from Vision.StandardNodes import ReadTable
ReadTable_157 = ReadTable(constrkw={}, name='ReadTable', library=stdlib)
masterNet.addNode(ReadTable_157, 253, 35)
ReadTable_157.inputPortByName['filename'].widget.set(
"Data/table_data_string.dat", run=False)
ReadTable_157.inputPortByName['sep'].widget.set(",", run=False)
apply(ReadTable_157.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore ReadTable named ReadTable in network masterNet"
print_exc()
ReadTable_157 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_158 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_158, 146, 200)
apply(Index_158.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_158 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_159 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_159, 295, 202)
apply(Index_159.inputPortByName['index'].widget.configure, (), {'max': 1})
Index_159.inputPortByName['index'].widget.set(1, run=False)
apply(Index_159.configure, (), {'expanded': True})
## saving node Set Matplotlib options ##
from Vision.matplotlibNodes import MatPlotLibOptions
Set_Matplotlib_options_50 = MatPlotLibOptions(
constrkw={}, name='Set Matplotlib options', library=matplotliblib)
masterNet.addNode(Set_Matplotlib_options_50, 360, 233)
Set_Matplotlib_options_50.inputPortByName['matplotlibOptions'].widget.set(
{'gridOn': 1}, run=False)
except:
print "WARNING: failed to restore MatPlotLibOptions named Set Matplotlib options in network masterNet"
print_exc()
Set_Matplotlib_options_50 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_51 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_51, 29, 202)
apply(Index_51.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_51 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_52 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_52, 209, 201)
apply(Index_52.inputPortByName['index'].widget.configure, (), {'max': 1})
Index_52.inputPortByName['index'].widget.set(1, run=False)
apply(Index_52.configure, (), {'expanded': True})
ReadTable_31 = ReadTable(constrkw={}, name='ReadTable', library=stdlib)
masterNet.addNode(ReadTable_31, 22, 5)
ReadTable_31.inputPortByName['filename'].widget.set(
"Data/histogram_data.dat", run=False)
ReadTable_31.inputPortByName['sep'].widget.set(",", run=False)
ReadTable_31.inputPortByName['datatype'].widget.set("float", run=False)
apply(ReadTable_31.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore ReadTable named ReadTable in network masterNet"
print_exc()
ReadTable_31 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_32 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_32, 255, 234)
apply(Index_32.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_32 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_33 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_33, 439, 233)
apply(Index_33.inputPortByName['index'].widget.configure, (), {'max': 1})
Index_33.inputPortByName['index'].widget.set(1, run=False)
apply(Index_33.configure, (), {'expanded': True})
ReadTable_10 = ReadTable(constrkw={}, name='ReadTable', library=stdlib)
masterNet.addNode(ReadTable_10, 73, 7)
ReadTable_10.inputPortByName['filename'].widget.set(
"Data/histogram_data_1.dat", run=False)
ReadTable_10.inputPortByName['sep'].widget.set(",", run=False)
ReadTable_10.inputPortByName['datatype'].widget.set("float", run=False)
apply(ReadTable_10.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore ReadTable named ReadTable in network masterNet"
print_exc()
ReadTable_10 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_11 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_11, 12, 208)
apply(Index_11.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_11 = None
try:
## saving node Plot ##
from Vision.matplotlibNodes import PlotNE
Plot_12 = PlotNE(constrkw={}, name='Plot', library=matplotliblib)
masterNet.addNode(Plot_12, 287, 332)
Plot_12.inputPortByName['lineStyle'].widget.set("dashed", run=False)
Plot_12.inputPortByName['color'].widget.set("red", run=False)
apply(Plot_12.configure, (), {'expanded': True})
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
LocalLigandDirectory_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
)
print_exc()
input_Ports_1 = None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_2.move(294, 448)
except:
print(
"WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
)
print_exc()
output_Ports_2 = None
try:
## saving node Make Zip File ##
from Vision.StandardNodes import MakeZipFileNE
Make_Zip_File_3 = MakeZipFileNE(constrkw={},
name='Make Zip File',
library=stdlib)
self.macroNetwork.addNode(Make_Zip_File_3, 136, 158)
Make_Zip_File_3.inputPortByName['input_directory'].configure(
*(), **{'defaultValue': None})
Make_Zip_File_3.inputPortByName['output_directory'].configure(
*(), **{'defaultValue': None})
Make_Zip_File_3.inputPortByName['output_name'].configure(
*(), **{'defaultValue': None})
Make_Zip_File_3.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MakeZipFileNE named Make Zip File in network self.macroNetwork"
)
print_exc()
Make_Zip_File_3 = None
try:
## saving node Entry ##
from Vision.StandardNodes import EntryNE
Entry_4 = EntryNE(constrkw={}, name='Entry', library=stdlib)
self.macroNetwork.addNode(Entry_4, 312, 18)
Entry_4.inputPortByName['entry'].configure(
*(), **{'defaultValue': None})
Entry_4.inputPortByName['entry'].widget.set(r"my_ligands.zip",
run=False)
Entry_4.configure(*(), **{'paramPanelImmediate': 1})
except:
print(
"WARNING: failed to restore EntryNE named Entry in network self.macroNetwork"
)
print_exc()
Entry_4 = None
try:
## saving node LigandDBUpload_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
LigandDBUpload_kryptonite_nbcr_net_5 = FunctionNode(
functionOrString='LigandDBUpload_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'username': '',
'userlib': '',
'password': '',
'localRun': False,
'execPath': '',
'desc': ''
},
constrkw={
'functionOrString': "'LigandDBUpload_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'username': '',
'userlib': '',
'password': '',
'localRun': False,
'execPath': '',
'desc': ''
}
},
name='LigandDBUpload_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(LigandDBUpload_kryptonite_nbcr_net_5,
136, 216)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'username'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'password'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'localRun'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'execPath'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'desc'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'username'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].rebindWidget()
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].unbindWidget()
