def putWaitMessageLF(self, message_str, foregap=1):
gridId = self.page_cursor[0] + str(self.page_cursor[1])
pyrvapi.rvapi_add_grid(gridId, False, self.page_cursor[0],
self.page_cursor[1], 0, 1, 1)
for i in range(foregap):
pyrvapi.rvapi_set_text(" ", gridId, i, 0, 1, 1)
pyrvapi.rvapi_set_text(
"<font style='font-size:120%;'>" + message_str + "</font>", gridId,
foregap, 0, 1, 1)
pyrvapi.rvapi_set_text("<div class='activity_bar'/>", gridId, foregap,
1, 1, 1)
self.page_cursor[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 putMessage(self, message_str):
pyrvapi.rvapi_set_text(message_str, self.page_cursor[0],
self.page_cursor[1], 0, 1, 1)
self.page_cursor[1] += 1
return
def putMessageLF(self, message_str):
pyrvapi.rvapi_set_text(
"<font style='font-size:120%;'>" + message_str + "</font>",
self.page_cursor[0], self.page_cursor[1], 0, 1, 1)
self.page_cursor[1] += 1
return
def run(body): # body is reference to the main Import class
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_integrated', 'xds_scaled', 'mtz_integrated'):
files_mtz.append((f_orig, f_fmt))
if not files_mtz:
return
unmergedSecId = "unmerged_mtz_sec_" + str(body.widget_no)
body.widget_no += 1
k = 0
for f_orig, f_fmt in files_mtz:
try:
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:
if k == 0:
body.file_stdout.write("\n" + "%" * 80 + "\n")
body.file_stdout.write("%%%%% UNMERGED DATA IMPORT\n")
body.file_stdout.write("%" * 80 + "\n")
pyrvapi.rvapi_add_section(unmergedSecId,
"Unmerged datasets",
body.report_page_id(),
body.rvrow, 0, 1, 1, False)
urow = 0
fileSecId = unmergedSecId
frow = 0
if len(files_mtz) > 1:
fileSecId = unmergedSecId + "_" + str(k)
pyrvapi.rvapi_add_section(fileSecId, "File " + f_orig,
unmergedSecId, urow, 0, 1, 1,
False)
urow += 1
pyrvapi.rvapi_set_text(
"<h2>Data analysis (Pointless)</h2>", fileSecId, frow,
0, 1, 1)
else:
pyrvapi.rvapi_set_text ( "<h2>Data analysis (Pointless)</h2>" + \
"<h3>File: " + f_orig + "</h3>",
fileSecId,frow,0,1,1 )
reportPanelId = fileSecId + "_report"
pyrvapi.rvapi_add_panel(reportPanelId, fileSecId, frow + 1, 0,
1, 1)
frow += 2
log_parser = pyrvapi_ext.parsers.generic_parser(
reportPanelId, False)
body.file_stdin = open(pointless_script(), 'w')
body.file_stdin.write (
"HKLIN " + p_mtzin + "\n" + \
"XMLOUT " + pointless_xml() + "\n"
)
body.file_stdin.close()
rc = command.call("pointless", [], "./", pointless_script(),
body.file_stdout, body.file_stderr,
log_parser)
body.unsetLogParser()
symmTablesId = fileSecId + "_" + symm_det()
pyrvapi.rvapi_add_section(symmTablesId,
"Symmetry determination tables",
fileSecId, frow, 0, 1, 1, True)
pyrvapi.rvapi_set_text(" ", fileSecId, frow + 1, 0, 1, 1)
frow += 2
#body.putSection ( symmTablesId,"Symmetry determination tables",True )
table_list = datred_utils.parse_xmlout(pointless_xml())
datred_utils.report(table_list, symmTablesId)
# dump_keyargs = dict(sort_keys=True, indent=4, separators=(',', ': '))
# print json.dumps(datred_utils.tabs_as_dict(tab_list), **dump_keyargs)
if rc.msg:
msg = "\n\n Pointless 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, "UNMERGED",
"Failed to process/import, ignored")
else:
mf = mtz.mtz_file(p_mtzin)
dset_list = datred_utils.point_symm_datasets(
pointless_xml(), f_fmt)
body.summary_row_0 = -1 # to signal the beginning of summary row
for dataset in dset_list:
# make HKL dataset annotation
unmerged = dtype_unmerged.DType(body.job_id)
