def getXYZMeta ( fpath,file_stdout,file_stderr,log_parser=None ):
# returns chain information as the following disctionary:
"""
{
'cryst' : {
'spaceGroup': 'P 21 21 21',
'a' : 64.897,
'b' : 78.323,
'c' : 38.792,
'alpha' : 90.00,
'beta' : 90.00,
'gamma' : 90.00
},
'xyz' : [
{ 'model':1,
'chains': [
{ 'id':'A', 'file':'rnase_model_1_A.pdb', 'type':'AA',
'seq':'DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLIDQTC',
'size':96, 'ligands':[] },
{ 'id':'B', 'file':'rnase_model_1_B.pdb', 'type':'AA',
'seq':'DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLIDQTC',
'size':96, 'ligands':['35S'] }
]
}
],
'ligands': ['35S']
}
"""
scr_file = open ( "pdbcur.script","w" )
scr_file.write ( "PDB_META\nEND\n" )
scr_file.close ()
# Start pdbcur
rc = command.call ( "pdbcur",['XYZIN',fpath],"./",
"pdbcur.script",file_stdout,file_stderr,log_parser )
# read pdbcur's json
jsonpath = os.path.splitext(fpath)[0] + ".json"
if not os.path.isfile(jsonpath):
return None
# read pdbcur's json
with open(jsonpath,'r') as json_file:
json_str = json_file.read()
json_file.close()
return XYZMeta ( json_str )
def run(body): # body is reference to the main Import class
files_xyz = []
for f in body.files_all:
fl = f.lower()
if fl.endswith(('.pdb', '.cif', '.mmcif', '.ent')):
files_xyz.append(f)
if len(files_xyz) <= 0:
return
body.file_stdout.write("\n" + "%" * 80 + "\n")
body.file_stdout.write("%%%%% IMPORT OF XYZ COORDINATES\n")
body.file_stdout.write("%" * 80 + "\n")
xyzSecId = "xyz_sec_" + str(body.widget_no)
body.widget_no += 1
pyrvapi.rvapi_add_section(xyzSecId, "XYZ Coordinates",
body.report_page_id(), body.rvrow, 0, 1, 1,
False)
k = 0
for f in files_xyz:
body.files_all.remove(f)
fpath = os.path.join(body.importDir(), f)
#coor.stripLigWat ( fpath,fpath ) # strip ligands and waters
# split input file to chains
scr_file = open("pdbcur.script", "w")
scr_file.write("SPLITTOCHAINS\nEND\n")
scr_file.close()
# Start pdbcur
rc = command.call("pdbcur", ['XYZIN', fpath], "./", "pdbcur.script",
body.file_stdout, body.file_stderr)
# read pdbcur's json
fnamesplit = os.path.splitext(f)
fpathsplit = os.path.join(body.importDir(), fnamesplit[0]) + ".json"
if not os.path.isfile(fpathsplit):
body.putSummaryLine_red(f, "UNKNOWN",
"Failed to recognise, ignored")
else:
with open(fpathsplit, 'r') as json_file:
json_str = json_file.read()
json_file.close()
#xyzmeta = eval(json_str)
xyzMeta = xyzmeta.XYZMeta(json_str)
if len(xyzMeta["xyz"]) <= 0:
body.putSummaryLine_red(f, "XYZ", "Empty file -- ignored")
else:
subSecId = xyzSecId
if len(files_xyz) > 1:
subSecId = xyzSecId + str(k)
pyrvapi.rvapi_add_section(subSecId, "Import " + f,
xyzSecId, k, 0, 1, 1, False)
xyz = dtype_xyz.DType(body.job_id)
xyz.setFile(f)
dtype_xyz.setXYZMeta(xyz, xyzMeta)
body.dataSerialNo += 1
xyz.makeDName(body.dataSerialNo)
os.rename(fpath, os.path.join(body.outputDir(), f))
xyz.makeUniqueFNames(body.outputDir())
body.outputDataBox.add_data(xyz)
xyzTableId = "xyz_" + str(k) + "_table"
body.putTable(xyzTableId, "", subSecId, 0)
jrow = 0
if len(files_xyz) <= 1:
body.putTableLine(xyzTableId, "File name",
"Imported file name", f, jrow)
jrow += 1
body.putTableLine(xyzTableId, "Assigned name",
"Assigned data name", xyz.dname, jrow)
crystData = getCrystData(xyzMeta)
body.putTableLine(xyzTableId, "Space group", "Space group",
crystData[0], jrow + 1)
body.putTableLine(
xyzTableId, "Cell parameters",
"Cell parameters (a,b,c, α,β,γ)",
crystData[1], jrow + 2)
contents = ""
nChains = 0
for model in xyzMeta["xyz"]:
for chain in model["chains"]:
