def fill_table(self, table_id, tdata, tooltips={}):
# Make column headers
for i in range(len(tdata[0])): # Skip name as it's the row header
h = tdata[0][i]
tt = tooltips[h] if h in tooltips else ""
pyrvapi.rvapi_put_horz_theader(table_id, h.encode('utf-8'), tt,
i) # Add table data
for i in range(1, len(tdata)):
for j in range(len(tdata[i])):
pyrvapi.rvapi_put_table_string(table_id, str(tdata[i][j]),
i - 1, j)
# Now colour the ensemble name cells
for i in range(len(tdata) - 1):
pyrvapi.rvapi_shape_table_cell(
table_id, # tableId
i, # row
0, # column
"", # tooltip
"", # cell_css
# "table-blue-vh", # cell_style
"table-blue", # cell_style
1, # rowSpan
1) # colSpan
return
def _refresh_table(self):
identifier = self._identifier.split("/")[1]
if self._column_sort_index:
self._sort_table_content_by_index()
for i, row in enumerate(self._content):
for j, cell_content in enumerate(row):
pyrvapi.rvapi_put_table_string(identifier, str(cell_content), i, j)
def create_table(self, df, table_id):
"""Function to create/display tables
Parameters
----------
df : :obj:`~pandas.DataFrame`
Input :obj:`~pandas.DataFrame` containing data to be plotted
table_id : str
Table ID
Returns
-------
object
table containing the results from SIMBAD
"""
num_labels = 0
for i, l in enumerate(df):
if i == 0:
pyrvapi.rvapi_put_horz_theader(table_id, "PDB_code", self._simbad_tooltips["PDB_code"], 0)
else:
pyrvapi.rvapi_put_horz_theader(table_id, l, self._simbad_tooltips[l], i)
num_labels = i
ir = len(df)
for i in range(0, ir):
for j in range(num_labels + 1):
if j == 0:
pyrvapi.rvapi_put_table_string(table_id, '<a href="http://www.ebi.ac.uk/pdbe/entry/pdb/{0}" '
'target="_blank">{1}</a>'.format(df.loc[i][j][0:4], df.loc[i][j]), i,
j)
else:
pyrvapi.rvapi_put_table_string(table_id, str(df.loc[i][j]), i, j)
def create_table(self, df, table_id):
"""Function to create/display tables
Parameters
----------
df : :obj:`~pandas.DataFrame`
Input :obj:`~pandas.DataFrame` containing data to be plotted
table_id : str
Table ID
Returns
-------
object
table containing the results from SIMBAD
"""
num_labels = 0
for i, l in enumerate(df):
if i == 0:
pyrvapi.rvapi_put_horz_theader(table_id, "PDB_code", self._simbad_tooltips["PDB_code"], 0)
else:
pyrvapi.rvapi_put_horz_theader(table_id, l, self._simbad_tooltips[l], i)
num_labels = i
ir = len(df)
for i in range(0, ir):
for j in range(num_labels + 1):
if j == 0:
pyrvapi.rvapi_put_table_string(table_id, '<a href="http://www.ebi.ac.uk/pdbe/entry/pdb/{0}" '
'target="_blank">{1}</a>'.format(df.loc[i][j][0:4], df.loc[i][j]), i,
j)
else:
pyrvapi.rvapi_put_table_string(table_id, str(df.loc[i][j]), i, j)
def makeRow ( name,parameter,row ):
pyrvapi.rvapi_put_vert_theader ( tableId,name,parameter.tooltip,row )
pyrvapi.rvapi_put_table_string ( tableId,parameter.type,row,0 )
pyrvapi.rvapi_put_table_string ( tableId,type(parameter.value).__name__,row,1 )
pyrvapi.rvapi_put_table_string ( tableId,parameter.label,row,2 )
pyrvapi.rvapi_put_table_string ( tableId,str(parameter.visible),row,3 )
pyrvapi.rvapi_put_table_string ( tableId,str(parameter.value),row,4 )
return
def fill_table(self, table_id, tdata, tooltips={}):
# Make column headers
for i in range(len(tdata[0])): # Skip name as it's the row header
h = tdata[0][i]
tt = tooltips[h] if h in tooltips else ""
pyrvapi.rvapi_put_horz_theader(table_id, h.encode('utf-8'), tt, i) # Add table data
for i in range(1, len(tdata)):
for j in range(len(tdata[i])):
pyrvapi.rvapi_put_table_string(table_id, str(tdata[i][j]), i - 1, j)
# REM - can use pyrvapi.rvapi_shape_table_cell to format cells is required
return
