def afterAddingToNetwork(self):
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
## loading libraries ##
from MolKit.VisionInterface.MolKitNodes import molkitlib
from DejaVu.VisionInterface.DejaVuNodes import vizlib
from Vision.StandardNodes import stdlib
## building macro network ##
WebMSMS = self
from traceback import print_exc
## loading libraries ##
from MolKit.VisionInterface.MolKitNodes import molkitlib
self.macroNetwork.getEditor().addLibraryInstance(molkitlib,"MolKit.VisionInterface.MolKitNodes", "molkitlib")
from DejaVu.VisionInterface.DejaVuNodes import vizlib
self.macroNetwork.getEditor().addLibraryInstance(vizlib,"DejaVu.VisionInterface.DejaVuNodes", "vizlib")
from Vision.StandardNodes import stdlib
self.macroNetwork.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")
try:
## saving node input Ports ##
input_Ports = self.macroNetwork.ipNode
input_Ports.move(13, 4)
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports=None
try:
## saving node output Ports ##
output_Ports = self.macroNetwork.opNode
output_Ports.move(256, 220)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports=None
try:
## saving node Assign Radii ##
from MolKit.VisionInterface.MolKitNodes import AssignRadii
Assign_Radii = AssignRadii(constrkw = {}, name='Assign Radii', library=molkitlib)
self.macroNetwork.addNode(Assign_Radii,30,68)
apply(Assign_Radii.getInputPortByName('molecules').configure, (), {'color': '#c64e70', 'cast': True, 'shape': 'oval'})
apply(Assign_Radii.getInputPortByName('united').configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'})
apply(Assign_Radii.getOutputPortByName('molecules').configure, (), {'color': '#c64e70', 'shape': 'oval'})
apply(Assign_Radii.getOutputPortByName('radii').configure, (), {'color': 'cyan', 'shape': 'oval'})
except:
print "WARNING: failed to restore AssignRadii named Assign Radii in network self.macroNetwork"
print_exc()
Assign_Radii=None
try:
## saving node Select Nodes ##
from MolKit.VisionInterface.MolKitNodes import NodeSelector
Select_Nodes = NodeSelector(constrkw = {}, name='Select Nodes', library=molkitlib)
self.macroNetwork.addNode(Select_Nodes,29,135)
apply(Select_Nodes.getInputPortByName('nodes').configure, (), {'color': '#c64e70', 'cast': True, 'shape': 'oval'})
apply(Select_Nodes.getInputPortByName('nodeType').configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'})
apply(Select_Nodes.getInputPortByName('selectionString').configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'})
apply(Select_Nodes.getOutputPortByName('nodes').configure, (), {'color': '#fe92a0', 'shape': 'oval'})
Select_Nodes.getInputPortByName("selectionString").widget.set(".*")
except:
print "WARNING: failed to restore NodeSelector named Select Nodes in network self.macroNetwork"
print_exc()
Select_Nodes=None
try:
## saving node Get xyzr ##
from Vision.StandardNodes import Generic
Get_xyzr = Generic(constrkw = {}, name='Get xyzr', library=stdlib)
self.macroNetwork.addNode(Get_xyzr,30,194)
apply(Get_xyzr.addInputPort, (), {'name': 'atoms', 'cast': True, 'datatype': 'AtomSet', 'height': 8, 'width': 12, 'shape': 'oval', 'color': '#fe92a0'})
apply(Get_xyzr.addOutputPort, (), {'name': 'output', 'datatype': 'string', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, atoms):
lines = ''
for atom in atoms:
lines += str(atom.coords[0]) + ' ' + str(atom.coords[1]) + ' ' + str(atom.coords[2]) + ' '+ str(atom.radius)
lines += "\\n"
self.outputData(output=lines)
"""
Get_xyzr.configure(function=code)
except:
print "WARNING: failed to restore Generic named Get xyzr in network self.macroNetwork"
print_exc()
Get_xyzr=None
try:
## saving node IndexedPolygons ##
from DejaVu.VisionInterface.GeometryNode import IndexedPolygonsNE
IndexedPolygons = IndexedPolygonsNE(constrkw = {}, name='IndexedPolygons', library=vizlib)
self.macroNetwork.addNode(IndexedPolygons,273,147)
apply(IndexedPolygons.getInputPortByName('coords').configure, (), {'color': 'purple', 'cast': True, 'shape': 'circle'})
apply(IndexedPolygons.getInputPortByName('indices').configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'})
apply(IndexedPolygons.getInputPortByName('vnormals').configure, (), {'cast': True, 'shape': 'circle'})
apply(IndexedPolygons.getInputPortByName('colors').configure, (), {'cast': True, 'shape': 'circle'})
apply(IndexedPolygons.getInputPortByName('name').configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'})
apply(IndexedPolygons.getInputPortByName('instanceMatrices').configure, (), {'cast': True})
apply(IndexedPolygons.getInputPortByName('geomOptions').configure, (), {'color': 'cyan', 'cast': True, 'shape': 'oval'})
apply(IndexedPolygons.getInputPortByName('parent').configure, (), {'color': 'red', 'cast': True, 'shape': 'rect'})
apply(IndexedPolygons.getOutputPortByName('indexedPolygons').configure, (), {'color': 'red', 'shape': 'rect'})
apply(IndexedPolygons.getOutputPortByName('allGeometries').configure, (), {'color': 'red', 'shape': 'rect'})
except:
print "WARNING: failed to restore IndexedPolygonsNE named IndexedPolygons in network self.macroNetwork"
print_exc()
IndexedPolygons=None
try:
## saving node MSMS WS ##
from Vision.StandardNodes import Generic
MSMS_WS = Generic(constrkw = {}, name='MSMS WS', library=stdlib)
self.macroNetwork.addNode(MSMS_WS,273,37)
apply(MSMS_WS.addInputPort, (), {'name': 'input_str', 'cast': True,
'datatype': 'string', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(MSMS_WS.addInputPort, (), {'name': 'density', 'datatype': 'float', 'required':False})
apply(MSMS_WS.getInputPortByName('density').createWidget, (),
{'descr':{'initialValue': 1.0, 'increment':0.1, 'type':'float',
'master': 'ParamPanel', 'oneTurn':10, 'min':1.0, 'labelCfg': {'text': 'density'}, 'class': 'NEDial'}})
apply(MSMS_WS.addInputPort, (), {'name': 'probe_radius', 'datatype': 'float', 'required':False})
apply(MSMS_WS.getInputPortByName('probe_radius').createWidget, (),
{'descr':{'initialValue': 1.5, 'increment':0.1, 'type':'float',
'master': 'ParamPanel', 'oneTurn':10, 'min':0.5, 'labelCfg': {'text': 'probe radius'}, 'class': 'NEDial'}})
apply(MSMS_WS.addInputPort, (), {'name': 'allComp', 'datatype': 'int', 'required':False})
apply(MSMS_WS.getInputPortByName('allComp').createWidget, (),
{'descr':{'initialValue': 0, 'master': 'ParamPanel', 'labelCfg':
{'text': 'all components'}, 'class': 'NECheckButton'}})
apply(MSMS_WS.addInputPort, (), {'name': 'getfile', 'datatype': 'boolean'})
apply(MSMS_WS.getInputPortByName('getfile').createWidget, (),
{'descr':{'master': 'ParamPanel', 'labelCfg': {'text': 'upload output'}, 'class': 'NECheckButton', 'initialValue':True }})
