", "Seq. Id. vs Q-score", "Q-score", "Seq. Id.", "qscore", "seqid", "#008B00") addPlot("p5", "Seq. Id. vs Nalign", "Normalised alignment length", "Seq. Id.", "nalign", "seqid", "#008B00") addPlot("p6", "Nalign vs. Q-score", "Q-score", "Normalised alignment length", "qscore", "nalign", "#8B8B00") else: self.putTitle("No PDB matches found") else: # pairwise or multiple alignment self.rvrow += 1 if nXYZ == 2: outFiles = self.restoreReportDocument().split("\n") elif nXYZ > 2: outFiles = [self.gesamt_xyz()] if len(outFiles) > 0: self.putTitle("Gesamt Output") # register output data from temporary location (files will be moved # to output directory by the registration procedure) ensemble = self.registerEnsemble( dtype_template.subtypeProtein(), outFiles[0]) if ensemble: self.putEnsembleWidget("ensemble_btn", "Superposed ensemble ", ensemble, -1) for i in range(1, len(outFiles) - 1): self.rvrow += 1 ensemble = self.registerEnsemble( dtype_template.subtypeProtein(), outFiles[i]) if ensemble: self.putEnsembleWidget("ensemble_" + str(i) + "_btn", "Superposed domain #" + str(i), ensemble, -1) else: self.putTitle("No Output Files Generated") # close execution logs and quit self.success() return
def create_summary_tab(self, ample_dict): # # Summary Tab # self._create_summary_tab() if not (ample_dict['single_model_mode'] or ample_dict['homologs'] or ample_dict['ideal_helices']) and \ bool(ample_dict['ensembles_data']) and not self.summary_tab_ensemble_sec_id: self.rm_pending_section() ensembles_data = ample_dict['ensembles_data'] self.summary_tab_ensemble_sec_id = "ensembles" pyrvapi.rvapi_add_section(self.summary_tab_ensemble_sec_id, "Ensembles", self.summary_tab_id, 0, 0, 1, 1, True) # Get the ensembling data d = ensembler.collate_cluster_data(ensembles_data) clusters = d['clusters'] rstr = "" rstr += "Ensemble Results<br/>" rstr += "----------------<br/><br/>" rstr += "Cluster method: {0}<br/>".format(d['cluster_method']) rstr += "Cluster score type: {0}<br/>".format( d['cluster_score_type']) rstr += "Truncation method: {0}<br/>".format( d['truncation_method']) rstr += "Percent truncation: {0}<br/>".format( d['percent_truncation']) rstr += "Side-chain treatments: {0}<br/>".format( d['side_chain_treatments']) rstr += "Number of clusters: {0}<br/><br/>".format( len(clusters.keys())) rstr += "Generated {0} ensembles<br/><br/>".format( len(ensembles_data)) pyrvapi.rvapi_add_text(rstr, self.summary_tab_ensemble_sec_id, 0, 0, 1, 1) ensemble_table = "ensemble_table" pyrvapi.rvapi_add_table1( self.summary_tab_ensemble_sec_id + "/" + ensemble_table, "Ensembling Results", 1, 0, 1, 1, True) # for cluster_num in sorted(clusters.keys()): # rstr += "\n" # rstr += "Cluster {0}\n".format(cluster_num) # rstr += "Number of models: {0}\n".format(clusters[cluster_num]['cluster_num_models']) # rstr += "Cluster centroid: {0}\n".format(clusters[cluster_num]['cluster_centroid']) # rstr += "\n" # tdata = cluster_table_data(clusters, cluster_num) # rstr += tableFormat.pprint_table(tdata) # cluster_num = 1 tdata = ensembler.cluster_table_data(clusters, cluster_num, d['side_chain_treatments']) self.fill_table(ensemble_table, tdata, tooltips=self._ensemble_tooltips) # # MRBUMP Results # if not self._got_mrbump_results(ample_dict): return self.summary_tab_id if not self.summary_tab_results_sec_id: self.rm_pending_section() # Only create the table once self.summary_tab_results_sec_id = "mrbump" pyrvapi.rvapi_add_section(self.summary_tab_results_sec_id, "MRBUMP", self.summary_tab_id, 0, 0, 1, 1, True) self.summary_tab_results_sec_table_id = "mrbump_table" pyrvapi.rvapi_add_table1( self.summary_tab_results_sec_id + "/" + self.summary_tab_results_sec_table_id, "MRBUMP Results", 1, 0, 1, 1, True) mrb_results = ample_dict['mrbump_results'] if not mrb_results == self.old_mrbump_results: # We set old_mrbump_results when we create the results_tab self.fill_table( self.summary_tab_results_sec_table_id, mrbump_util.ResultsSummary().results_table(mrb_results), tooltips=self._mrbump_tooltips) # # Survey section # if not self.summary_tab_survey_sec_id and not self.ccp4i2: # Only create the table once self.summary_tab_survey_sec_id = "survey" pyrvapi.rvapi_add_section(self.summary_tab_survey_sec_id, "Feedback", self.summary_tab_id, 0, 0, 1, 1, True) rstr = "<h2>How did we do?</h2><h3>Please follow this link and leave some feedback:</h3><a href='{0}' style='color: blue'>{0}</a>".format( ample_util.survey_url) pyrvapi.rvapi_add_text(rstr, self.summary_tab_survey_sec_id, 0, 0, 1, 1) return self.summary_tab_id