def run(body): # body is reference to the main Import class
files_map = []
for f in body.files_all:
fl = f.lower();
if fl.endswith(('.map', '.mrc')):
files_map.append ( f )
if len(files_map) <= 0:
return
body.file_stdout.write ( "\n" + "%"*80 + "\n" )
body.file_stdout.write ( "%%%%% Map volume data\n" )
body.file_stdout.write ( "%"*80 + "\n" )
mapSecId = "map_sec_" + str(body.widget_no)
body.widget_no += 1
pyrvapi.rvapi_add_section ( mapSecId, "Map", body.report_page_id(),
body.rvrow, 0, 1, 1, False )
k = 0
for f in files_map:
body.files_all.remove ( f )
pyrvapi.rvapi_put_table_string ( body.import_summary_id(), f, body.summary_row, 0 )
fpath = os.path.join ( body.importDir(), f );
with mrcfile.mmap(fpath) as mrc:
msg = "MAP {0} x {1} x {2}".format(mrc.header.nx, mrc.header.ny, mrc.header.nz)
pyrvapi.rvapi_put_table_string ( body.import_summary_id(), msg, body.summary_row, 1 )
map_ = dtype_map.DType ( body.job_id )
map_.subtype = ['final_map']
map_.setFile ( f )
body.dataSerialNo += 1
map_.makeDName ( body.dataSerialNo )
body.outputDataBox.add_data ( map_ )
# Essential to rename uploaded file to put it in output directory
# Might be better to use the standard register() method instead if possible?
# Currently the file ends up remaining in the upload directory on the front end,
# even though it's removed on the number cruncher...
os.rename ( fpath, os.path.join(body.outputDir(), f) )
body.file_stdout.write ( "... processed: " + f + "\n" )
k += 1
body.rvrow += 1
pyrvapi.rvapi_flush()
return
def makeTable(tableDict, tableId, holderId, row, col, rowSpan, colSpan):
#
# Table dictionary example:
#
# { title: "Table Title", # empty string by default
# state: 0, # -1,0,1, -100,100
# class: "table-blue", # "table-blue" by default
# css : "text-align:right;", # "text-align:rigt;" by default
# horzHeaders : [ # either empty list or full header structures for all columns
# { label: "Size" , tooltip: "" },
# { label: "Weight", tooltip: "" },
# .....
# ],
# rows : [
# { header: { label: "1st row", tooltip: "" }, # header may be missing
# data : [ "string1","string2", ... ]
# },
# ......
# ]
# }
#
pyrvapi.rvapi_add_table(tableId, __get_item("title", tableDict, ""),
holderId, row, col, rowSpan, colSpan,
__get_item("state", tableDict, 0))
if ("class" in tableDict) or ("css" in tableDict):
pyrvapi.rvapi_set_table_style(
tableId, __get_item("class", tableDict, "table-blue"),
__get_item("css", tableDict, "text-align:right;"))
if "horzHeaders" in tableDict:
for i in range(len(tableDict["horzHeaders"])):
header = tableDict["horzHeaders"][i]
pyrvapi.rvapi_put_horz_theader(tableId, header["label"],
header["tooltip"], i)
if "rows" in tableDict:
for i in range(len(tableDict["rows"])):
trow = tableDict["rows"][i]
if "header" in trow:
pyrvapi.rvapi_put_vert_theader(tableId,
trow["header"]["label"],
trow["header"]["tooltip"], i)
data = trow["data"]
for j in range(len(data)):
pyrvapi.rvapi_put_table_string(tableId, data[j], i, j)
return
def run(self):
# Prepare seqalign input
# fetch input data
seq = self.input_data.data.seq
seqfile = open ( self.file_seq_path(),'wb' )
nseq = 0 # number of sequences
smap = {} # map of sequence names
seqtype = "" # for checking sequence types
for s in seq:
s1 = self.makeClass ( s )
if s1._type=='DataSequence':
nseq += 1
seqname = "s" + str(nseq).zfill(3)
smap[seqname] = {}
smap[seqname]["name" ] = s1.dname
smap[seqname]["align"] = ""
seqfile.write ( "\n>" + seqname +
"\n" + s1.getSequence(self.inputDir()) + "\n" )
stype = s1.getType()
if not seqtype:
seqtype = stype
elif seqtype!=stype:
seqtype = "x"
else:
chains = s1.xyzmeta.xyz[0].chains