apply(MSMS_WS.addOutputPort, (), {'name': 'vertices', 'datatype': 'coordinates3D', 'height': 8, 'width': 12, 'shape': 'rect', 'color': 'green'})
apply(MSMS_WS.addOutputPort, (), {'name': 'indices', 'datatype': 'faceIndices', 'height': 8, 'width': 12, 'shape': 'rect', 'color': 'purple'})
apply(MSMS_WS.addOutputPort, (), {'name': 'vnormals', 'datatype': 'normals3D', 'height': 8, 'width': 12, 'shape': 'rect', 'color': 'blue'})
MSMS_WS.host = self.host
MSMS_WS.opal_service = self.opal_service
code = """def doit(self, input_str, probe_radius, density, allComp, getfile):
self.opal_service.inputFile.Set_name('msms.xyzr')
self.opal_service.inputFile.Set_contents(input_str)
options = '-if msms.xyzr -of ws_out '
options += '-probe_radius ' + str(probe_radius)
options += ' -density ' + str(density)
if allComp:
options += ' -all_components'
self.opal_service.req._argList = options
inputFiles = []
inputFiles.append(self.opal_service.inputFile)
self.opal_service.req._inputFile = inputFiles
resp = self.opal_service.run('msmsServicePort')
if resp:
for files in resp._outputFile:
if files._url.split('/')[-1] == 'ws_out.face':
face_file = files._url
if files._url.split('/')[-1] == 'ws_out.vert':
vert_file = files._url
if getfile:
from Pmv.msmsParser import MSMSParser
msmsParser = MSMSParser()
import urllib
opener = urllib.FancyURLopener({})
in_file = opener.open(face_file)
msmsParser.getFaces(in_file.readlines())
in_file = opener.open(vert_file)
msmsParser.getVert(in_file.readlines())
self.outputData(vertices = msmsParser.vertices, indices = msmsParser.faces,
vnormals = msmsParser.normals)
else:
self.outputData(vertices = vert_file, indices = face_file,
vnormals = None)
"""
MSMS_WS.configure(function=code)
except:
print "WARNING: failed to restore Generic named MSMS WS in network self.macroNetwork"
print_exc()
MSMS_WS=None
self.macroNetwork.freeze()
## saving connections for network WebMSMS ##
if Assign_Radii is not None and Select_Nodes is not None:
self.macroNetwork.connectNodes(
Assign_Radii, Select_Nodes, "molecules", "nodes", blocking=True)
if Select_Nodes is not None and Get_xyzr is not None:
self.macroNetwork.connectNodes(
Select_Nodes, Get_xyzr, "nodes", "atoms", blocking=True)
if Get_xyzr is not None and MSMS_WS is not None:
self.macroNetwork.connectNodes(
Get_xyzr, MSMS_WS, "output", "input_str", blocking=True)
if MSMS_WS is not None and IndexedPolygons is not None:
self.macroNetwork.connectNodes(
MSMS_WS, IndexedPolygons, "vertices", "coords", blocking=True)
if MSMS_WS is not None and IndexedPolygons is not None:
self.macroNetwork.connectNodes(
MSMS_WS, IndexedPolygons, "indices", "indices", blocking=True)
if MSMS_WS is not None and IndexedPolygons is not None:
self.macroNetwork.connectNodes(
MSMS_WS, IndexedPolygons, "vnormals", "vnormals", blocking=True)
output_Ports = self.macroNetwork.opNode
if IndexedPolygons is not None and output_Ports is not None:
self.macroNetwork.connectNodes(
IndexedPolygons, output_Ports, "indexedPolygons", "new", blocking=True)
input_Ports = self.macroNetwork.ipNode
if input_Ports is not None and Assign_Radii is not None:
self.macroNetwork.connectNodes(
input_Ports, Assign_Radii, "new", "molecules", blocking=True)
self.macroNetwork.unfreeze()
WebMSMS.shrink()
## reset modifications ##
WebMSMS.resetTags()
WebMSMS.buildOriginalList()
def afterAddingToNetwork(self):
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