def run(self): # Check the existence of PDB archive self.checkPDB() # Prepare mrbump input # fetch input data seq = self.input_data.data.seq[0] hkl = None if hasattr(self.input_data.data, 'hkl'): # optional data parameter hkl = self.input_data.data.hkl[0] # make a file with input script self.open_stdin() if hkl: self.write_stdin ( "JOBID " + self.outdir_name() + "\n" + \ "MDLS False\n" + \ "MDLC True\n" + \ "MDLD False\n" + \ "MDLP False\n" + \ "MDLM False\n" + \ "MDLU False\n" + \ "MRPROG molrep phaser\n" + \ "SHELX False\n" + \ "BUCC True\n" + \ "BCYC 5\n" + \ "ARPW False\n" + \ "CHECK False\n" + \ "UPDATE False\n" + \ "PICKLE False\n" + \ "MRNUM 10\n" + \ "USEE True\n" + \ "SCOP False\n" + \ "DEBUG False\n" + \ "RLEVEL 95\n" + \ "GESE False\n" + \ "GEST False\n" + \ "AMPT False\n" + \ "PDBLOCAL " + os.environ["PDB_DIR"] + "\n" + \ "LABIN F=" + hkl.dataset.Fmean.value + \ " SIGF=" + hkl.dataset.Fmean.sigma + \ " FreeR_flag=" + hkl.dataset.FREE + "\n" + \ "LITE False\n" + \ "END\n" ) else: self.write_stdin ( "JOBID " + self.outdir_name() + "\n" + \ "MDLS False\n" + \ "MDLC True\n" + \ "MDLD False\n" + \ "MDLP False\n" + \ "MDLM False\n" + \ "MDLU False\n" + \ "CHECK False\n" + \ "UPDATE False\n" + \ "PICKLE False\n" + \ "MRNUM 5\n" + \ "USEE True\n" + \ "SCOP False\n" + \ "DEBUG False\n" + \ "RLEVEL 95\n" + \ "GESE True\n" + \ "GEST True\n" + \ "AMPT False\n" + \ "IGNORE 5tha\n" + \ "DOPHMMER True\n" + \ "PDBLOCAL " + os.environ["PDB_DIR"] + "\n" + \ "DOHHPRED False\n" + \ "END\n" ) self.close_stdin() # make command-line parameters for mrbump run on a SHELL-type node cmd = ["seqin", os.path.join(self.inputDir(), seq.files[0])] if hkl: cmd += ["hklin", os.path.join(self.inputDir(), hkl.files[0])] # prepare report parser self.setGenericLogParser(self.mrbump_report(), True) # Start mrbump self.runApp("mrbump", cmd) self.unsetLogParser() # check solution and register data search_dir = "search_" + self.outdir_name() if os.path.isdir(search_dir): if hkl: molrep_dir = os.path.join(search_dir, "results", "solution", "mr", "molrep", "refine") if os.path.isdir(molrep_dir): dirlist = os.listdir(molrep_dir) xyzfile = None #mtzfile = None for filename in dirlist: if filename.startswith("refmac"): if filename.endswith(".pdb"): xyzfile = os.path.join(molrep_dir, filename) #if filename.endswith(".mtz"): #mtzfile = os.path.join(molrep_dir,filename) structure = self.finaliseStructure(xyzfile, "mrbump", hkl, None, [seq], 1, False) if structure: # update structure revision revision = self.makeClass( self.input_data.data.revision[0]) revision.setStructureData(structure) self.registerRevision(revision) else: self.putTitle("No solution found") else: models_found = False ensembles_found = False models_dir = os.path.join(search_dir, "models") if os.path.isdir(models_dir): mdirlist = os.listdir(models_dir) domainNo = 1 dirName = "domain_" + str(domainNo) while dirName in mdirlist: secrow = 0 domains_dir = os.path.join(models_dir, dirName) dirlist = os.listdir(domains_dir) for filename in dirlist: if filename.endswith(".pdb"): if not models_found: models_found = True self.putTitle("Results") if secrow == 0: secId = "domain_sec_" + str(domainNo) self.putSection(secId, "Domain " + str(domainNo)) pyrvapi.rvapi_add_text( "<h2>Models found:</h2>", secId, secrow, 0, 1, 1) secrow += 1 xyz = self.registerXYZ( os.path.join(domains_dir, filename)) if xyz: xyz.addDataAssociation(seq.dataId) pyrvapi.rvapi_add_data( "model_" + str(self.dataSerialNo) + "_btn", "Model #" + str(self.dataSerialNo).zfill(2), # always relative to job_dir from job_dir/html os.path.join("..", self.outputDir(), xyz.files[0]), "xyz", secId, secrow, 0, 1, 1, -1) secrow += 1 ensembles_dir = os.path.join(domains_dir, "ensembles") ensembleSerNo = 0 if os.path.isdir(ensembles_dir): for filename in os.listdir(ensembles_dir): if filename.endswith(".pdb"): if not ensembles_found: pyrvapi.rvapi_add_text( "<h2>Ensembles made:</h2>", secId, secrow, 0, 1, 1) ensembles_found = True secrow += 1 ensembleSerNo += 1 ensemble = self.registerEnsemble( seq, os.path.join(ensembles_dir, filename)) if ensemble: ensemble.addDataAssociation(seq.dataId) self.putEnsembleWidget1( secId, "ensemble_" + str(ensembleSerNo) + "_btn", "Ensemble #" + str(ensembleSerNo).zfill(2), ensemble, -1, secrow, 1) secrow += 1 domainNo += 1 dirName = "domain_" + str(domainNo) # ---------------------------------------------------------------- if not models_found: self.putTitle("No models found") else: self.putTitle("No resuts produced") # close execution logs and quit self.success() return
def write_output(items, json_file=None, xml_file=None, xmlroot=None, docid=None, output=None): # in non-i2 mode items are added to the output dictionary which is dumped to json if json_file is not None: if 'result' in items: result = items['result'] for solution in output['solutions']: if solution['id'] == result['id']: solution.update({'acornCC': result['acornCC']}) else: output.update(items) temp_filename = json_file + '.tmp' with open(temp_filename, 'w') as jsonfile: print(json.dumps(output, sort_keys=True, indent=2, separators=(',', ': ')), file=jsonfile) if os.path.exists(json_file): import uuid tmpfile = str(uuid.uuid4()) os.rename(json_file, tmpfile) os.remove(tmpfile) os.rename(temp_filename, json_file) return output elif xmlroot is None and xml_file is not None: xmlroot = etree.Element('Fragon') return xmlroot elif docid is None: jsrview_dir = os.path.join(os.environ['CCP4'], 