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'password'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'localRun'].widget.set(0, run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'execPath'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'desc'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore FunctionNode named LigandDBUpload_kryptonite_nbcr_net in network self.macroNetwork"
)
print_exc()
LigandDBUpload_kryptonite_nbcr_net_5 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_6 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_6, 136, 273)
Index_6.inputPortByName['data'].configure(*(),
**{'defaultValue': None})
Index_6.inputPortByName['index'].configure(
*(), **{'defaultValue': None})
Index_6.outputPortByName['data'].configure(
*(), **{'datatype': 'string'})
Index_6.inputPortByName['index'].widget.configure(
*(), **{
'max': 7,
'min': -8
})
Index_6.inputPortByName['index'].widget.set(0, run=False)
Index_6.configure(*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Index named Index in network self.macroNetwork"
)
print_exc()
Index_6 = None
try:
## saving node ReplaceURL ##
from WebServices.VisionInterface.WSNodes import ReplaceURLNode
ReplaceURL_7 = ReplaceURLNode(constrkw={},
name='ReplaceURL',
library=wslib)
self.macroNetwork.addNode(ReplaceURL_7, 328, 327)
ReplaceURL_7.inputPortByName['url'].configure(
*(), **{'defaultValue': None})
ReplaceURL_7.inputPortByName['newfilename'].configure(
*(), **{'defaultValue': None})
ReplaceURL_7.inputPortByName['url'].rebindWidget()
ReplaceURL_7.inputPortByName['url'].widget.set(r"", run=False)
ReplaceURL_7.inputPortByName['url'].unbindWidget()
ReplaceURL_7.configure(*(), **{'paramPanelImmediate': 1})
except:
print(
"WARNING: failed to restore ReplaceURLNode named ReplaceURL in network self.macroNetwork"
)
print_exc()
ReplaceURL_7 = None
try:
## saving node CreateLigandDBObj ##
from Vision.StandardNodes import Generic
CreateLigandDBObj_8 = Generic(constrkw={},
name='CreateLigandDBObj',
library=stdlib)
self.macroNetwork.addNode(CreateLigandDBObj_8, 217, 385)
CreateLigandDBObj_8.addInputPort(
*(), **{
'singleConnection': True,
'name': 'ligand_lib_url',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
CreateLigandDBObj_8.addInputPort(
*(), **{
'singleConnection': True,
'name': 'log_file',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': False,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
CreateLigandDBObj_8.addOutputPort(
*(), **{
'name': 'ligand_db_obj',
'datatype': 'LigandDB',
'height': 8,
'width': 12,
'shape': 'rect',
'color': '#FFCCFF'
})
code = """def doit(self, ligand_lib_url, log_file):
if log_file == None:
log_file = "ligand_lib_uploads.log"
log_file = os.path.abspath(log_file)
if log_file != None:
from time import strftime
now = strftime("%Y-%m-%d %H:%M:%S")
log_str = '''On ''' + now + ''', you uploaded a ligand library to: \n'''
log_str = log_str + ligand_lib_url + '''\n\n'''
f = open(log_file, '''a''')
f.write(log_str)
print "This ligand library upload has been recorded in " + log_file
from AutoDockTools.VisionInterface.Adt.LigandDB import LigandDB
ligand_db_obj = LigandDB(url_lib=ligand_lib_url)
pass
## to ouput data on port ligand_db_obj use
self.outputData(ligand_db_obj=ligand_db_obj)
"""
CreateLigandDBObj_8.configure(function=code)
CreateLigandDBObj_8.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Generic named CreateLigandDBObj in network self.macroNetwork"
)
print_exc()
CreateLigandDBObj_8 = None
try:
## saving node get_paths ##
from Vision.StandardNodes import Generic
get_paths_9 = Generic(constrkw={},
name='get_paths',
library=stdlib)
self.macroNetwork.addNode(get_paths_9, 136, 105)
get_paths_9.addInputPort(
*(), **{
'singleConnection': True,
'name': 'directory',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
get_paths_9.addInputPort(
*(), **{
'singleConnection': True,
'name': 'zip_name',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'input_directory',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'output_directory',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'output_name',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'output_basedir',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, directory, zip_name):
input_directory = os.path.abspath(directory)
if not(os.path.exists(input_directory)):
print "ERROR: ligand input directory " + input_directory + " does not exist"
return '''stop'''
output_directory = os.path.abspath('''.''')
output_name = zip_name
output_basedir = zip_name.rstrip('''.zip''')
pass
self.outputData(input_directory=input_directory, output_directory=output_directory, output_name=zip_name, output_basedir=output_basedir)
## to ouput data on port input_directory use
## self.outputData(input_directory=data)
## to ouput data on port output_directory use
## self.outputData(output_directory=data)
## to ouput data on port output_name use
## self.outputData(output_name=data)
## to ouput data on port output_basedir use
## self.outputData(output_basedir=data)
"""
get_paths_9.configure(function=code)
get_paths_9.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Generic named get_paths in network self.macroNetwork"
)
print_exc()
get_paths_9 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network LocalLigandDirectory ##
if Make_Zip_File_3 is not None and LigandDBUpload_kryptonite_nbcr_net_5 is not None:
try:
self.macroNetwork.connectNodes(
Make_Zip_File_3,
LigandDBUpload_kryptonite_nbcr_net_5,
"zipfile",
"userlib",
blocking=True,
splitratio=[0.67700056401206909, 0.41786522052018427])
except:
print(
"WARNING: failed to restore connection between Make_Zip_File_3 and LigandDBUpload_kryptonite_nbcr_net_5 in network self.macroNetwork"
)
if LigandDBUpload_kryptonite_nbcr_net_5 is not None and Index_6 is not None:
try:
self.macroNetwork.connectNodes(
LigandDBUpload_kryptonite_nbcr_net_5,
Index_6,
"result",
"data",
blocking=True,
splitratio=[0.27868065815947218, 0.69101010116597561])
except:
print(
"WARNING: failed to restore connection between LigandDBUpload_kryptonite_nbcr_net_5 and Index_6 in network self.macroNetwork"
)
if Index_6 is not None and ReplaceURL_7 is not None:
try:
self.macroNetwork.connectNodes(
Index_6,
ReplaceURL_7,
"data",
"url",
blocking=True,
splitratio=[0.0, 0.50910496731074983])
except:
print(
"WARNING: failed to restore connection between Index_6 and ReplaceURL_7 in network self.macroNetwork"
)
if ReplaceURL_7 is not None and CreateLigandDBObj_8 is not None:
try:
self.macroNetwork.connectNodes(
ReplaceURL_7,
CreateLigandDBObj_8,
"newurl",
"ligand_lib_url",
blocking=True,
splitratio=[0.7375258387145982, 0.34433018843468416])
except:
print(
"WARNING: failed to restore connection between ReplaceURL_7 and CreateLigandDBObj_8 in network self.macroNetwork"
)
output_Ports_2 = self.macroNetwork.opNode
if CreateLigandDBObj_8 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
CreateLigandDBObj_8,
output_Ports_2,
"ligand_db_obj",