for c in chains:
if s1.chainSel=="(all)" or s1.chainSel==c.id:
nseq += 1
seqname = "s" + str(nseq).zfill(3)
smap[seqname] = {}
smap[seqname]["name"] = s1.dname + ":" + c.id
smap[seqname]["align"] = ""
seqfile.write ( "\n>" + seqname +
"\n" + c.seq + "\n" )
stype = c.type.lower()
if not seqtype:
seqtype = stype
elif seqtype!=stype:
seqtype = "x"
seqfile.close()
if nseq<2:
self.putTitle ( "Input Error" )
self.putMessage ( "Number of sequences is less than 2" )
elif seqtype=="" or seqtype=="x":
self.putTitle ( "Input Error" )
self.putMessage ( "Inconsistent sequence types (mixed protein, dna and rna)" )
else:
if seqtype!="protein":
seqtype = "dna"
cmd = [self.file_seq_path(),"-type="+seqtype,"-stats="+self.file_stat_path()]
# Start clustalw2
self.runApp ( os.path.join(os.environ["CCP4"],"libexec","clustalw2"),cmd )
# check solution file and display results
if os.path.isfile(self.file_aln_path()) and os.path.isfile(self.file_stat_path()):
len_max = "0"
len_min = "0"
len_avg = "0"
len_dev = "0"
len_med = "0"
id_max = "0"
id_min = "0"
id_avg = "0"
id_dev = "0"
id_med = "0"
lines = [line.rstrip('\n') for line in open(self.file_stat_path(),'r')]
for l in lines:
w = l.split(" ")
if w[0]=="seqlen":
if w[1]=="longest:" : len_max = w[2]
if w[1]=="shortest:": len_min = w[2]
if w[1]=="avg:" : len_avg = w[2]
if w[1]=="std-dev:" : len_dev = w[2]
if w[1]=="median:" : len_med = w[2]
if w[0]=="aln":
if w[1]=="pw-id":
if w[2]=="highest:": id_max = w[3]
if w[2]=="lowest:" : id_min = w[3]
if w[2]=="avg:" : id_avg = w[3]
if w[2]=="std-dev:": id_dev = w[3]
if w[2]=="median:" : id_med = w[3]
lines = [line.rstrip('\n') for line in open(self.file_aln_path(),'r')]
smap["align"] = ""
i = 0
while i < len(lines):
if lines[i].startswith("s"):
for j in range(nseq):
smap[lines[i][:4]]["align"] += lines[i][16:]
i += 1
smap["align"] += lines[i][16:]
i += 1
len_cmb = len(smap["align"])
id_cmb = 0
for c in smap["align"]:
if c=="*":
id_cmb += 1
if float(len_avg)>0:
id_cmb = id_cmb/float(len_avg)
id_cmb = "%.2f" % id_cmb
tableId = "stat_table"
self.putTable ( tableId,"<span style='font-size:1.25em'>" +
"Alignment statistics</span>",
self.report_page_id(),self.rvrow,0 )
self.setTableHorzHeaders ( tableId,["Length","Score"],
["Sequence length","Sequence ID"] )
self.putTableLine2 ( tableId,"Highest",len_max,id_max,0 )
self.putTableLine2 ( tableId,"Lowest" ,len_min,id_min,1 )
self.putTableLine2 ( tableId,"Average",len_avg,id_avg,2 )
self.putTableLine2 ( tableId,"Std-Dev",len_dev,id_dev,3 )
self.putTableLine2 ( tableId,"Median" ,len_med,id_med,4 )
self.putTableLine2 ( tableId,"Combined",str(len_cmb),
"<b>"+id_cmb+"%</b>",5 )
self.rvrow += 2
self.putMessage ( " " )
tableId = "align_table"
self.putTable ( tableId,"<span style='font-size:1.25em'>" +
"Aligned sequences</span>",
self.report_page_id(),self.rvrow,100 )
self.setTableHorzHeaders ( tableId,["Sequence","Alignment"],
["Sequence","Alignment"] )
for r in range(nseq):
sname = "s" + str(r+1).zfill(3)
self.putTableLine ( tableId,str(r+1),"",smap[sname]["name"],r )
pyrvapi.rvapi_put_table_string ( tableId,
self.seqHTML(smap[sname]["align"],smap["align"]),r,1 )
pyrvapi.rvapi_shape_table_cell ( tableId,r,1,"",
"background:black;color:yellow","",1,1 );
else:
self.putTitle ( "Alignment was not generated" )
# close execution logs and quit
self.success()
return
def putTableLine2 ( self,tableId,header,v1,v2,row ):
self.putTableLine ( tableId,header,"",v1,row )
pyrvapi.rvapi_put_table_string ( tableId,v2,row,1 )
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 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