dataset["symm_summary"] = table_list
unmerged.importUnmergedData(mf, dataset)
body.dataSerialNo += 1
unmerged.makeDName(body.dataSerialNo)
outFileName = unmerged.dataId + ".mtz"
body.file_stdin = open(pointless_script(), 'w')
body.file_stdin.write (
"NAME PROJECT x CRYSTAL y DATASET z\n" + \
"HKLIN " + p_mtzin + "\n" + \
"HKLOUT " + os.path.join(body.outputDir(),outFileName) + "\n" + \
"COPY\n" + \
"ORIGINALLATTICE\n"
)
for offset, first, last in unmerged.dataset.runs:
body.file_stdin.write("RUN 1 FILE 1 BATCH " +
str(first) + " to " +
str(last) + "\n")
body.file_stdin.write("END\n")
body.file_stdin.close()
rc = command.call("pointless", [], "./",
pointless_script(), body.file_stdout,
body.file_stderr, None)
if rc.msg:
msg = "\n\n Pointless failed with message:\n\n" + \
rc.msg + \
"\n\n File " + outFileName + \
" cannot be processed.\n\n"
body.file_stdout.write(msg)
body.file_stderr.write(msg)
body.putSummaryLine_red(
outFileName, "UNMERGED",
"Failed to process/import, ignored")
else:
unmerged.files[0] = outFileName
subSecId = fileSecId
if len(dset_list) > 1:
subSecId = fileSecId + str(k)
pyrvapi.rvapi_add_section(
subSecId,
"Import " + unmerged.dataset.name,
fileSecId, frow, 0, 1, 1, False)
frow += 1
mtzTableId = "unmerged_mtz_" + str(k) + "_table"
unmerged.makeUniqueFNames(body.outputDir())
body.outputDataBox.add_data(unmerged)
makeUnmergedTable(body, mtzTableId, subSecId,
unmerged, 0)
pyrvapi.rvapi_set_text (
" <br><hr/><h3>Created Reflection Data Set (unmerged)</h3>" + \
"<b>Assigned name:</b> " + unmerged.dname + \
"<br> ",subSecId,frow,0,1,1 )
pyrvapi.rvapi_add_data(
"hkl_data_" + str(body.dataSerialNo),
"Unmerged reflections",
# always relative to job_dir from job_dir/html
os.path.join("..", body.outputDir(),
unmerged.files[0]),
"hkl:hkl",
subSecId,
frow + 1,
0,
1,
1,
-1)
frow += 2
if body.summary_row_0 < 0:
body.putSummaryLine(f_orig, "UNMERGED",
unmerged.dname)
else:
body.addSummaryLine("UNMERGED", unmerged.dname)
k += 1
pyrvapi.rvapi_flush()
# move imported file into output directory
os.rename(
p_mtzin,
os.path.join(body.outputDir(), os.path.basename(p_mtzin)))
body.file_stdout.write("... processed: " + f_orig + "\n ")
trace = ''
except:
trace = ''.join(traceback.format_exception(*sys.exc_info()))
body.file_stdout.write(trace)
if trace:
body.fail(trace, 'import failed')
body.rvrow += 1
pyrvapi.rvapi_flush()
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 putSRFDiagram(
body, # reference on Basic class
hkl, # hkl data object
dirPath, # directory with hkl object files (outputDir)
reportDir, # directory with html report (reportDir)
holderId, # rvapi holder of SRF widget
row,
col, # rvapi coordinates for SRF widget
rowSpan,
colSpan, # coordinate spans for STF widget
file_stdout, # standard output stream
file_stderr, # standard error stream
log_parser=None # log file parser
):
fpath = hkl.getFilePath(dirPath, 0)
Fmean = hkl.getMeta("Fmean.value", "")
sigF = hkl.getMeta("Fmean.sigma", "")
if Fmean == "" or sigF == "":
file_stderr.write ( "Fmean and sigFmean columns not found in " +\
hkl.files[0] + " -- SRF not calculated\n" )
return [-1, "Fmean and sigFmean columns not found"]
scr_file = open("molrep_srf.script", "w")
scr_file.write ( "file_f " + fpath +\
"\nlabin F=" + Fmean + " SIGF=" + sigF + "\n" )
scr_file.close()
"""
cols = hkl.getMeanColumns()
if cols[2]!="F":