## loading libraries ##
from MolKit.VisionInterface.MolKitNodes import molkitlib
from DejaVu.VisionInterface.DejaVuNodes import vizlib
from Vision.StandardNodes import stdlib
## building macro network ##
WebMSMS = self
from traceback import print_exc
## loading libraries ##
from MolKit.VisionInterface.MolKitNodes import molkitlib
self.macroNetwork.getEditor().addLibraryInstance(
molkitlib, "MolKit.VisionInterface.MolKitNodes", "molkitlib")
from DejaVu.VisionInterface.DejaVuNodes import vizlib
self.macroNetwork.getEditor().addLibraryInstance(
vizlib, "DejaVu.VisionInterface.DejaVuNodes", "vizlib")
from Vision.StandardNodes import stdlib
self.macroNetwork.getEditor().addLibraryInstance(
stdlib, "Vision.StandardNodes", "stdlib")
try:
## saving node input Ports ##
input_Ports = self.macroNetwork.ipNode
input_Ports.move(13, 4)
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports = None
try:
## saving node output Ports ##
output_Ports = self.macroNetwork.opNode
output_Ports.move(256, 220)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports = None
try:
## saving node Assign Radii ##
from MolKit.VisionInterface.MolKitNodes import AssignRadii
Assign_Radii = AssignRadii(constrkw={},
name='Assign Radii',
library=molkitlib)
self.macroNetwork.addNode(Assign_Radii, 30, 68)
apply(
Assign_Radii.getInputPortByName('molecules').configure, (), {
'color': '#c64e70',
'cast': True,
'shape': 'oval'
})
apply(
Assign_Radii.getInputPortByName('united').configure, (), {
'color': 'yellow',
'cast': True,
'shape': 'circle'
})
apply(
Assign_Radii.getOutputPortByName('molecules').configure, (), {
'color': '#c64e70',
'shape': 'oval'
})
apply(
Assign_Radii.getOutputPortByName('radii').configure, (), {
'color': 'cyan',
'shape': 'oval'
})
except:
print "WARNING: failed to restore AssignRadii named Assign Radii in network self.macroNetwork"
print_exc()
Assign_Radii = None
try:
## saving node Select Nodes ##
from MolKit.VisionInterface.MolKitNodes import NodeSelector
Select_Nodes = NodeSelector(constrkw={},
name='Select Nodes',
library=molkitlib)
self.macroNetwork.addNode(Select_Nodes, 29, 135)
apply(
Select_Nodes.getInputPortByName('nodes').configure, (), {
'color': '#c64e70',
'cast': True,
'shape': 'oval'
})
apply(
Select_Nodes.getInputPortByName('nodeType').configure, (), {
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(
Select_Nodes.getInputPortByName('selectionString').configure,
(), {
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(
Select_Nodes.getOutputPortByName('nodes').configure, (), {
'color': '#fe92a0',
'shape': 'oval'
})
Select_Nodes.getInputPortByName("selectionString").widget.set(".*")
except:
print "WARNING: failed to restore NodeSelector named Select Nodes in network self.macroNetwork"
print_exc()
Select_Nodes = None
try:
## saving node Get xyzr ##
from Vision.StandardNodes import Generic
Get_xyzr = Generic(constrkw={}, name='Get xyzr', library=stdlib)
self.macroNetwork.addNode(Get_xyzr, 30, 194)
apply(
Get_xyzr.addInputPort, (), {
'name': 'atoms',
'cast': True,
'datatype': 'AtomSet',
'height': 8,
'width': 12,
'shape': 'oval',
'color': '#fe92a0'
})
apply(
Get_xyzr.addOutputPort, (), {
'name': 'output',
'datatype': 'string',
'height': 12,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, atoms):
lines = ''
for atom in atoms:
lines += str(atom.coords[0]) + ' ' + str(atom.coords[1]) + ' ' + str(atom.coords[2]) + ' '+ str(atom.radius)