'share', 'jsrview') pyrvapi.rvapi_init_document('fragon_results', os.getcwd(), 'Fragon %s results' % items['Fragon'], 1, 7, jsrview_dir, None, None, None, None) pyrvapi.rvapi_add_tab('tab1', 'Fragon results', True) pyrvapi.rvapi_add_section('status', 'Current status', 'tab1', 0, 0, 1, 1, True) pyrvapi.rvapi_add_text( 'The job is currently running. Updates will be shown here after fragment placement and density modification.', 'status', 0, 0, 1, 1) pyrvapi.rvapi_flush() output.update(items) return 'tab1', output elif xml_file is not None: # in i2 mode new items are added to the etree as this preserves the order in the xml for key in items: if key == 'Fragon': version_node = etree.SubElement(xmlroot, 'Version') version_node.text = output['Fragon'] elif key == 'callback': callback = items['callback'] if callback[0] == 'progress': try: progress_node = xmlroot.xpath( '//Fragon/phaser_progress')[0] except IndexError: progress_node = etree.SubElement( xmlroot, 'phaser_progress') progress_node.text = callback[1] elif callback[0] == 'Best LLG/TFZ': best_llg_node = etree.SubElement(xmlroot, 'best_llg') best_llg_node.text = callback[1]['llg'] best_tfz_node = etree.SubElement(xmlroot, 'best_tfz') best_tfz_node.text = callback[1]['tfz'] elif key == 'solutions': solutions = items['solutions'] try: solutions_node = xmlroot.xpath('//Fragon/solutions')[0] except IndexError: solutions_node = etree.SubElement(xmlroot, 'solutions') if len(solutions) > 0: solutions_node.text = json.dumps(solutions) else: node = etree.SubElement(xmlroot, key) node.text = items[key].__str__() temp_filename = 'program.xml.tmp' with open(temp_filename, 'w') as xmlfile: xmlfile.write(etree.tostring(xmlroot, pretty_print=True)) if os.path.exists(xml_file): import uuid tmpfile = str(uuid.uuid4()) os.rename(xml_file, tmpfile) os.remove(tmpfile) os.rename(temp_filename, xml_file) elif docid is not None: for key in items: if key == 'copies': if items['copies'] > 1: pyrvapi.rvapi_set_text( 'Running Phaser to place %d fragments' % items['copies'], 'status', 0, 0, 1, 1) else: pyrvapi.rvapi_set_text( 'Running Phaser to place the fragment', 'status', 0, 0, 1, 1) pyrvapi.rvapi_add_tab('tab2', 'Phaser log file', False) pyrvapi.rvapi_append_content(output['root'] + '_Phaser.log', True, 'tab2') pyrvapi.rvapi_flush() output.update(items) elif key == 'callback': callback = items['callback'] if callback[0] == 'progress': pyrvapi.rvapi_set_text( 'Current Phaser stage: %s' % callback[1], 'status', 1, 0, 1, 1) pyrvapi.rvapi_flush() elif callback[0] == 'Best LLG': pyrvapi.rvapi_set_text( 'Current best solution Log Likelihood Gain (LLG): %s Translation Function Z-score (TFZ): %s' % (callback[1], output['best_tfz']), 'status', 2, 0, 1, 1) pyrvapi.rvapi_flush() elif callback[0] == 'Best TFZ': output.update({'best_tfz': callback[1]}) elif key == 'solutions': solutions = items['solutions'] top_llg = sorted(solutions, key=lambda r: r['llg'], reverse=True)[0]['llg'] top_tfz = sorted(solutions, key=lambda r: r['llg'], reverse=True)[0]['tfz'] top_acornCC = sorted([ solution['acornCC'] if solution['acornCC'] not in ['Running', '-', None] else None for solution in solutions ], reverse=True)[0] if len(solutions) == 1: pyrvapi.rvapi_set_text( 'Phaser has found a single solution with Log Likelihood Gain (LLG) of %0.2f and Translation Function Z-score (TFZ) of %0.2f' % (top_llg, top_tfz), 'status', 0, 0, 1, 1) else: pyrvapi.rvapi_set_text( 'Phaser has found %d solutions. The top solution has Log Likelihood Gain (LLG) of %0.2f and Translation Function Z-score (TF Z-score) of %0.2f' % (output['num_phaser_solutions'], top_llg, top_tfz), 'status', 0, 0, 1, 1) if output['num_phaser_solutions'] > len(solutions): pyrvapi.rvapi_set_text( 'Attempting to improve phases for the top %d solutions by density modification with ACORN' % len(solns), 'status', 1, 0, 1, 1) else: pyrvapi.rvapi_set_text( 'Attempting to improve phases by density modification with ACORN', 'status', 1, 0, 1, 1) if top_acornCC is not None: pyrvapi.rvapi_set_text( 'The best solution so far has a correlation coefficient from density modification of %0.3f' % top_acornCC, 'status', 2, 0, 1, 1) else: pyrvapi.rvapi_set_text('', 'status', 2, 0, 1, 1) pyrvapi.rvapi_add_table('results_table', 'Phaser solutions', 'tab1', 1, 0, 1, 1, 1) pyrvapi.rvapi_put_horz_theader('results_table', 'Solution number', '', 0) pyrvapi.rvapi_put_horz_theader('results_table', 'Space group', '', 1) pyrvapi.rvapi_put_horz_theader('results_table', 'LLG', 'Phaser Log Likelihood Gain', 2) pyrvapi.rvapi_put_horz_theader( 'results_table', 'TF Z-score', 'Phaser Translation Function Z-score', 3) pyrvapi.rvapi_put_horz_theader( 'results_table', 'CC', 'CC from ACORN density modification', 4) for solution in solutions: pyrvapi.rvapi_put_table_string('results_table', '%d' % solution['number'], solution['number'] - 1, 0) pyrvapi.rvapi_put_table_string('results_table', solution['sg'], solution['number'] - 1, 1) pyrvapi.rvapi_put_table_string('results_table', '%0.2f' % solution['llg'], solution['number'] - 