file_stderr.write ( "Fmean and sigFmean columns not found in " +\
hkl.files[0] + " -- SRF not calculated\n" )
return [-1,"Fmean and sigFmean columns not found"]
scr_file = open ( "molrep_srf.script","w" )
scr_file.write ( "file_f " + fpath +\
"\nlabin F=" + cols[0] + " SIGF=" + cols[1] + "\n" )
scr_file.close ()
"""
# Start molrep
rc = command.call("molrep", ["-i"], "./", "molrep_srf.script", file_stdout,
file_stderr, log_parser)
if not os.path.isfile("molrep_rf.ps"):
file_stderr.write ( "\nSRF postscript was not generated for " +\
hkl.files[0] + "\n" )
return [-2, rc.msg]
rc = command.call("ps2pdf", ["molrep_rf.ps"], "./", None, file_stdout,
file_stderr, log_parser)
if not os.path.isfile("molrep_rf.pdf"):
file_stderr.write ( "\nSRF pdf was not generated for " +\
hkl.files[0] + "\n" )
return [-3, rc.msg]
pdfpath = os.path.splitext(hkl.files[0])[0] + ".pdf"
os.rename("molrep_rf.pdf", os.path.join(reportDir, pdfpath))
subsecId = body.getWidgetId(holderId) + "_srf"
pyrvapi.rvapi_add_section(subsecId, "Self-Rotation Function", holderId,
row, col, rowSpan, colSpan, False)
pyrvapi.rvapi_set_text ( "<object data=\"" + pdfpath +\
"\" type=\"application/pdf\" " +\
"style=\"border:none;width:100%;height:1000px;\"></object>",
subsecId,0,0,1,1 )
pyrvapi.rvapi_flush()
return [0, "Ok"]
def importData(self):
self.putWaitMessageLF("<b>1. Input Data Import</b>")
#self.rvrow -= 1
# -------------------------------------------------------------------
# import uploaded data
# make import tab and redirect output to it
pyrvapi.rvapi_add_tab(self.import_page_id(), "1. Input Data Import",
False)
self.setReportWidget(self.import_page_id())
fstdout = self.file_stdout
fstderr = self.file_stderr
self.file_stdout = open(self.import_stdout_path(), 'w')
self.file_stderr = open(self.import_stderr_path(), 'w')
# create tabs for import standard outputs
if self.navTreeId:
pyrvapi.rvapi_set_tab_proxy(self.navTreeId, self.import_page_id())
pyrvapi.rvapi_add_tab(self.import_log_page_id(), "Log file", False)
pyrvapi.rvapi_append_content(
os.path.join("..",
self.import_stdout_path() + '?capsize'), True,
self.import_log_page_id())
pyrvapi.rvapi_add_tab(self.import_err_page_id(), "Errors", False)
pyrvapi.rvapi_append_content(
os.path.join("..",
self.import_stderr_path() + '?capsize'), True,
self.import_err_page_id())
self.putTitle("CCP4go Automated Structure Solver: Data Import")
super(CCP4go, self).import_all()
# redirect everything back to report page and original standard streams
self.file_stdout.close()
self.file_stderr.close()
self.file_stdout = fstdout
self.file_stderr = fstderr
self.resetReportPage()
if self.navTreeId:
pyrvapi.rvapi_set_tab_proxy(self.navTreeId, "")
# -------------------------------------------------------------------
# fetch data for CCP4go pipeline
self.unm = None # unmerged dataset
self.hkl = None # selected merged dataset
self.seq = None # list of sequence objects
self.xyz = None # coordinates (model/apo)
self.hkl_alt = {} # alternative-space group merged datasets
if "DataUnmerged" in self.outputDataBox.data:
self.unm = self.outputDataBox.data["DataUnmerged"][0]
if "DataHKL" in self.outputDataBox.data:
maxres = 10000.0
for i in range(len(self.outputDataBox.data["DataHKL"])):
res = self.outputDataBox.data["DataHKL"][i].getHighResolution(
True)
if res < maxres:
maxres = res
self.hkl = self.outputDataBox.data["DataHKL"][i]
