def rm_pending_section(self):
if self.summary_tab_pending_sec_id:
pyrvapi.rvapi_flush()
pyrvapi.rvapi_remove_widget(self.summary_tab_pending_sec_id)
pyrvapi.rvapi_flush()
self.summary_tab_pending_sec_id = None
return
def create_results_tab(self, ample_dict):
if self.ccp4i2 or not self.summary_tab_id or not self._got_mrbump_results(
ample_dict):
return
mrb_results = ample_dict.get('mrbump_results')
if mrb_results == self.old_mrbump_results:
return
self.old_mrbump_results = mrb_results
if not self.results_tab_id:
self.results_tab_id = "results_tab"
pyrvapi.rvapi_insert_tab(self.results_tab_id, "Results",
self.summary_tab_id, False)
# Delete old sections:
pyrvapi.rvapi_flush()
for section_id in self.results_tab_sections:
pyrvapi.rvapi_remove_widget(section_id)
pyrvapi.rvapi_flush()
self.results_tab_sections = []
ensemble_results = ample_dict[
'ensembles_data'] if 'ensembles_data' in ample_dict[
'ensembles_data'] else None
mrbsum = mrbump_util.ResultsSummary(
results=mrb_results[0:min(len(mrb_results), mrbump_util.TOP_KEEP)])
mrbsum.sortResults(prioritise="SHELXE_CC")
self.results_section(
self.results_tab_id, mrbsum.results, ensemble_results,
"Top {0} SHELXE Results".format(mrbump_util.TOP_KEEP))
mrbsum.sortResults(prioritise="PHASER_TFZ")
# Add seperator between results - doesn't work as not deleted on refresh
# pyrvapi.rvapi_add_text("<br/><hr/><br/>", self.results_tab_id, 0, 0, 1, 1)
self.results_section(
self.results_tab_id, mrbsum.results, ensemble_results,
"Top {0} PHASER Results".format(mrbump_util.TOP_KEEP))
return self.results_tab_id
def rm_pending_section(self):
if self.summary_tab_pending_sec_id:
pyrvapi.rvapi_flush()
pyrvapi.rvapi_remove_widget(self.summary_tab_pending_sec_id)
pyrvapi.rvapi_flush()
self.summary_tab_pending_sec_id = None
return
def create_results_tab(self, ample_dict):
if self.ccp4i2 or not self.summary_tab_id or not self._got_mrbump_results(ample_dict):
return
mrb_results = ample_dict.get('mrbump_results')
if mrb_results == self.old_mrbump_results:
return
self.old_mrbump_results = mrb_results
if not self.results_tab_id:
self.results_tab_id = "results_tab"
pyrvapi.rvapi_insert_tab(self.results_tab_id,
"Results", self.summary_tab_id, False)
# Delete old sections:
pyrvapi.rvapi_flush()
for section_id in self.results_tab_sections:
pyrvapi.rvapi_remove_widget(section_id)
pyrvapi.rvapi_flush()
self.results_tab_sections = []
ensemble_results = ample_dict['ensembles_data'] if 'ensembles_data' in ample_dict['ensembles_data'] else None
mrbsum = mrbump_util.ResultsSummary(results=mrb_results[0:min(len(mrb_results),mrbump_util.TOP_KEEP)])
mrbsum.sortResults(prioritise="SHELXE_CC")
self.results_section(self.results_tab_id,
mrbsum.results,
ensemble_results,
"Top {0} SHELXE Results".format(mrbump_util.TOP_KEEP))
mrbsum.sortResults(prioritise="PHASER_TFZ")
self.results_section(self.results_tab_id,
mrbsum.results,
ensemble_results,
"Top {0} PHASER Results".format(mrbump_util.TOP_KEEP))
return self.results_tab_id
def create_results_tab(self, ample_dict):
if self.ccp4i2 or not self.summary_tab_id: return
if not self._got_mrbump_results(ample_dict): return
mrb_results = ample_dict['mrbump_results']
if mrb_results == self.old_mrbump_results: return
self.old_mrbump_results = mrb_results
if not self.results_tab_id:
self.results_tab_id = "results_tab"
# Insert results tab before summary tab
pyrvapi.rvapi_insert_tab(
self.results_tab_id, "Results", self.summary_tab_id,
False) # Last arg is "open" - i.e. show or hide
# Delete old sections:
pyrvapi.rvapi_flush()
for section_id in self.results_tab_sections:
pyrvapi.rvapi_remove_widget(section_id)
pyrvapi.rvapi_flush()
self.results_tab_sections = []
ensemble_results = ample_dict[
'ensembles_data'] if 'ensembles_data' in ample_dict[
'ensembles_data'] else None
mrbsum = mrbump_util.ResultsSummary(
results=mrb_results[0:min(len(mrb_results), mrbump_util.TOP_KEEP)])
mrbsum.sortResults(prioritise="SHELXE_CC")
self.results_section(
self.results_tab_id, mrbsum.results, ensemble_results,
"Top {0} SHELXE Results".format(mrbump_util.TOP_KEEP))
mrbsum.sortResults(prioritise="PHASER_TFZ")
self.results_section(
self.results_tab_id, mrbsum.results, ensemble_results,
"Top {0} PHASER Results".format(mrbump_util.TOP_KEEP))
return self.results_tab_id
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