1, 2) pyrvapi.rvapi_put_table_string('results_table', '%0.2f' % solution['tfz'], solution['number'] - 1, 3) if solution['acornCC'] in ['Running', '-']: pyrvapi.rvapi_put_table_string( 'results_table', solution['acornCC'].replace('-', ''), solution['number'] - 1, 4) elif solution['acornCC'] is None: pyrvapi.rvapi_put_table_string('results_table', 'Not tested', solution['number'] - 1, 4) else: pyrvapi.rvapi_put_table_string( 'results_table', '%0.3f' % solution['acornCC'], solution['number'] - 1, 4) output.update(items) pyrvapi.rvapi_flush() elif key == 'cc_best': solutions = output['solutions'] top_llg = sorted(solutions, key=lambda r: r['llg'], reverse=True)[0]['llg'] top_tfz = sorted(solutions, key=lambda r: r['llg'], reverse=True)[0]['tfz'] top_acornCC = sorted([ solution['acornCC'] if solution['acornCC'] not in ['Running', '-', None] else None for solution in solutions ], reverse=True)[0] pyrvapi.rvapi_set_section_state('status', False) pyrvapi.rvapi_add_section('results', 'Results', 'tab1', 2, 0, 1, 1, True) pyrvapi.rvapi_add_text( 'Phaser found %d solutions. The top solution had Log Likelihood Gain (LLG) of %0.2f and Translation Function Z-score (TFZ) of %0.2f' % (output['num_phaser_solutions'], top_llg, top_tfz), 'results', 0, 0, 1, 1) pyrvapi.rvapi_add_text( 'The best solution has a correlation coefficient from density modification of %0.3f' % top_acornCC, 'results', 1, 0, 1, 1) if top_acornCC > 0.15: pyrvapi.rvapi_add_text( 'This suggests the structure has been solved and the phases from ACORN will enable automated model building', 'results', 2, 0, 1, 1) else: pyrvapi.rvapi_add_text( 'Sorry this does not suggest a solution', 'results', 3, 0, 1, 1) pyrvapi.rvapi_flush() elif key == 'best_solution_id': pdbout = output['name'] + '_phaser_solution.pdb' mtzout = output['name'] + '_acorn_phases.mtz' pyrvapi.rvapi_add_data( 'best', 'Best fragment placement and electron density', pdbout, 'xyz', 'tab1', 3, 0, 1, 1, True) pyrvapi.rvapi_append_to_data('best', mtzout, 'hkl:map') else: output.update(items) return output
def add_text(self, content): pyrvapi.rvapi_add_text(content, self._identifier, 0, 0, 1, 1)
def results_section(self, results_tab_id, mrb_results, ensemble_results, section_title): # # Results Tab # if not mrb_results: return # Create unique identifier for this section by using the id # All ids will have this appended to avoid clashes uid = str(uuid.uuid4()) section_id = section_title.replace(" ", "_") + uid self.results_tab_sections.append(section_id) # Add to list so we can remove if we update pyrvapi.rvapi_add_panel(section_id, results_tab_id, 0, 0, 1, 1) pyrvapi.rvapi_add_text("<h3>{0}</h3>".format(section_title), section_id, 0, 0, 1, 1) results_tree = "results_tree" + section_id pyrvapi.rvapi_add_tree_widget(results_tree, section_title, section_id, 0, 0, 1, 1) for r in mrb_results: name = r['ensemble_name'] container_id = "sec_{0}".format(name) + uid pyrvapi.rvapi_add_panel(container_id, results_tree, 0, 0, 1, 1) header = "<h3>Results for ensemble: {0}</h3>".format(name) pyrvapi.rvapi_add_text(header, container_id, 0, 0, 1, 1) sec_table = "sec_table_{0}".format(name) + uid title = "Results table: {0}".format(name) title = "Summary" pyrvapi.rvapi_add_section(sec_table, title, container_id, 0, 0, 1, 1, True) table_id = "table_{0}".format(name) + uid pyrvapi.rvapi_add_table(table_id, "", sec_table, 1, 0, 1, 1, False) tdata = mrbump_util.ResultsSummary().results_table([r]) self.fill_table(table_id, tdata, tooltips=self._mrbump_tooltips) # Ensemble if ensemble_results: epdb = self.ensemble_pdb(r, ensemble_results) if epdb: sec_ensemble = "sec_ensemble_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_ensemble, "Ensemble Search Model", container_id, 0, 0, 1, 1, False) data_ensemble = "data_ensemble_{0}".format(name) + uid pyrvapi.rvapi_add_data(data_ensemble, "Ensemble PDB", self.fix_path(epdb), "XYZOUT", sec_ensemble, 2, 0, 1, 1, True) # PHASER if os.path.isfile(str(r['PHASER_logfile'])) or (os.path.isfile(str(r['PHASER_pdbout'])) and os.path.isfile(str(r['PHASER_mtzout']))): sec_phaser = "sec_phaser_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_phaser, "PHASER Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['PHASER_pdbout'])) and os.path.isfile(str(r['PHASER_mtzout'])): data_phaser = "data_phaser_out_{0}".format(name) + uid pyrvapi.rvapi_add_data(data_phaser, "PHASER PDB", os.path.splitext(self.fix_path(r['PHASER_pdbout']))[0], "xyz:map", sec_phaser, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data(data_phaser, self.fix_path(r['PHASER_mtzout']), "xyz:map") if os.path.isfile(str(r['PHASER_logfile'])): pyrvapi.rvapi_add_data("data_phaser_logfile_{0}".format(name), "PHASER Logfile", self.fix_path(r['PHASER_logfile']), "text", sec_phaser, 2, 0, 1, 1, True) # REFMAC if os.path.isfile(str(r['REFMAC_logfile'])) or (os.path.isfile(str(r['REFMAC_pdbout'])) and os.path.isfile(str(r['REFMAC_mtzout']))): sec_refmac = "sec_refmac_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_refmac, "REFMAC Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['REFMAC_pdbout'])) and os.path.isfile(str(r['REFMAC_mtzout'])): data_refmac = "data_refmac_out_{0}".format(name) + uid pyrvapi.rvapi_add_data(data_refmac, "REFMAC PDB", os.path.splitext(self.fix_path(r['REFMAC_pdbout']))[0], "xyz:map", sec_refmac, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data(data_refmac, self.fix_path(r['REFMAC_mtzout']), "xyz:map") if os.path.isfile(str(r['REFMAC_logfile'])): pyrvapi.rvapi_add_data("data_refmac_logfile_{0}".format(name), "REFMAC Logfile", self.fix_path(r['REFMAC_logfile']), "text", sec_refmac, 2, 0, 1, 1, True) # Buccaner if os.path.isfile(str(r['BUCC_logfile'])) or (os.path.isfile(str(r['BUCC_pdbout'])) and os.path.isfile(str(r['BUCC_mtzout']))): sec_bucc = "sec_bucc_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_bucc, "BUCCANEER Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['BUCC_pdbout'])) and os.path.isfile(str(r['BUCC_mtzout'])): data_bucc = "data_bucc_out_{0}".format(name) + uid pyrvapi.rvapi_add_data(data_bucc, "BUCC PDB", os.path.splitext(self.fix_path(r['BUCC_pdbout']))[0], "xyz:map", sec_bucc, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data(data_bucc, self.fix_path(r['BUCC_mtzout']), "xyz:map") if os.path.isfile(str(r['BUCC_logfile'])): pyrvapi.rvapi_add_data("data_bucc_logfile_{0}".format(name), "BUCC Logfile", self.fix_path(r['BUCC_logfile']), "text", sec_bucc, 2, 0, 1, 1, True) # Arpwarp if os.path.isfile(str(r['ARP_logfile'])) or (os.path.isfile(str(r['ARP_pdbout'])) and os.path.isfile(str(r['ARP_mtzout']))): sec_arp = "sec_arp_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_arp, "ARPWARP Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['ARP_pdbout'])) and os.path.isfile(str(r['ARP_mtzout'])): data_arp = "data_arp_out_{0}".format(name) + uid pyrvapi.rvapi_add_data(data_arp, "ARP PDB", os.path.splitext(self.fix_path(r['ARP_pdbout']))[0], "xyz:map", sec_arp, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data(data_arp, self.fix_path(r['ARP_mtzout']), "xyz:map") if os.path.isfile(str(r['ARP_logfile'])): pyrvapi.rvapi_add_data("data_arp_logfile_{0}".format(name), "ARP Logfile", self.fix_path(r['ARP_logfile']), "text", sec_arp, 2, 0, 1, 1, True) # SHELXE if os.path.isfile(str(r['SHELXE_logfile'])) or (os.path.isfile(str(r['SHELXE_pdbout'])) and os.path.isfile(str(r['SHELXE_mtzout']))): sec_shelxe = "sec_shelxe_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_shelxe, "SHELXE Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['SHELXE_pdbout'])) and os.path.isfile(str(r['SHELXE_mtzout'])): data_shelxe = "data_shelxe_out_{0}".format(name) + uid pyrvapi.rvapi_add_data(data_shelxe, "SHELXE PDB", os.path.splitext(self.fix_path(r['SHELXE_pdbout']))[0], "xyz:map", sec_shelxe, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data(data_shelxe, self.fix_path(r['SHELXE_mtzout']), "xyz:map") if os.path.isfile(str(r['SHELXE_logfile'])): pyrvapi.rvapi_add_data("data_shelxe_logfile_{0}".format(name), "SHELXE Logfile", self.fix_path(r['SHELXE_logfile']), "text", sec_shelxe, 2, 0, 1, 1, True) # Buccaner Rebuild if os.path.isfile(str(r['SXRBUCC_logfile'])) or (os.path.isfile(str(r['SXRBUCC_pdbout'])) and os.path.isfile(str(r['SXRBUCC_mtzout']))): sec_sxrbucc = "sec_sxrbucc_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_sxrbucc, "BUCCANEER SHELXE Trace Rebuild Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['SXRBUCC_pdbout'])) and os.path.isfile(str(r['SXRBUCC_mtzout'])): data_sxrbucc = "data_sxrbucc_out_{0}".format(name) + uid pyrvapi.rvapi_add_data(data_sxrbucc, "SXRBUCC PDB", os.path.splitext(self.fix_path(r['SXRBUCC_pdbout']))[0], "xyz:map", sec_sxrbucc, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data(data_sxrbucc, self.fix_path(r['SXRBUCC_mtzout']), "xyz:map") if os.path.isfile(str(r['SXRBUCC_logfile'])): pyrvapi.rvapi_add_data("data_sxrbucc_logfile_{0}".format(name), "SXRBUCC Logfile", self.fix_path(r['SXRBUCC_logfile']), "text", sec_sxrbucc, 2, 0, 1, 1, True) # Arpwarp Rebuild if os.path.isfile(str(r['SXRARP_logfile'])) or (os.path.isfile(str(r['SXRARP_pdbout'])) and os.path.isfile(str(r['SXRARP_mtzout']))): sec_sxrarp = "sec_sxrarp_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_sxrarp, "ARPWARP SHELXE Trace Redbuild Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['SXRARP_pdbout'])) and os.path.isfile(str(r['SXRARP_mtzout'])): data_sxrarp = "data_sxrarp_out_{0}".format(name) + uid pyrvapi.rvapi_add_data(data_sxrarp, "SXRARP PDB", os.path.splitext(self.fix_path(r['SXRARP_pdbout']))[0], "xyz:map", sec_sxrarp, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data(data_sxrarp, self.fix_path(r['SXRARP_mtzout']), "xyz:map") if os.path.isfile(str(r['SXRARP_logfile'])): pyrvapi.rvapi_add_data("data_sxrarp_logfile_{0}".format(name), "SXRARP Logfile", self.fix_path(r['SXRARP_logfile']), "text", sec_sxrarp, 2, 0, 1, 1, True) pyrvapi.rvapi_set_tree_node(results_tree, container_id, "{0}".format(name), "auto", "") return