"new",
blocking=True,
splitratio=[0.25450332220506922, 0.49254602433654382])
except:
print(
"WARNING: failed to restore connection between CreateLigandDBObj_8 and output_Ports_2 in network self.macroNetwork"
)
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and get_paths_9 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
get_paths_9,
"new",
"directory",
blocking=True,
splitratio=[0.73592256661833422, 0.40050624233195609])
except:
print(
"WARNING: failed to restore connection between input_Ports_1 and get_paths_9 in network self.macroNetwork"
)
if Entry_4 is not None and get_paths_9 is not None:
try:
self.macroNetwork.connectNodes(
Entry_4,
get_paths_9,
"string",
"zip_name",
blocking=True,
splitratio=[0.74641701362897139, 0.56047721560743557])
except:
print(
"WARNING: failed to restore connection between Entry_4 and get_paths_9 in network self.macroNetwork"
)
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
Make_Zip_File_3,
"input_directory",
"input_directory",
blocking=True,
splitratio=[0.24975092021298884, 0.59053364249853169])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
)
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
Make_Zip_File_3,
"output_name",
"output_name",
blocking=True,
splitratio=[0.44934886807300634, 0.5145630699734256])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
)
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
Make_Zip_File_3,
"output_directory",
"output_directory",
blocking=True,
splitratio=[0.65054191214838031, 0.31030412383438832])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
)
if get_paths_9 is not None and ReplaceURL_7 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
ReplaceURL_7,
"output_basedir",
"newfilename",
blocking=True,
splitratio=[0.5380996717918376, 0.39023381726820411])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and ReplaceURL_7 in network self.macroNetwork"
)
if input_Ports_1 is not None and CreateLigandDBObj_8 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
CreateLigandDBObj_8,
"new",
"log_file",
blocking=True,
splitratio=[0.49268182912115838, 0.67412763774649975])
except:
print(
"WARNING: failed to restore connection between input_Ports_1 and CreateLigandDBObj_8 in network self.macroNetwork"
)
if ReplaceURL_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
ReplaceURL_7,
output_Ports_2,
"newurl",
"new",
blocking=True,
splitratio=[0.67446600768034171, 0.74989471765767979])
except:
print(
"WARNING: failed to restore connection between ReplaceURL_7 and output_Ports_2 in network self.macroNetwork"
)
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(
name='Make_Zip_File_input_directory')
input_Ports_1.outputPorts[2].configure(
name='CreateLigandDBObj_log_file')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[2].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(
name='CreateLigandDBObj_ligand_db_obj')
output_Ports_2.inputPorts[2].configure(name='ReplaceURL_newurl')
## configure MacroNode input ports
LocalLigandDirectory_0.inputPorts[0].configure(
name='Make_Zip_File_input_directory')
LocalLigandDirectory_0.inputPorts[0].configure(datatype='string')
LocalLigandDirectory_0.inputPorts[1].configure(
name='CreateLigandDBObj_log_file')
LocalLigandDirectory_0.inputPorts[1].configure(datatype='string')
## configure MacroNode output ports
LocalLigandDirectory_0.outputPorts[0].configure(
name='CreateLigandDBObj_ligand_db_obj')
LocalLigandDirectory_0.outputPorts[0].configure(datatype='LigandDB')
LocalLigandDirectory_0.outputPorts[1].configure(
name='ReplaceURL_newurl')
LocalLigandDirectory_0.outputPorts[1].configure(datatype='string')
LocalLigandDirectory_0.shrink()
## reset modifications ##
LocalLigandDirectory_0.resetTags()
LocalLigandDirectory_0.buildOriginalList()
try:
## saving node ErrorBar ##
from Vision.matplotlibNodes import ErrorBarNE
ErrorBar_39 = ErrorBarNE(constrkw = {}, name='ErrorBar', library=matplotliblib)
masterNet.addNode(ErrorBar_39,190,338)
ErrorBar_39.inputPortByName['format'].widget.set("o", run=False)
except:
print "WARNING: failed to restore ErrorBarNE named ErrorBar in network masterNet"
print_exc()
ErrorBar_39=None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_40 = Index(constrkw = {}, name='Index', library=stdlib)
masterNet.addNode(Index_40,4,199)
apply(Index_40.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_40=None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_41 = Index(constrkw = {}, name='Index', library=stdlib)
masterNet.addNode(Index_41,143,197)
apply(Index_41.inputPortByName['index'].widget.configure, (), {'max': 3})
Index_41.inputPortByName['index'].widget.set(1, run=False)
apply(Index_41.configure, (), {'expanded': True})
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
TrajQR_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
apply(input_Ports_1.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1 = None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
apply(output_Ports_2.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_2.move(183, 405)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2 = None
try:
## saving node Make_Zip_File ##
from Vision.StandardNodes import MakeZipFileNE
Make_Zip_File_3 = MakeZipFileNE(constrkw={},
name='Make_Zip_File',
library=stdlib)
self.macroNetwork.addNode(Make_Zip_File_3, 47, 75)
apply(Make_Zip_File_3.inputPortByName['input_directory'].configure,
(), {'defaultValue': None})
apply(
Make_Zip_File_3.inputPortByName['output_directory'].configure,
(), {'defaultValue': None})
apply(Make_Zip_File_3.inputPortByName['output_name'].configure, (),
{'defaultValue': None})
apply(Make_Zip_File_3.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MakeZipFileNE named Make_Zip_File in network self.macroNetwork"
print_exc()
Make_Zip_File_3 = None
try:
## saving node TrajQR_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
TrajQR_kryptonite_nbcr_net_4 = FunctionNode(
functionOrString='TrajQR_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'license': False,
'rmsd': '',
'qh_filename': 'qh.tre',
'qr_filename': 'qr.out',
'compressed_pdbs': '',
'localRun': False,
'execPath': ''
},
constrkw={
'functionOrString': "'TrajQR_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'license': False,
'rmsd': '',
'qh_filename': 'qh.tre',
'qr_filename': 'qr.out',
'compressed_pdbs': '',
'localRun': False,
'execPath': ''
}
},
name='TrajQR_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(TrajQR_kryptonite_nbcr_net_4, 279, 135)
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['license'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].configure,
(), {
'defaultValue': None,
'required': True
})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['qh_filename'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['qr_filename'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.
