def __init__(self, parent, title, opened=False):
self._identifier = self.unique_id("tree")
super(Tree, self).__init__(parent)
self._title = title
self._opened = opened
pyrvapi.rvapi_add_tree_widget(
self._identifier, self._title, self._parent.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)
# 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 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 __init__(self, args=None):
# args = optional replacement for sys.argv to allow this class to be
# called from within other Python programs (such as tests)
rvapi_v = "...................."
pyrvapi.rvapi_version(rvapi_v)
rvapi_v = rvapi_v.split(".")
self.rvapi_version[0] = int(rvapi_v[0])
self.rvapi_version[1] = int(rvapi_v[1])
self.rvapi_version[2] = int(rvapi_v[2].replace("\x00", ""))
self.workdir = os.getcwd()
self.output_meta["retcode"] = ""
self.output_meta["report_row"] = 0
self.output_meta["results"] = {}
self.output_meta["resorder"] = []
self.file_stdout = sys.stdout
self.file_stderr = sys.stderr
# first parse command-line parameters
if args is None:
args = sys.argv[1:]
narg = 0
while narg < len(args):
key = args[narg]
narg += 1
if key == "--sge" or key == "--mp": self.exeType = key
elif key == "--no-simbad12": self.trySimbad12 = False
elif key == "--no-morda": self.tryMoRDa = False
elif key == "--no-crank2": self.tryCrank2 = False
elif key == "--no-fitligands": self.tryFitLigands = False
elif narg < len(args):
value = args[narg]
if key == "--wkdir": self.workdir = value
elif key == "--rdir": self.reportdir = value
elif key == "--outdir": self.outputdir = value
elif key == "--rvapi-prefix": self.rvapi_prefix = value
elif key == "--rvapi-document": self.rvapi_doc_path = value
elif key == "--jobid": self.jobId = value
elif key == "--qname": self.queueName = value
elif key == "--njobs": self.nSubJobs = int(value)
else:
self.output_meta[
"retcode"] = "[01-001] unknown command line parameter"
self.stderr(" *** unrecognised command line parameter " +
key)
narg += 1
# read data from standard input
self.stdout("\n INPUT DATA:" +
"\n -----------------------------------------------")
ilist = sys.stdin.read().splitlines()
for i in range(len(ilist)):
s = ilist[i].strip()
if s.startswith("HKLIN"):
self.hklpath = s.replace("HKLIN", "", 1).strip()
self.stdout("\n HKLIN " + self.hklpath)
elif s.startswith("SEQIN"):
self.seqpath = s.replace("SEQIN", "", 1).strip()
self.stdout("\n SEQIN " + self.seqpath)
elif s.startswith("XYZIN"):
self.xyzpath = s.replace("XYZIN", "", 1).strip()
self.stdout("\n XYZIN " + self.xyzpath)
elif s.startswith("HATOMS"):
self.ha_type = s.replace("HATOMS", "", 1).strip()
self.stdout("\n HATOMS " + self.ha_type)
elif s.startswith("LIGAND"):
lst = filter(None, s.replace("LIGAND", "", 1).split(" "))
self.ligands.append(lst)
self.stdout("\n LIGAND " + lst[0])
if len(lst) > 1:
self.stdout(" " + lst[1])
elif s:
self.output_meta[
"retcode"] = "[01-002] unrecognised input line"
self.stderr(" *** unrecognised input line " + s + "\n")
self.stdout("\n -----------------------------------------------\n")
# initialise work directory structure
self.scriptsdir = os.path.join(self.workdir, "scripts")
if not os.path.isdir(self.scriptsdir):
os.mkdir(self.scriptsdir)
outdir = os.path.join(self.workdir, self.outputdir)
if not os.path.isdir(outdir):
os.mkdir(outdir)
# initialise RVAPI report
self.layout = 4
if self.compare_rvapi_version([1, 0, 15]) <= 0:
self.layout = 0
self.page_cursor = [self.summaryTabId, 0]
if not self.rvapi_doc_path: # initialise rvapi report document
report_type = 1 # report with tabs
if not self.rvapi_prefix or not self.reportdir:
report_type = 0x00100000 # report will not be created
rdir = self.reportdir
if not rdir:
rdir = "report"
rdir = os.path.join(self.workdir,
rdir) # has to be full path because of Crank-2
if not os.path.isdir(rdir):
os.mkdir(rdir)
# initialise HTML report document; note that we use absolute path for
# the report directory, which is necessary for passing RVAPI document
# to applications via creation of the rvapi_document file with
# pyrvapi.rvapi_store_document2(..)
pyrvapi.rvapi_init_document(
"jscofe_report", # document Id
rdir, # report directory
"Title", # title (immaterial)
report_type, # HTML report to be produced
self.layout, # Report will start with plain page
self.rvapi_prefix, # where to look for js support
None,
None,
"task.tsk",
"i2.xml")
if self.layout == 0:
# Add tree widget
pyrvapi.rvapi_add_tree_widget(
self.navTreeId, # tree widget reference (Id)
"Workflow", # tree widget title
"body", # reference to widget holder (grid)
0, # holder row
0, # holder column
1, # row span
1 # column span
)
pyrvapi.rvapi_set_tab_proxy(self.navTreeId, "")
self.page_cursor = self.addTab(self.summaryTabId, "Summary", True)
self.putMessage(
"<h2>CCP4go (Combined Automated Structure Solution)</h2>")
else: # continue rvapi document given
pyrvapi.rvapi_restore_document2(self.rvapi_doc_path)
meta = pyrvapi.rvapi_get_meta()
#self.stdout ( "\n META = " + meta )
if meta:
d = json.loads(meta)
if "jobId" in d: self.jobId = d["jobId"]
if "stageNo" in d: self.stage_no = d["stageNo"]
if "sge_q" in d: self.SGE = True
if "sge_tc" in d: self.nSubJobs = d["sge_tc"]
if "summaryTabId" in d:
self.summaryTabId = d["summaryTabId"]
self.page_cursor[0] = self.summaryTabId
if "summaryTabRow" in d:
self.summaryTabRow = d["summaryTabRow"]
self.page_cursor[1] = self.summaryTabRow
if "navTreeId" in d:
self.navTreeId = d["navTreeId"]
pyrvapi.rvapi_set_tab_proxy(self.navTreeId, "")
if "outputDir" in d: self.outputdir = d["outputDir"]
if "outputName" in d: self.outputname = d["outputName"]
#self.stdout ( "\n summaryTabId = " + self.summaryTabId )
#self.stdout ( "\n summaryTabRow = " + str(self.summaryTabRow) )
#self.stdout ( "\n layout = " + str(self.layout) )
#self.stdout ( "\n navTreeId = " + self.navTreeId + "\n" )
#self.putMessage ( "<h2>YYYYYYYYYYYYYYY</h2>" )
#self.page_cursor = self.addTab ( "new","New",True )
#self.putMessage ( "<h2>ZZZZZZZZZZZZZZZZ</h2>" )
#self.file_stdout.write ( "nSubJobs=" + str(self.nSubJobs) + "\n" )
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:
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