if chain["type"] != "UNK":
nChains += 1
if len(contents) > 0:
contents += "<br>"
contents += "Model " + str(model['model']) + ", chain " + \
chain['id'] + ": " + str(chain['size']) + \
" residues, type: " + chain['type']
if len(xyzMeta["ligands"]) > 0:
if len(contents) > 0:
contents += "<br>"
contents += "Ligands:"
for name in xyzMeta["ligands"]:
contents += " " + name
body.putTableLine(xyzTableId, "Contents", "File contents",
contents, jrow + 3)
pyrvapi.rvapi_add_data(
xyzTableId + "_structure_btn",
xyz.dname + " ",
# always relative to job_dir from job_dir/html
os.path.join("..", body.outputDir(), xyz.files[0]),
"xyz",
subSecId,
1,
0,
1,
1,
-1)
body.putSummaryLine(f, "XYZ", xyz.dname)
"""
if nChains>1:
irow = 2
for model in xyzMeta["xyz"]:
for chain in model['chains']:
if chain["type"] != "UNK":
fname = fnamesplit[0] + "_" + str(model['model']) + "_" + \
chain['id'] + fnamesplit[1]
xyz = dtype_xyz.DType ( body.job_id )
xyz.setFile ( fname )
mdl = {}
mdl['model'] = model['model']
mdl['chains'] = [chain]
xyz_meta = {}
xyz_meta["cryst"] = xyzMeta["cryst"]
xyz_meta["xyz"] = [mdl]
xyz_meta["ligands"] = chain["ligands"]
dtype_xyz.setXYZMeta ( xyz,xyz_meta )
body.dataSerialNo += 1
xyz.makeDName ( body.dataSerialNo )
os.rename ( os.path.join(body.importDir(),fname),
os.path.join(body.outputDir(),fname) )
xyz.makeUniqueFNames ( body.outputDir() )
body.outputDataBox.add_data ( xyz )
xyzTableId = "xyz_" + str(k) + "_" + str(model['model']) + \
"_" + chain['id'] + "_table"
body.putMessage1 ( subSecId ," ",irow )
body.putTable ( xyzTableId,"",subSecId,irow+1 )
body.putTableLine ( xyzTableId,"Assigned name",
"Assigned data name",xyz.dname,0 )
crystData = getCrystData ( xyz_meta )
body.putTableLine ( xyzTableId,"Space group",
"Space group",crystData[0],1 )
body.putTableLine ( xyzTableId,"Cell parameters",
"Cell parameters (a,b,c, α,β,γ)",
crystData[1],2 )
contents = "Model " + str(model['model']) + ", chain " + \
chain['id'] + ": " + str(chain['size'])
contents += " residues, type: " + chain['type']
if len(xyz.xyzmeta["ligands"])>0:
contents += "<br>Ligands:"
for name in xyz.xyzmeta["ligands"]:
contents += " " + name
body.putTableLine ( xyzTableId,"Contents",
"File contents",contents,3 )
pyrvapi.rvapi_add_data ( xyzTableId+"_structure_btn",xyz.dname,
# always relative to job_dir from job_dir/html
os.path.join("..",body.outputDir(),xyz.files[0]),
"xyz",subSecId,irow+2,0,1,1,-1 )
#fdebug = open ( "_debug.txt",'a' )
#fdebug.write ( fname + "\n")
#fdebug.close()
body.addSummaryLine ( "XYZ",xyz.dname )
irow += 3
"""
body.file_stdout.write("... processed: " + f + "\n")
k += 1
body.rvrow += 1
pyrvapi.rvapi_flush()
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 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 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"]
file_stdout.write(
" wrong command specification 'pycofe.tasks.rvapiapp' (" +
task.rvapi_command + ")")
signal.TaskReadFailure().quitApp()
# ============================================================================
# Run job
file_stdout.write("[" + job_id.zfill(4) + "] RVAPI Application " +
app.upper() + "\n\n")
file_stderr.write(" ")
rc = command.call(app,
args,
"./",
None,
file_stdout,
file_stderr,
log_parser=None)
# ============================================================================
# close execution logs and quit
file_stdout.close()
file_stderr.close()
if rc.msg == "":
signal.Success().quitApp()
elif messagebox:
messagebox.displayMessage(
"Failed to launch", "<b>Failed to launch " + task.rvapi_command +