inputPortByName['compressed_pdbs'].configure, (), {
'defaultValue': None,
'required': True
})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['localRun'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['execPath'].
configure, (), {'defaultValue': None})
TrajQR_kryptonite_nbcr_net_4.inputPortByName['license'].widget.set(
0, run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].rebindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].widget.set(
r"", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].unbindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'qh_filename'].widget.set(r"qh.tre", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'qr_filename'].widget.set(r"qr.out", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'compressed_pdbs'].rebindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'compressed_pdbs'].widget.set(r"", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'compressed_pdbs'].unbindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'localRun'].widget.set(0, run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'execPath'].widget.set(r"", run=False)
apply(TrajQR_kryptonite_nbcr_net_4.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named TrajQR_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
TrajQR_kryptonite_nbcr_net_4 = None
try:
## saving node SelectOnExtension ##
from Vision.StandardNodes import SelectOnExtension
SelectOnExtension_5 = SelectOnExtension(constrkw={},
name='SelectOnExtension',
library=stdlib)
self.macroNetwork.addNode(SelectOnExtension_5, 279, 192)
apply(SelectOnExtension_5.inputPortByName['filenames'].configure,
(), {'defaultValue': None})
apply(SelectOnExtension_5.inputPortByName['extension'].configure,
(), {'defaultValue': None})
SelectOnExtension_5.inputPortByName['extension'].widget.set(
r".out", run=False)
apply(SelectOnExtension_5.configure, (),
{'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore SelectOnExtension named SelectOnExtension in network self.macroNetwork"
print_exc()
SelectOnExtension_5 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_6 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_6, 123, 281)
apply(
Index_6.inputPortByName['data'].configure, (), {
'datatype': 'list',
'defaultValue': None,
'originalDatatype': 'None'
})
apply(Index_6.inputPortByName['index'].configure, (),
{'defaultValue': None})
apply(Index_6.outputPortByName['data'].configure, (),
{'datatype': 'string'})
apply(Index_6.inputPortByName['index'].widget.configure, (), {
'max': 0,
'min': -1
})
Index_6.inputPortByName['index'].widget.set(0, run=False)
apply(Index_6.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Index named Index in network self.macroNetwork"
print_exc()
Index_6 = None
try:
## saving node GetSelectedPDBs ##
from Vision.StandardNodes import Generic
GetSelectedPDBs_7 = Generic(constrkw={},
name='GetSelectedPDBs',
library=stdlib)
self.macroNetwork.addNode(GetSelectedPDBs_7, 200, 346)
apply(
GetSelectedPDBs_7.addInputPort, (), {
'singleConnection': True,
'name': 'trajqr_url',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
apply(
GetSelectedPDBs_7.addInputPort, (), {
'singleConnection': True,
'name': 'pdb_in_dir',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
apply(
GetSelectedPDBs_7.addInputPort, (), {
'singleConnection': True,
'name': 'pdb_out_dir',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
apply(
GetSelectedPDBs_7.addOutputPort, (), {
'name': 'pdb_out_dir',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, trajqr_url, pdb_in_dir, pdb_out_dir):
pdb_in_dir = os.path.abspath(pdb_in_dir)
pdb_out_dir = os.path.abspath(pdb_out_dir)
import urllib
import shutil
pdb_list = []
f = urllib.urlopen(trajqr_url)
for i in f.readlines():
pdb_file = i.strip('''
''')+'''.pdb'''
infile = pdb_in_dir + os.sep + pdb_file
outfile = pdb_out_dir + os.sep + pdb_file
shutil.copyfile(infile, outfile)
f.close
pass
## to ouput data on port pdb_list use
self.outputData(pdb_out_dir=pdb_out_dir)
"""
GetSelectedPDBs_7.configure(function=code)
apply(GetSelectedPDBs_7.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Generic named GetSelectedPDBs in network self.macroNetwork"
print_exc()
GetSelectedPDBs_7 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network TrajQR ##
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
Make_Zip_File_3,
"new",
"input_directory",
blocking=True,
splitratio=[0.67469172328672133, 0.50941480178765064])
except:
print "WARNING: failed to restore connection between input_Ports_1 and Make_Zip_File_3 in network self.macroNetwork"
if input_Ports_1 is not None and TrajQR_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
TrajQR_kryptonite_nbcr_net_4,
"new",
"rmsd",
blocking=True,
splitratio=[0.45681934134493246, 0.33803410340720857])
except:
print "WARNING: failed to restore connection between input_Ports_1 and TrajQR_kryptonite_nbcr_net_4 in network self.macroNetwork"
if Make_Zip_File_3 is not None and TrajQR_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
Make_Zip_File_3,
TrajQR_kryptonite_nbcr_net_4,
"zipfile",
"compressed_pdbs",
blocking=True,
splitratio=[0.71081093868178202, 0.43908686250860129])
except:
print "WARNING: failed to restore connection between Make_Zip_File_3 and TrajQR_kryptonite_nbcr_net_4 in network self.macroNetwork"
if TrajQR_kryptonite_nbcr_net_4 is not None and SelectOnExtension_5 is not None:
try:
self.macroNetwork.connectNodes(
TrajQR_kryptonite_nbcr_net_4,
SelectOnExtension_5,
"result",
"filenames",
blocking=True,
splitratio=[0.63533198718963335, 0.2560040659014205])
except:
print "WARNING: failed to restore connection between TrajQR_kryptonite_nbcr_net_4 and SelectOnExtension_5 in network self.macroNetwork"
if SelectOnExtension_5 is not None and Index_6 is not None:
try:
self.macroNetwork.connectNodes(
SelectOnExtension_5,
Index_6,
"matching",
"data",