lines += "\\n"
self.outputData(output=lines)
"""
Get_xyzr.configure(function=code)
except:
print "WARNING: failed to restore Generic named Get xyzr in network self.macroNetwork"
print_exc()
Get_xyzr = None
try:
## saving node IndexedPolygons ##
from DejaVu.VisionInterface.GeometryNode import IndexedPolygonsNE
IndexedPolygons = IndexedPolygonsNE(constrkw={},
name='IndexedPolygons',
library=vizlib)
self.macroNetwork.addNode(IndexedPolygons, 273, 147)
apply(
IndexedPolygons.getInputPortByName('coords').configure, (), {
'color': 'purple',
'cast': True,
'shape': 'circle'
})
apply(
IndexedPolygons.getInputPortByName('indices').configure, (), {
'color': 'yellow',
'cast': True,
'shape': 'circle'
})
apply(
IndexedPolygons.getInputPortByName('vnormals').configure, (), {
'cast': True,
'shape': 'circle'
})
apply(
IndexedPolygons.getInputPortByName('colors').configure, (), {
'cast': True,
'shape': 'circle'
})
apply(
IndexedPolygons.getInputPortByName('name').configure, (), {
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(
IndexedPolygons.getInputPortByName(
'instanceMatrices').configure, (), {'cast': True})
apply(
IndexedPolygons.getInputPortByName('geomOptions').configure,
(), {
'color': 'cyan',
'cast': True,
'shape': 'oval'
})
apply(
IndexedPolygons.getInputPortByName('parent').configure, (), {
'color': 'red',
'cast': True,
'shape': 'rect'
})
apply(
IndexedPolygons.getOutputPortByName(
'indexedPolygons').configure, (), {
'color': 'red',
'shape': 'rect'
})
apply(
IndexedPolygons.getOutputPortByName('allGeometries').configure,
(), {
'color': 'red',
'shape': 'rect'
})
except:
print "WARNING: failed to restore IndexedPolygonsNE named IndexedPolygons in network self.macroNetwork"
print_exc()
IndexedPolygons = None
try:
## saving node MSMS WS ##
from Vision.StandardNodes import Generic
MSMS_WS = Generic(constrkw={}, name='MSMS WS', library=stdlib)
self.macroNetwork.addNode(MSMS_WS, 273, 37)
apply(
MSMS_WS.addInputPort, (), {
'name': 'input_str',
'cast': True,
'datatype': 'string',
'height': 12,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(MSMS_WS.addInputPort, (), {
'name': 'density',
'datatype': 'float',
'required': False
})
apply(
MSMS_WS.getInputPortByName('density').createWidget, (), {
'descr': {
'initialValue': 1.0,
'increment': 0.1,
'type': 'float',
'master': 'ParamPanel',
'oneTurn': 10,
'min': 1.0,
'labelCfg': {
'text': 'density'
},
'class': 'NEDial'
}
})
apply(MSMS_WS.addInputPort, (), {
'name': 'probe_radius',
'datatype': 'float',
'required': False
})
apply(
MSMS_WS.getInputPortByName('probe_radius').createWidget, (), {
'descr': {
'initialValue': 1.5,
'increment': 0.1,
'type': 'float',
'master': 'ParamPanel',
'oneTurn': 10,
'min': 0.5,
'labelCfg': {
'text': 'probe radius'
},
'class': 'NEDial'
}
})
apply(MSMS_WS.addInputPort, (), {
'name': 'allComp',
'datatype': 'int',
'required': False
})
apply(
MSMS_WS.getInputPortByName('allComp').createWidget, (), {
'descr': {
'initialValue': 0,
'master': 'ParamPanel',
'labelCfg': {
'text': 'all components'
},
'class': 'NECheckButton'
}
})
apply(MSMS_WS.addInputPort, (), {
'name': 'getfile',
'datatype': 'boolean'
})
apply(
MSMS_WS.getInputPortByName('getfile').createWidget, (), {
'descr': {
'master': 'ParamPanel',
'labelCfg': {
'text': 'upload output'
},
'class': 'NECheckButton',