def display_summary_tab(self): """Function to create the MoRDa Database results tab Returns ------- object Page containing a summary of the best results from SIMBAD """ self._create_summary_tab() if self.lattice_df is None: lattice_score = 1 else: try: lattice_score = self.lattice_df['final_r_free'][0] except IndexError: lattice_score = 1 if self.contaminant_df is None: contaminant_score = 1 else: try: contaminant_score = self.contaminant_df['final_r_free'][0] except IndexError: contaminant_score = 1 if self.morda_db_df is None: morda_db_score = 1 else: try: morda_db_score = self.morda_db_df['final_r_free'][0] except IndexError: morda_db_score = 1 section_title = 'SIMBAD Summary' uid = str(uuid.uuid4()) sec = section_title.replace(" ", "_") + uid tab = self.summary_tab_id if lattice_score == 1 and contaminant_score == 1 and morda_db_score == 1: msg = "No solution was found by SIMBAD" pyrvapi.rvapi_add_section(sec, section_title, tab, 0, 0, 1, 1, True) pyrvapi.rvapi_add_text(msg, sec, 2, 0, 1, 1) else: if lattice_score <= contaminant_score and lattice_score <= morda_db_score: pdb_code = self.lattice_df.loc[0][0] r_fact = self.lattice_df['final_r_fact'][0] r_free = self.lattice_df['final_r_free'][0] source = "latt" elif contaminant_score <= lattice_score and contaminant_score <= morda_db_score: pdb_code = self.contaminant_df.loc[0][0] r_fact = self.contaminant_df['final_r_fact'][0] r_free = self.contaminant_df['final_r_free'][0] source = "cont" elif morda_db_score <= lattice_score and morda_db_score <= contaminant_score: pdb_code = self.morda_db_df.loc[0][0] r_fact = self.morda_db_df['final_r_fact'][0] r_free = self.morda_db_df['final_r_free'][0] source = "morda" else: logger.debug('Unexpected result') return mr_workdir = os.path.join(self.work_dir, 'output_files', pdb_code) mr_log = os.path.join(mr_workdir, '{0}_mr.log'.format(pdb_code)) ref_log = os.path.join(mr_workdir, '{0}_ref.log'.format(pdb_code)) ref_pdb = os.path.join(mr_workdir, '{0}_refinement_output.pdb'.format(pdb_code)) ref_map = os.path.join(mr_workdir, '{0}_refmac_2fofcwt.map'.format(pdb_code)) ref_mtz = os.path.join(mr_workdir, '{0}_refinement_output.mtz'.format(pdb_code)) diff_map = os.path.join(mr_workdir, '{0}_refmac_fofcwt.map'.format(pdb_code)) msg = 'The best search model found by SIMBAD was {0}. \ This gave an R/Rfact of {1:.3f} and an R/Rfree of {2:.3f}. \ An R/Rfree lower than 0.450 is indicative of a \ solution. Values above this may also be indicative of a correct solution \ but you should examine the maps through the graphical map viewer for \ verification.'.format(pdb_code, r_fact, r_free) pyrvapi.rvapi_add_section(sec, section_title, tab, 0, 0, 1, 1, True) pyrvapi.rvapi_add_text(msg, sec, 2, 0, 1, 1) section_title = 'Best SIMBAD result Downloads' uid = str(uuid.uuid4()) download_sec = section_title.replace(" ", "_") + uid pyrvapi.rvapi_add_section(download_sec, section_title, tab, 0, 0, 1, 1, True) section_title = 'Best SIMBAD result Log Files' uid = str(uuid.uuid4()) logfile_sec = section_title.replace(" ", "_") + uid pyrvapi.rvapi_add_section(logfile_sec, section_title, tab, 0, 0, 1, 1, False) pdb, mtz, map_, dmap, mr_log, ref_log = list( self.adjust_paths_of_files([ref_pdb, ref_mtz, ref_map, diff_map, mr_log, ref_log])) for e in self.rvapi_meta.results: if e["name"] == pdb_code and e["source"] == source: e["best"] = True self.output_result_files(download_sec, dmap, map_, mtz, pdb) self.output_log_files(logfile_sec, mr_log, ref_log)
def results_section(self, results_tab_id, mrb_results, ensemble_results, section_title): # # Results Tab # if not mrb_results: return # Create unique identifier for this section by using the id # All ids will have this appended to avoid clashes uid = str(uuid.uuid4()) section_id = section_title.replace(" ", "_") + uid self.results_tab_sections.append( section_id) # Add to list so we can remove if we update pyrvapi.rvapi_add_panel(section_id, results_tab_id, 0, 0, 1, 1) pyrvapi.rvapi_add_text("<h3>{0}</h3>".format(section_title), section_id, 0, 0, 1, 1) results_tree = "results_tree" + section_id pyrvapi.rvapi_add_tree_widget(results_tree, section_title, section_id, 0, 0, 1, 1) for r in mrb_results: name = r['ensemble_name'] # container_id="sec_{0}".format(name) # pyrvapi.rvapi_add_section(container_id,"Results for: {0}".format(name),results_tree,0,0,1,1,True) container_id = "sec_{0}".format(name) + uid pyrvapi.rvapi_add_panel(container_id, results_tree, 0, 0, 1, 1) header = "<h3>Results for ensemble: {0}</h3>".format(name) pyrvapi.rvapi_add_text(header, container_id, 0, 0, 1, 1) sec_table = "sec_table_{0}".format(name) + uid title = "Results table: {0}".format(name) title = "Summary" pyrvapi.rvapi_add_section(sec_table, title, container_id, 0, 0, 1, 1, True) table_id = "table_{0}".format(name) + uid pyrvapi.rvapi_add_table(table_id, "", sec_table, 1, 0, 1, 1, False) tdata = mrbump_util.ResultsSummary().results_table([r]) self.fill_table(table_id, tdata, tooltips=self._mrbump_tooltips) # Ensemble