blocking=True,
splitratio=[0.65832290589891362, 0.21624347250969889])
except:
print "WARNING: failed to restore connection between SelectOnExtension_5 and Index_6 in network self.macroNetwork"
if Index_6 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
Index_6,
GetSelectedPDBs_7,
"data",
"trajqr_url",
blocking=True,
splitratio=[0.51754619993986595, 0.63949220525823236])
except:
print "WARNING: failed to restore connection between Index_6 and GetSelectedPDBs_7 in network self.macroNetwork"
if input_Ports_1 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
GetSelectedPDBs_7,
"Make_Zip_File_input_directory",
"pdb_in_dir",
blocking=True,
splitratio=[0.7121964126696847, 0.42697952864467786])
except:
print "WARNING: failed to restore connection between input_Ports_1 and GetSelectedPDBs_7 in network self.macroNetwork"
if input_Ports_1 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
GetSelectedPDBs_7,
"new",
"pdb_out_dir",
blocking=True,
splitratio=[0.62460995639428174, 0.60275185701976297])
except:
print "WARNING: failed to restore connection between input_Ports_1 and GetSelectedPDBs_7 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if GetSelectedPDBs_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
GetSelectedPDBs_7,
output_Ports_2,
"pdb_out_dir",
"new",
blocking=True,
splitratio=[0.7431176169343523, 0.73697976585137526])
except:
print "WARNING: failed to restore connection between GetSelectedPDBs_7 and output_Ports_2 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(
name='Make_Zip_File_input_directory')
input_Ports_1.outputPorts[2].configure(
name='TrajQR_kryptonite_nbcr_net_rmsd')
input_Ports_1.outputPorts[3].configure(
name='GetSelectedPDBs_pdb_out_dir')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(
name='GetSelectedPDBs_pdb_out_dir')
## configure MacroNode input ports
TrajQR_0.inputPorts[0].configure(name='Make_Zip_File_input_directory')
TrajQR_0.inputPorts[0].configure(datatype='string')
TrajQR_0.inputPorts[1].configure(
name='TrajQR_kryptonite_nbcr_net_rmsd')
TrajQR_0.inputPorts[1].configure(datatype='string')
TrajQR_0.inputPorts[2].configure(name='GetSelectedPDBs_pdb_out_dir')
TrajQR_0.inputPorts[2].configure(datatype='string')
## configure MacroNode output ports
TrajQR_0.outputPorts[0].configure(name='GetSelectedPDBs_pdb_out_dir')
TrajQR_0.outputPorts[0].configure(datatype='string')
TrajQR_0.shrink()
## reset modifications ##
TrajQR_0.resetTags()
TrajQR_0.buildOriginalList()
ReadTable_180 = None
try:
## saving node Vline ##
from Vision.matplotlibNodes import VlineNE
Vline_181 = VlineNE(constrkw={}, name='Vline', library=matplotliblib)
masterNet.addNode(Vline_181, 117, 358)
except:
print "WARNING: failed to restore VlineNE named Vline in network masterNet"
print_exc()
Vline_181 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_182 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_182, 12, 187)
apply(Index_182.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_182 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_183 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_183, 161, 188)
apply(Index_183.inputPortByName['index'].widget.configure, (), {'max': 2})
Index_183.inputPortByName['index'].widget.set(1, run=False)
apply(Index_183.configure, (), {'expanded': True})
def afterAddingToNetwork(self):
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
## loading libraries ##
from MolKit.VisionInterface.MolKitNodes import molkitlib
from Vision.StandardNodes import stdlib
## building macro network ##
recluster_11 = self
from traceback import print_exc
## loading libraries ##
from MolKit.VisionInterface.MolKitNodes import molkitlib
self.macroNetwork.getEditor().addLibraryInstance(
molkitlib, "MolKit.VisionInterface.MolKitNodes", "molkitlib")
from Vision.StandardNodes import stdlib
self.macroNetwork.getEditor().addLibraryInstance(
stdlib, "Vision.StandardNodes", "stdlib")
try:
## saving node input Ports ##
input_Ports_12 = self.macroNetwork.ipNode
input_Ports_12.move(172, 137)
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_12 = None
try:
## saving node output Ports ##
output_Ports_13 = self.macroNetwork.opNode
output_Ports_13.move(172, 479)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_13 = None
try:
## saving node Docking ##
from Vision.StandardNodes import Generic
Docking_16 = Generic(constrkw={}, name='Docking', library=stdlib)
self.macroNetwork.addNode(Docking_16, 189, 250)
apply(
Docking_16.addInputPort, (), {
'name': 'docking_logs',
'cast': True,
'datatype': 'list',
'balloon':
'list of docking log files to be read into as a single Docking',
'height': 12,
'width': 12,
'shape': 'oval',
'color': 'cyan'
})
apply(
Docking_16.addInputPort, (), {
'name': 'rmsTool',
'cast': True,
'datatype': 'None',
'balloon': 'rmsTool to be used for clustering',
'required': False,
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
apply(
Docking_16.addOutputPort, (), {
'name': 'docking',
'datatype': 'None',
'balloon': 'docking instance',
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
code = """def doit(self, docking_logs, rmsTool):
from AutoDockTools.Docking import Docking
d = Docking()
for f in docking_logs:
d.readDlg(f)
d.clusterer.rmsTool = rmsTool
self.outputData(docking = d)
## to ouput data on port docking use
## self.outputData(docking=data)
"""
Docking_16.configure(function=code)
except:
print "WARNING: failed to restore Generic named Docking in network self.macroNetwork"
print_exc()
Docking_16 = None
try:
## saving node rmsTool ##
from Vision.StandardNodes import Generic
rmsTool_17 = Generic(constrkw={}, name='rmsTool', library=stdlib)
self.macroNetwork.addNode(rmsTool_17, 206, 197)
apply(
rmsTool_17.addInputPort, (), {
'name': 'crds',
'cast': True,
'datatype': 'coordinates3D',
'balloon':
'coordinates to use as reference for rms calculation.',
'height': 8,
