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)