if "DataSequence" in self.outputDataBox.data:
self.seq = self.outputDataBox.data["DataSequence"]
if "DataXYZ" in self.outputDataBox.data:
self.xyz = self.outputDataBox.data["DataXYZ"][0]
# -------------------------------------------------------------------
# make data summary table
panelId = "summary_section"
pyrvapi.rvapi_set_text("", self.report_page_id(), self.rvrow, 0, 1, 1)
self.putSection(panelId, "<b>1. Input summary</b>")
tableId = "ccp4go_summary_table"
#self.putTable ( tableId,"<font style='font-style:normal;font-size:125%;'>" +
# "1. Input Data</font>",self.report_page_id(),
# self.rvrow,0 )
#self.rvrow += 1
self.putTable(tableId, "Input data", panelId, 0, 0)
self.setTableHorzHeaders(
tableId, ["Assigned Name", "View"],
["Name of the assocuated data object", "Data view and export"])
def addDataLine(name, tooltip, object, nrow):
if object:
self.putTableLine(tableId, name, tooltip, object.dname,
nrow[0])
self.putInspectButton(object, "View", tableId, nrow[0] + 1, 2)
nrow[0] += 1
return
nrow = [0]
addDataLine("Unmerged Reflections", "Reflection data", self.unm, nrow)
addDataLine("Merged Reflections", "Reflection data", self.hkl, nrow)
if self.seq:
if len(self.seq) < 2:
addDataLine("Sequence", "Sequence data", self.seq[0], nrow)
else:
for i in range(len(self.seq)):
addDataLine("Sequence #" + str(i + 1), "Sequence data",
self.seq[i], nrow)
addDataLine("Structure", "Homologue structure", self.xyz, nrow)
if self.task.ha_type:
self.putTableLine(tableId, "Anomalous scatterers",
"Chemical type of anomalous scatterers",
self.task.ha_type, nrow[0])
nrow[0] += 1
for i in range(len(self.task.ligands)):
ligand = self.task.ligands[i]
if ligand.source != "none":
dline = "[" + ligand.code + "] "
if ligand.source == "smiles":
m = 0
for j in range(len(ligand.smiles)):
if m > 40:
dline += "<br> "
m = 0
dline += ligand.smiles[j]
m += 1
self.putTableLine(tableId, "Ligand #" + str(i + 1),
"Ligand description", dline, nrow[0])
nrow[0] += 1
return
def makeOutputData(self, resdir, meta):
if not "row" in meta or not "nResults" in meta:
return
#if meta["nResults"]<1:
# return
row = meta["row"]
panel_id = "output_panel_" + str(row)
title = "Details"
if "title" in meta:
row -= 1
pyrvapi.rvapi_set_text("", self.report_page_id(), row, 0, 1, 1)
title = meta["title"]
if "merged" in meta: # output from the data reduction part
# import reflection data and place HKL widgets
pyrvapi.rvapi_add_section(
panel_id, "<b>" + str(meta["stage_no"]) +
". Data processing results (<i>Spg=" + meta["spg"] +
"</i>)</b>", self.report_page_id(), row, 0, 1, 1, False)
self.setReportWidget(panel_id)
self.import_dir = "./"
self.import_table_id = None
# clean upload directory
#shutil.rmtree(dirpath)
#os.mkdir(dirpath)
self.files_all = [meta["mtz"]]
import_merged.run(self, "Import merged HKL")
# get reference to imported structure
self.hkl = self.outputDataBox.data["DataHKL"][0]
elif "ligands" in meta:
# check in generated ligands
pyrvapi.rvapi_add_section(panel_id, title, self.report_page_id(),
row, 0, 1, 1, False)
self.setReportWidget(panel_id)
if meta["nResults"] > 0:
#self.putMessage ( "<h3>Generated ligand structure(s)</h3>" )
for code in meta["ligands"]:
self.putMessage(" ")
self.putMessageLF("<b>Code: " + code + "</b>")
self.finaliseLigand(code, meta["ligands"][code]["xyz"],
meta["ligands"][code]["cif"], False,
"")
else:
self.putMessage("<h3>No ligand structure(s) generated</h3>")
self.putMessage("<i>This is likely to be a program error, " +
"please report</i>")
else: # look for structure
pyrvapi.rvapi_add_section(panel_id, title, self.report_page_id(),
row, 0, 1, 1, False)
self.setReportWidget(panel_id)
if meta["nResults"] > 0:
hkl_sol = self.hkl
# check if space group changed
if "spg" in meta:
spgkey = meta["spg"].replace(" ", "")
if spgkey in self.hkl_alt:
hkl_sol = self.hkl_alt[spgkey]
elif "hkl" in meta:
self.putMessage("<h3>Space group changed to " +
meta["spg"] + "</h3>")
self.import_dir = "./"
self.import_table_id = None
hkl0 = self.outputDataBox.data["DataHKL"]
id0 = []
for i in range(len(hkl0)):
id0 += [hkl0[i].dataId]
self.files_all = [meta["hkl"]]
import_merged.run(
self,
"Import merged HKL reindexed in " + meta["spg"])
self.rvrow += 10
# get reference to imported structure
hkl0 = self.outputDataBox.data["DataHKL"]
hkl_sol = None
for i in range(len(hkl0)):
if not hkl0[i].dataId in id0:
hkl_sol = hkl0[i]
self.hkl_alt[spgkey] = hkl_sol
# register structure data
libPath = None
if "lib" in meta:
libPath = meta["lib"]
structure = self.registerStructure(meta["pdb"], meta["mtz"],
meta["map"], meta["dmap"],
libPath, True)
if structure:
structure.addDataAssociation(hkl_sol.dataId)
structure.setRefmacLabels(hkl_sol)
structure.addMRSubtype()
structure.addXYZSubtype()
if "libindex" in meta:
structure.addLigands(meta["libindex"])
self.putMessage(" ") # just vertical spacer
self.putStructureWidget(
"structure_btn_" + str(row),
meta["name"] + " structure and electron density",
structure)
if resdir.lower().startswith("simbad"):
self.import_dir = resdir
self.import_table_id = None
asudef.revisionFromStructure(
self,
hkl_sol,
structure,
"simbad_" + meta["pdbcode"],
useSequences=self.seq,
make_revision=(self.seq == None))
self.id_modifier += 1
if not self.seq: # sequence was imported in asudef
self.seq = self.outputDataBox.data["DataSequence"]
elif resdir == "dimple_mr":
self.import_dir = resdir
self.import_table_id = None
asudef.revisionFromStructure(
self,
hkl_sol,
structure,
"dimple",
useSequences=self.seq,
make_revision=(self.seq == None))
self.id_modifier += 1
if not self.seq: # sequence was imported in asudef
self.seq = self.outputDataBox.data["DataSequence"]
else:
self.putMessage("Structure Data cannot be formed " +
"(probably a bug)")
else:
self.putMessageLF("No solution found.")
self.putMessage(" ") # just vertical spacer
"""
{"results":
{ "simbad12_results":
{"mtz": "output/simbad12_results/simbad.mtz",
"map": "output/simbad12_results/simbad.map",
"name": "Simbad-LC",
"nResults": 1,
"rfree": 0.347,
"dmap": "output/simbad12_results/simbad_dmap.map",
"rfactor": 0.3792,
"pdb": "output/simbad12_results/simbad.pdb",
"columns": {"PHI": "PHIC_ALL_LS", "SIGF": "SIGF", "DELFWT": "DELFWT", "F": "F", "FREE": "FreeR_flag", "FOM": "FOM", "PHDELWT": "PHDELWT"}, "row": 5}, "buccaneer": {"mtz": "output/buccaneer/buccaneer.mtz", "map": "output/buccaneer/buccaneer.map", "name": "Buccanneer", "nResults": 1, "rfree": 0.3671, "dmap": "output/buccaneer/buccaneer_dmap.map", "rfactor": 0.3151, "pdb": "output/buccaneer/buccaneer.pdb", "columns": {"PHI": "PHIC_ALL_LS", "SIGF": "SIGF", "DELFWT": "DELFWT", "F": "F", "FREE": "FreeR_flag", "FOM": "FOM", "PHDELWT": "PHDELWT"},
"row": 8
}
},
"retcode": "solved",
"report_row": 9
}
"""
self.resetReportPage()
return