'width': 12,
'shape': 'rect',
'color': 'green'
})
apply(
rmsTool_17.addOutputPort, (), {
'name': 'rmsTool',
'datatype': 'None',
'balloon': 'rmsTool created using crds as reference',
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
code = """def doit(self, crds):
from mglutil.math.rmsd import RMSDCalculator
rmsTool = RMSDCalculator(crds)
self.outputData(rmsTool = rmsTool)
"""
rmsTool_17.configure(function=code)
except:
print "WARNING: failed to restore Generic named rmsTool in network self.macroNetwork"
print_exc()
rmsTool_17 = None
try:
## saving node Read Molecule ##
from MolKit.VisionInterface.MolKitNodes import ReadMolecule
Read_Molecule_18 = ReadMolecule(constrkw={},
name='Read Molecule',
library=molkitlib)
self.macroNetwork.addNode(Read_Molecule_18, 243, 16)
apply(Read_Molecule_18.inputPortByName['filename'].configure, (), {
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(Read_Molecule_18.outputPortByName['MolSets'].configure, (), {
'color': '#c64e70',
'shape': 'oval'
})
Read_Molecule_18.inputPortByName['filename'].widget.set(
"ind.pdbqt", run=False)
except:
print "WARNING: failed to restore ReadMolecule named Read Molecule in network self.macroNetwork"
print_exc()
Read_Molecule_18 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_19 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_19, 243, 66)
apply(
Index_19.inputPortByName['data'].configure, (), {
'datatype': 'MoleculeSet',
'cast': True,
'shape': 'oval',
'color': '#c64e70'
})
apply(Index_19.inputPortByName['index'].configure, (), {
'color': 'yellow',
'cast': True,
'shape': 'circle'
})
apply(Index_19.outputPortByName['data'].configure, (), {
'color': 'white',
'shape': 'diamond'
})
except:
print "WARNING: failed to restore Index named Index in network self.macroNetwork"
print_exc()
Index_19 = None
try:
## saving node Get allAtoms.coords ##
from Vision.StandardNodes import GetAttr
Get_allAtoms_coords_20 = GetAttr(constrkw={},
name='Get allAtoms.coords',
library=stdlib)
self.macroNetwork.addNode(Get_allAtoms_coords_20, 243, 115)
apply(Get_allAtoms_coords_20.inputPortByName['objects'].configure,
(), {
'color': 'white',
'cast': True,
'shape': 'diamond'
})
apply(Get_allAtoms_coords_20.inputPortByName['attr'].configure, (),
{
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(Get_allAtoms_coords_20.outputPortByName['attrs'].configure,
(), {
'color': 'cyan',
'shape': 'oval'
})
apply(
Get_allAtoms_coords_20.inputPortByName['attr'].widget.
configure, (), {
'choices':
('AAradii', 'AtomRadiiPatterns', 'NodesFromName', 'ROOT',
'TORSDOF', '_MarkTree', '__cmp__', '__doc__', '__eq__',
'__hash__', '__init__', '__module__', '__ne__',
'__repr__', '__str__', '_atomRadius', '_copyNode',
'_copy_atom_attr', '_fit_atom_into_tree',
'_numberOfDeletedNodes', 'addBond', 'adopt', 'allAtoms',
'assignUniqIndex', 'atmNum', 'attach_nonbonded_fragments',
'bonds', 'bondsflag', 'buildBondsBhtree',
'buildBondsByDistance', 'buildBondsByDistanceOnAtoms',
'buildBrokenBonds', 'chains', 'childByName', 'children',
'childrenName', 'childrenSetClass', 'closerThan',
'compare', 'compiled_patterns', 'configureProgressBar',
'copy', 'defaultRadii', 'deleteSubTree', 'dump',
'elementType', 'findLevels', 'findType', 'full_name',
'get', 'getAtoms', 'getCenter', 'getNext',
'getParentOfType', 'getPrevious', 'getRoot',
'getTypeList', 'hasBonds', 'hasSS', 'isAbove', 'isBelow',
'levels', 'makeNameUniq', 'merge', 'mergeNPH', 'name',
'ndihe', 'p', 'parent', 'parser', 'read', 'remove',
'removeAllHydrogens', 'removeBond', 'secondaryStructure',
'secondaryStructureFromFile',
'secondaryStructureFromStride', 'setClass', 'split',
'subTree', 'top', 'torTree', 'updateProgressBar', 'write')
})
Get_allAtoms_coords_20.inputPortByName['attr'].widget.set(
"allAtoms.coords", run=False)
apply(Get_allAtoms_coords_20.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore GetAttr named Get allAtoms.coords in network self.macroNetwork"
print_exc()
Get_allAtoms_coords_20 = None
try:
## saving node Get clusterer ##
from Vision.StandardNodes import GetAttr
Get_clusterer_21 = GetAttr(constrkw={},
name='Get clusterer',
library=stdlib)
self.macroNetwork.addNode(Get_clusterer_21, 189, 306)
apply(Get_clusterer_21.inputPortByName['objects'].configure, (), {
'color': 'white',
'cast': True,
'shape': 'diamond'
})
apply(Get_clusterer_21.inputPortByName['attr'].configure, (), {
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(Get_clusterer_21.outputPortByName['attrs'].configure, (), {
'color': 'cyan',
'shape': 'oval'
})
apply(
Get_clusterer_21.inputPortByName['attr'].widget.configure, (),
{
'choices':
('__doc__', '__init__', '__module__', 'addConformations',
'ch', 'clusterer', 'clusterer_dict', 'defaultParser',
'dlo_list', 'flex_res', 'ligMol', 'parser', 'readDlg',
'readEntropiaResults', 'readXMLResults', 'set_ligand',
'version', 'warnings', 'writeConformation',
'write_current_conformation')
})
Get_clusterer_21.inputPortByName['attr'].widget.set("clusterer",
run=False)
apply(Get_clusterer_21.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore GetAttr named Get clusterer in network self.macroNetwork"
print_exc()
Get_clusterer_21 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_22 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_22, 188, 383)
apply(Index_22.inputPortByName['data'].configure, (), {
'datatype': 'list',
'cast': True,
'shape': 'oval',
'color': 'cyan'
})
apply(Index_22.inputPortByName['index'].configure, (), {
'color': 'yellow',
'cast': True,
'shape': 'circle'
})
apply(Index_22.outputPortByName['data'].configure, (), {
'color': 'white',
'shape': 'diamond'
})
except:
print "WARNING: failed to restore Index named Index in network self.macroNetwork"
print_exc()
Index_22 = None
try:
## saving node make clustering ##
from Vision.StandardNodes import Generic
make_clustering_23 = Generic(constrkw={},