if ensemble_results: epdb = self.ensemble_pdb(r, ensemble_results) if epdb: sec_ensemble = "sec_ensemble_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_ensemble, "Ensemble Search Model", container_id, 0, 0, 1, 1, False) data_ensemble = "data_ensemble_{0}".format(name) + uid pyrvapi.rvapi_add_data(data_ensemble, "Ensemble PDB", self.fix_path(epdb), "XYZOUT", sec_ensemble, 2, 0, 1, 1, True) # PHASER if os.path.isfile(str(r['PHASER_logfile'])) or ( os.path.isfile(str(r['PHASER_pdbout'])) and os.path.isfile(str(r['PHASER_mtzout']))): sec_phaser = "sec_phaser_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_phaser, "PHASER Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['PHASER_pdbout'])) and os.path.isfile( str(r['PHASER_mtzout'])): data_phaser = "data_phaser_out_{0}".format(name) + uid pyrvapi.rvapi_add_data( data_phaser, "PHASER PDB", os.path.splitext(self.fix_path(r['PHASER_pdbout']))[0], "xyz:map", sec_phaser, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data( data_phaser, self.fix_path(r['PHASER_mtzout']), "xyz:map") if os.path.isfile(str(r['PHASER_logfile'])): pyrvapi.rvapi_add_data( "data_phaser_logfile_{0}".format(name), "PHASER Logfile", self.fix_path(r['PHASER_logfile']), "text", sec_phaser, 2, 0, 1, 1, True) # REFMAC if os.path.isfile(str(r['REFMAC_logfile'])) or ( os.path.isfile(str(r['REFMAC_pdbout'])) and os.path.isfile(str(r['REFMAC_mtzout']))): sec_refmac = "sec_refmac_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_refmac, "REFMAC Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['REFMAC_pdbout'])) and os.path.isfile( str(r['REFMAC_mtzout'])): data_refmac = "data_refmac_out_{0}".format(name) + uid pyrvapi.rvapi_add_data( data_refmac, "REFMAC PDB", os.path.splitext(self.fix_path(r['REFMAC_pdbout']))[0], "xyz:map", sec_refmac, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data( data_refmac, self.fix_path(r['REFMAC_mtzout']), "xyz:map") if os.path.isfile(str(r['REFMAC_logfile'])): pyrvapi.rvapi_add_data( "data_refmac_logfile_{0}".format(name), "REFMAC Logfile", self.fix_path(r['REFMAC_logfile']), "text", sec_refmac, 2, 0, 1, 1, True) # Buccaner if os.path.isfile(str(r['BUCC_logfile'])) or ( os.path.isfile(str(r['BUCC_pdbout'])) and os.path.isfile(str(r['BUCC_mtzout']))): sec_bucc = "sec_bucc_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_bucc, "BUCCANEER Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['BUCC_pdbout'])) and os.path.isfile( str(r['BUCC_mtzout'])): data_bucc = "data_bucc_out_{0}".format(name) + uid pyrvapi.rvapi_add_data( data_bucc, "BUCC PDB", os.path.splitext(self.fix_path(r['BUCC_pdbout']))[0], "xyz:map", sec_bucc, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data( data_bucc, self.fix_path(r['BUCC_mtzout']), "xyz:map") if os.path.isfile(str(r['BUCC_logfile'])): pyrvapi.rvapi_add_data( "data_bucc_logfile_{0}".format(name), "BUCC Logfile", self.fix_path(r['BUCC_logfile']), "text", sec_bucc, 2, 0, 1, 1, True) # Arpwarp if os.path.isfile(str(r['ARP_logfile'])) or ( os.path.isfile(str(r['ARP_pdbout'])) and os.path.isfile(str(r['ARP_mtzout']))): sec_arp = "sec_arp_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_arp, "ARPWARP Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['ARP_pdbout'])) and os.path.isfile( str(r['ARP_mtzout'])): data_arp = "data_arp_out_{0}".format(name) + uid pyrvapi.rvapi_add_data( data_arp, "ARP PDB", os.path.splitext(self.fix_path(r['ARP_pdbout']))[0], "xyz:map", sec_arp, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data( data_arp, self.fix_path(r['ARP_mtzout']), "xyz:map") if os.path.isfile(str(r['ARP_logfile'])): pyrvapi.rvapi_add_data("data_arp_logfile_{0}".format(name), "ARP Logfile", self.fix_path(r['ARP_logfile']), "text", sec_arp, 2, 0, 1, 1, True) # SHELXE if os.path.isfile(str(r['SHELXE_logfile'])) or ( os.path.isfile(str(r['SHELXE_pdbout'])) and os.path.isfile(str(r['SHELXE_mtzout']))): sec_shelxe = "sec_shelxe_{0}".format(name) + uid pyrvapi.rvapi_add_section(sec_shelxe, "SHELXE Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['SHELXE_pdbout'])) and os.path.isfile( str(r['SHELXE_mtzout'])): data_shelxe = "data_shelxe_out_{0}".format(name) + uid pyrvapi.rvapi_add_data( data_shelxe, "SHELXE PDB", os.path.splitext(self.fix_path(r['SHELXE_pdbout']))[0], "xyz:map", sec_shelxe, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data( data_shelxe, self.fix_path(r['SHELXE_mtzout']), "xyz:map") if os.path.isfile(str(r['SHELXE_logfile'])): pyrvapi.rvapi_add_data( "data_shelxe_logfile_{0}".format(name), "SHELXE Logfile", self.fix_path(r['SHELXE_logfile']), "text", sec_shelxe, 2, 0, 1, 1, True) # Buccaner Rebuild if os.path.isfile(str(r['SXRBUCC_logfile'])) or ( os.path.isfile(str(r['SXRBUCC_pdbout'])) and os.path.isfile(str(r['SXRBUCC_mtzout']))): sec_sxrbucc = "sec_sxrbucc_{0}".format(name) + uid pyrvapi.rvapi_add_section( sec_sxrbucc, "BUCCANEER SHELXE Trace Rebuild Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['SXRBUCC_pdbout'])) and