'initialValue': True
}
})
apply(
MSMS_WS.addOutputPort, (), {
'name': 'vertices',
'datatype': 'coordinates3D',
'height': 8,
'width': 12,
'shape': 'rect',
'color': 'green'
})
apply(
MSMS_WS.addOutputPort, (), {
'name': 'indices',
'datatype': 'faceIndices',
'height': 8,
'width': 12,
'shape': 'rect',
'color': 'purple'
})
apply(
MSMS_WS.addOutputPort, (), {
'name': 'vnormals',
'datatype': 'normals3D',
'height': 8,
'width': 12,
'shape': 'rect',
'color': 'blue'
})
MSMS_WS.host = self.host
MSMS_WS.opal_service = self.opal_service
code = """def doit(self, input_str, probe_radius, density, allComp, getfile):
self.opal_service.inputFile.Set_name('msms.xyzr')
self.opal_service.inputFile.Set_contents(input_str)
options = '-if msms.xyzr -of ws_out '
options += '-probe_radius ' + str(probe_radius)
options += ' -density ' + str(density)
if allComp:
options += ' -all_components'
self.opal_service.req._argList = options
inputFiles = []
inputFiles.append(self.opal_service.inputFile)
self.opal_service.req._inputFile = inputFiles
resp = self.opal_service.run('msmsServicePort')
if resp:
for files in resp._outputFile:
if files._url.split('/')[-1] == 'ws_out.face':
face_file = files._url
if files._url.split('/')[-1] == 'ws_out.vert':
vert_file = files._url
if getfile:
from Pmv.msmsParser import MSMSParser
msmsParser = MSMSParser()
import urllib
opener = urllib.FancyURLopener({})
in_file = opener.open(face_file)
msmsParser.getFaces(in_file.readlines())
in_file = opener.open(vert_file)
msmsParser.getVert(in_file.readlines())
self.outputData(vertices = msmsParser.vertices, indices = msmsParser.faces,
vnormals = msmsParser.normals)
else:
self.outputData(vertices = vert_file, indices = face_file,
vnormals = None)
"""
MSMS_WS.configure(function=code)
except:
print "WARNING: failed to restore Generic named MSMS WS in network self.macroNetwork"
print_exc()
MSMS_WS = None
self.macroNetwork.freeze()
## saving connections for network WebMSMS ##
if Assign_Radii is not None and Select_Nodes is not None:
self.macroNetwork.connectNodes(Assign_Radii,
Select_Nodes,
"molecules",
"nodes",
blocking=True)
if Select_Nodes is not None and Get_xyzr is not None:
self.macroNetwork.connectNodes(Select_Nodes,
Get_xyzr,
"nodes",
"atoms",
blocking=True)
if Get_xyzr is not None and MSMS_WS is not None:
self.macroNetwork.connectNodes(Get_xyzr,
MSMS_WS,
"output",
"input_str",
blocking=True)
if MSMS_WS is not None and IndexedPolygons is not None:
self.macroNetwork.connectNodes(MSMS_WS,
IndexedPolygons,
"vertices",
"coords",
blocking=True)
if MSMS_WS is not None and IndexedPolygons is not None:
self.macroNetwork.connectNodes(MSMS_WS,
IndexedPolygons,
"indices",
"indices",
blocking=True)
if MSMS_WS is not None and IndexedPolygons is not None:
self.macroNetwork.connectNodes(MSMS_WS,
IndexedPolygons,
"vnormals",
"vnormals",
blocking=True)
output_Ports = self.macroNetwork.opNode
if IndexedPolygons is not None and output_Ports is not None:
self.macroNetwork.connectNodes(IndexedPolygons,
output_Ports,
"indexedPolygons",
"new",
blocking=True)
input_Ports = self.macroNetwork.ipNode
if input_Ports is not None and Assign_Radii is not None:
self.macroNetwork.connectNodes(input_Ports,
Assign_Radii,
"new",
"molecules",
blocking=True)
self.macroNetwork.unfreeze()
WebMSMS.shrink()
## reset modifications ##
WebMSMS.resetTags()
WebMSMS.buildOriginalList()