name='make clustering',
library=stdlib)
self.macroNetwork.addNode(make_clustering_23, 189, 432)
apply(
make_clustering_23.addInputPort, (), {
'name': 'clusterer',
'cast': True,
'datatype': 'None',
'balloon': 'clusterer which will make the new clustering',
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
apply(
make_clustering_23.addInputPort, (), {
'name': 'tolerance',
'cast': True,
'datatype': 'float',
'balloon': 'rms tolerance for the new clustering',
'height': 12,
'width': 12,
'shape': 'circle',
'color': 'green'
})
apply(
make_clustering_23.addOutputPort, (), {
'name': 'clustering',
'datatype': 'None',
'balloon': 'clustering at newest rms',
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
code = """def doit(self, clusterer, tolerance):
clusterer.make_clustering(tolerance)
self.outputData(clustering = clusterer.clustering_dict[tolerance])
"""
make_clustering_23.configure(function=code)
except:
print "WARNING: failed to restore Generic named make clustering in network self.macroNetwork"
print_exc()
make_clustering_23 = None
try:
## saving node Dial ##
from Vision.StandardNodes import DialNE
Dial_24 = DialNE(constrkw={}, name='Dial', library=stdlib)
self.macroNetwork.addNode(Dial_24, 233, 380)
apply(Dial_24.inputPortByName['dial'].configure, (), {
'color': 'green',
'cast': True,
'shape': 'circle'
})
apply(Dial_24.inputPortByName['mini'].configure, (), {
'color': 'green',
'cast': True,
'shape': 'circle'
})
apply(Dial_24.inputPortByName['maxi'].configure, (), {
'color': 'green',
'cast': True,
'shape': 'circle'
})
apply(Dial_24.outputPortByName['value'].configure, (), {
'color': 'green',
'shape': 'circle'
})
Dial_24.inputPortByName['dial'].widget.set(3.0, run=False)
apply(Dial_24.configure, (), {'expanded': False})
except:
print "WARNING: failed to restore DialNE named Dial in network self.macroNetwork"
print_exc()
Dial_24 = None
self.macroNetwork.freeze()
## saving connections for network recluster ##
if rmsTool_17 is not None and Docking_16 is not None:
try:
self.macroNetwork.connectNodes(rmsTool_17,
Docking_16,
"rmsTool",
"rmsTool",
blocking=True)
except:
print "WARNING: failed to restore connection between rmsTool_17 and Docking_16 in network self.macroNetwork"
if Read_Molecule_18 is not None and Index_19 is not None:
try:
self.macroNetwork.connectNodes(Read_Molecule_18,
Index_19,
"MolSets",
"data",
blocking=True)
except:
print "WARNING: failed to restore connection between Read_Molecule_18 and Index_19 in network self.macroNetwork"
if Index_19 is not None and Get_allAtoms_coords_20 is not None:
try:
self.macroNetwork.connectNodes(Index_19,
Get_allAtoms_coords_20,
"data",
"objects",
blocking=True)
except:
print "WARNING: failed to restore connection between Index_19 and Get_allAtoms_coords_20 in network self.macroNetwork"
if Get_allAtoms_coords_20 is not None and rmsTool_17 is not None:
try:
self.macroNetwork.connectNodes(Get_allAtoms_coords_20,
rmsTool_17,
"attrs",
"crds",
blocking=True)
except:
print "WARNING: failed to restore connection between Get_allAtoms_coords_20 and rmsTool_17 in network self.macroNetwork"
if Docking_16 is not None and Get_clusterer_21 is not None:
try:
self.macroNetwork.connectNodes(Docking_16,
Get_clusterer_21,
"docking",
"objects",
blocking=True)
except:
print "WARNING: failed to restore connection between Docking_16 and Get_clusterer_21 in network self.macroNetwork"
if Get_clusterer_21 is not None and Index_22 is not None:
try:
self.macroNetwork.connectNodes(Get_clusterer_21,
Index_22,
"attrs",
"data",
blocking=True)
except:
print "WARNING: failed to restore connection between Get_clusterer_21 and Index_22 in network self.macroNetwork"
if Index_22 is not None and make_clustering_23 is not None:
try:
self.macroNetwork.connectNodes(Index_22,
make_clustering_23,
"data",
"clusterer",
blocking=True)
except:
print "WARNING: failed to restore connection between Index_22 and make_clustering_23 in network self.macroNetwork"
if Dial_24 is not None and make_clustering_23 is not None:
try:
self.macroNetwork.connectNodes(Dial_24,
make_clustering_23,
"value",
"tolerance",
blocking=True)
except:
print "WARNING: failed to restore connection between Dial_24 and make_clustering_23 in network self.macroNetwork"
output_Ports_13 = self.macroNetwork.opNode
if make_clustering_23 is not None and output_Ports_13 is not None:
try:
self.macroNetwork.connectNodes(make_clustering_23,
output_Ports_13,
"clustering",
"new",
blocking=True)
except:
print "WARNING: failed to restore connection between make_clustering_23 and output_Ports_13 in network self.macroNetwork"
input_Ports_12 = self.macroNetwork.ipNode
if input_Ports_12 is not None and Docking_16 is not None:
try:
self.macroNetwork.connectNodes(input_Ports_12,
Docking_16,
"new",
"docking_logs",
blocking=True)
except:
print "WARNING: failed to restore connection between input_Ports_12 and Docking_16 in network self.macroNetwork"
self.macroNetwork.unfreeze()
recluster_11.shrink()
## reset modifications ##
recluster_11.resetTags()
recluster_11.buildOriginalList()
try:
## saving node Plot ##
from Vision.matplotlibNodes import PlotNE
Plot_57 = PlotNE(constrkw = {}, name='Plot', library=matplotliblib)
masterNet.addNode(Plot_57,31,351)
Plot_57.inputPortByName['lineStyle'].widget.set("dotted", run=False)
apply(Plot_57.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore PlotNE named Plot in network masterNet"
print_exc()
Plot_57=None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_58 = Index(constrkw = {}, name='Index', library=stdlib)
masterNet.addNode(Index_58,215,173)
apply(Index_58.inputPortByName['index'].widget.configure, (), {'max': 4})
Index_58.inputPortByName['index'].widget.set(2, run=False)
apply(Index_58.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_58=None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_59 = Index(constrkw = {}, name='Index', library=stdlib)