os.path.isfile( str(r['SXRBUCC_mtzout'])): data_sxrbucc = "data_sxrbucc_out_{0}".format(name) + uid pyrvapi.rvapi_add_data( data_sxrbucc, "SXRBUCC PDB", os.path.splitext(self.fix_path( r['SXRBUCC_pdbout']))[0], "xyz:map", sec_sxrbucc, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data( data_sxrbucc, self.fix_path(r['SXRBUCC_mtzout']), "xyz:map") if os.path.isfile(str(r['SXRBUCC_logfile'])): pyrvapi.rvapi_add_data( "data_sxrbucc_logfile_{0}".format(name), "SXRBUCC Logfile", self.fix_path(r['SXRBUCC_logfile']), "text", sec_sxrbucc, 2, 0, 1, 1, True) # Arpwarp Rebuild if os.path.isfile(str(r['SXRARP_logfile'])) or ( os.path.isfile(str(r['SXRARP_pdbout'])) and os.path.isfile(str(r['SXRARP_mtzout']))): sec_sxrarp = "sec_sxrarp_{0}".format(name) + uid pyrvapi.rvapi_add_section( sec_sxrarp, "ARPWARP SHELXE Trace Redbuild Outputs", container_id, 0, 0, 1, 1, False) if os.path.isfile(str(r['SXRARP_pdbout'])) and os.path.isfile( str(r['SXRARP_mtzout'])): data_sxrarp = "data_sxrarp_out_{0}".format(name) + uid pyrvapi.rvapi_add_data( data_sxrarp, "SXRARP PDB", os.path.splitext(self.fix_path(r['SXRARP_pdbout']))[0], "xyz:map", sec_sxrarp, 2, 0, 1, 1, True) pyrvapi.rvapi_append_to_data( data_sxrarp, self.fix_path(r['SXRARP_mtzout']), "xyz:map") if os.path.isfile(str(r['SXRARP_logfile'])): pyrvapi.rvapi_add_data( "data_sxrarp_logfile_{0}".format(name), "SXRARP Logfile", self.fix_path(r['SXRARP_logfile']), "text", sec_sxrarp, 2, 0, 1, 1, True) pyrvapi.rvapi_set_tree_node(results_tree, container_id, "{0}".format(name), "auto", "") return
def display_summary_tab(self): """Function to create the MoRDa Database results tab Returns ------- object Page containing a summary of the best results from SIMBAD """ self._create_summary_tab() if self.lattice_df is None: lattice_score = 1 else: try: lattice_score = self.lattice_df['final_r_free'][0] except IndexError: lattice_score = 1 if self.contaminant_df is None: contaminant_score = 1 else: try: contaminant_score = self.contaminant_df['final_r_free'][0] except IndexError: contaminant_score = 1 if self.morda_db_df is None: morda_db_score = 1 else: try: morda_db_score = self.morda_db_df['final_r_free'][0] except IndexError: morda_db_score = 1 section_title = 'SIMBAD Summary' uid = str(uuid.uuid4()) sec = section_title.replace(" ", "_") + uid tab = self.summary_tab_id if lattice_score == 1 and contaminant_score == 1 and morda_db_score == 1: msg = "No solution was found by SIMBAD" pyrvapi.rvapi_add_section(sec, section_title, tab, 0, 0, 1, 1, True) pyrvapi.rvapi_add_text(msg, sec, 2, 0, 1, 1) else: if lattice_score <= contaminant_score and lattice_score <= morda_db_score: pdb_code = self.lattice_df.loc[0][0] r_fact = self.lattice_df['final_r_fact'][0] r_free = self.lattice_df['final_r_free'][0] source = "latt" elif contaminant_score <= lattice_score and contaminant_score <= morda_db_score: pdb_code = self.contaminant_df.loc[0][0] r_fact = self.contaminant_df['final_r_fact'][0] r_free = self.contaminant_df['final_r_free'][0] source = "cont" elif morda_db_score <= lattice_score and morda_db_score <= contaminant_score: pdb_code = self.morda_db_df.loc[0][0] r_fact = self.morda_db_df['final_r_fact'][0] r_free = self.morda_db_df['final_r_free'][0] source = "morda" else: logger.debug('Unexpected result') return mr_workdir = os.path.join(self.work_dir, 'output_files', pdb_code) mr_log = os.path.join(mr_workdir, '{0}_mr.log'.format(pdb_code)) ref_log = os.path.join(mr_workdir, '{0}_ref.log'.format(pdb_code)) ref_pdb = os.path.join(mr_workdir, '{0}_refinement_output.pdb'.format(pdb_code)) ref_map = os.path.join(mr_workdir, '{0}_refmac_2fofcwt.map'.format(pdb_code)) ref_mtz = os.path.join(mr_workdir, '{0}_refinement_output.mtz'.format(pdb_code)) diff_map = os.path.join(mr_workdir, '{0}_refmac_fofcwt.map'.format(pdb_code)) msg = 'The best search model found by SIMBAD was {0}. \ This gave an R/Rfact of {1:.3f} and an R/Rfree of {2:.3f}. \ An R/Rfree lower than 0.450 is indicative of a \ solution. Values above this may also be indicative of a correct solution \ but you should examine the maps through the graphical map viewer for \ verification'.format(pdb_code, r_fact, r_free) pyrvapi.rvapi_add_section(sec, section_title, tab, 0, 0, 1, 1, True) pyrvapi.rvapi_add_text(msg, sec, 2, 0, 1, 1) section_title = 'Best SIMBAD result Downloads' uid = str(uuid.uuid4()) download_sec = section_title.replace(" ", "_") + uid pyrvapi.rvapi_add_section(download_sec, section_title, tab, 0, 0, 1, 1, True) section_title = 'Best SIMBAD result Log Files' uid = str(uuid.uuid4()) logfile_sec = section_title.replace(" ", "_") + uid pyrvapi.rvapi_add_section(logfile_sec, section_title, tab, 0, 0, 1, 1, False) pdb, mtz, map_, dmap, mr_log, ref_log = list( self.adjust_paths_of_files([ref_pdb, ref_mtz, ref_map, diff_map, mr_log, ref_log])) for e in self.rvapi_meta.results: if e["name"] == pdb_code and e["source"] == source: e["best"] = True self.output_result_files(download_sec, dmap, map_, mtz, pdb) self.output_log_files(logfile_sec, mr_log, ref_log)