masterNet.addNode(Index_59,379,173)
apply(Index_59.inputPortByName['index'].widget.configure, (), {'max': 4})
library=matplotliblib)
masterNet.addNode(Draw_Area_114, 352, 158)
Draw_Area_114.inputPortByName['title'].widget.set(
"About as simple as it gets, folks", run=False)
Draw_Area_114.inputPortByName['xlabel'].widget.set("time(s)", run=False)
Draw_Area_114.inputPortByName['ylabel'].widget.set("voltage(mV)",
run=False)
except:
print "WARNING: failed to restore MPLDrawAreaNE named Draw Area in network masterNet"
print_exc()
Draw_Area_114 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_115 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_115, 4, 189)
apply(Index_115.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_115 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_116 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_116, 175, 188)
apply(Index_116.inputPortByName['index'].widget.configure, (), {'max': 1})
Index_116.inputPortByName['index'].widget.set(1, run=False)
apply(Index_116.configure, (), {'expanded': True})
ReadTable_108 = ReadTable(constrkw={}, name='ReadTable', library=stdlib)
masterNet.addNode(ReadTable_108, 39, 7)
ReadTable_108.inputPortByName['filename'].widget.set("Data/pie_data.dat",
run=False)
ReadTable_108.inputPortByName['sep'].widget.set(",", run=False)
ReadTable_108.inputPortByName['datatype'].widget.set("float", run=False)
apply(ReadTable_108.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore ReadTable named ReadTable in network masterNet"
print_exc()
ReadTable_108 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_109 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_109, 81, 177)
apply(Index_109.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_109 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_110 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_110, 250, 175)
apply(Index_110.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
apply(
ReadTable_5.inputPortByName['numOfBottomLinesToJump'].widget.configure,
(), {'oneTurn': 10.0})
ReadTable_5.inputPortByName['numOfBottomLinesToJump'].widget.set(0,
run=False)
ReadTable_5.inputPortByName['sep'].widget.set(r",", run=False)
ReadTable_5.inputPortByName['datatype'].widget.set(r"float", run=False)
except:
print "WARNING: failed to restore ReadTable named ReadTable in network masterNet"
print_exc()
ReadTable_5 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_6 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_6, 32, 189)
Index_6.inputPortByName['index'].widget.set(0, run=False)
apply(Index_6.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_6 = None
#masterNet.run()
masterNet.freeze()
## saving connections for network ImageFigure ##
if Draw_Area_1 is not None and Histogram_0 is not None:
try:
masterNet.connectNodes(
constrkw={}, name='Set Matplotlib options', library=matplotliblib)
masterNet.addNode(Set_Matplotlib_options_23, 148, 330)
Set_Matplotlib_options_23.inputPortByName['matplotlibOptions'].widget.set(
{
'gridOn': 1,
'whichgrid': 'major'
}, run=False)
except:
print "WARNING: failed to restore MatPlotLibOptions named Set Matplotlib options in network masterNet"
print_exc()
Set_Matplotlib_options_23 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_24 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_24, 28, 182)
apply(Index_24.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_24 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_25 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_25, 178, 174)
apply(Index_25.inputPortByName['index'].widget.configure, (), {'max': 3})
Index_25.inputPortByName['index'].widget.set(1, run=False)
apply(Index_25.configure, (), {'expanded': True})
constrkw={}, name='Set Matplotlib options', library=matplotliblib)
masterNet.addNode(Set_Matplotlib_options_201, 212, 363)
Set_Matplotlib_options_201.inputPortByName['matplotlibOptions'].widget.set(
{
'gridOn': 1,
'whichgrid': 'major'
}, run=False)
except:
print "WARNING: failed to restore MatPlotLibOptions named Set Matplotlib options in network masterNet"
print_exc()
Set_Matplotlib_options_201 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_202 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_202, 28, 182)
apply(Index_202.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_202 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_203 = Index(constrkw={}, name='Index', library=stdlib)
masterNet.addNode(Index_203, 178, 174)
apply(Index_203.inputPortByName['index'].widget.configure, (), {'max': 3})
Index_203.inputPortByName['index'].widget.set(1, run=False)
apply(Index_203.configure, (), {'expanded': True})
from Vision.StandardNodes import ReadTable
ReadTable_163 = ReadTable(constrkw = {}, name='ReadTable', library=stdlib)
masterNet.addNode(ReadTable_163,135,21)
ReadTable_163.inputPortByName['filename'].widget.set("Data/text_align_data.dat", run=False)
ReadTable_163.inputPortByName['sep'].widget.set(",", run=False)
ReadTable_163.inputPortByName['datatype'].widget.set("float", run=False)
apply(ReadTable_163.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore ReadTable named ReadTable in network masterNet"
print_exc()
ReadTable_163=None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_164 = Index(constrkw = {}, name='Index', library=stdlib)
masterNet.addNode(Index_164,4,168)
apply(Index_164.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore Index named Index in network masterNet"
print_exc()
Index_164=None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_165 = Index(constrkw = {}, name='Index', library=stdlib)
masterNet.addNode(Index_165,139,171)
apply(Index_165.inputPortByName['index'].widget.configure, (), {'max': 3})
Index_165.inputPortByName['index'].widget.set(1, run=False)
apply(Index_165.configure, (), {'expanded': True})