def test_06_MSMS():
# test the MSMS node
net = ed.currentNetwork
net.runOnNewData.value = True
node1 = ReadMolecule(library=molkitlib)
net.addNode(node1, 20, 20)
node1.inputPorts[0].widget.set(os.path.abspath("1crn.pdb"))
# assign radii
node2 = AssignRadii(library=molkitlib)
net.addNode(node2, 275, 62)
net.connectNodes(node1, node2, "MolSets", "molecules")
node2.toggleNodeExpand_cb()
# select nodes
node3 = NodeSelector(library=molkitlib)
net.addNode(node3, 14, 153)
net.connectNodes(node2, node3, "molecules", "nodes")
node3.toggleNodeExpand_cb()
# msms
node4 = AtomsAsMSMS(library=molkitlib)
net.addNode(node4, 263, 267)
net.connectNodes(node3, node4, "nodes", "atoms")
net.connectNodes(node2, node4, "radii", "radii")
pause()
# check data
from mslib import MSMS
assert isinstance(node4.outputPorts[0].data, MSMS),\
"Expected %s, got %s"%(MSMS, node4.outputPorts[0].data.__class__)
assert len(node4.outputPorts[0].data.coords) == 327,\
"Expected 327, got %s"%len(node4.outputPorts[0].data.coords)
# just for the fun of it, click the united radii checkbutton a couple times
node2.inputPorts[1].widget.set(1)
node2.inputPorts[1].widget.set(0)
node2.inputPorts[1].widget.set(1)
node2.inputPorts[1].widget.set(0)
def test_06_MSMS():
# test the MSMS node
net = ed.currentNetwork
net.runOnNewData.value = True
node1 = ReadMolecule(library=molkitlib)
net.addNode(node1, 20, 20)
node1.inputPorts[0].widget.set(os.path.abspath("1crn.pdb"))
# assign radii
node2 = AssignRadii(library=molkitlib)
net.addNode(node2, 275, 62)
net.connectNodes(node1, node2, "MolSets", "molecules")
node2.toggleNodeExpand_cb()
# select nodes
node3 = NodeSelector(library=molkitlib)
net.addNode(node3, 14, 153)
net.connectNodes(node2, node3, "molecules", "nodes")
node3.toggleNodeExpand_cb()
# msms
node4 = AtomsAsMSMS(library=molkitlib)
net.addNode(node4, 263, 267)
net.connectNodes(node3, node4, "nodes", "atoms")
net.connectNodes(node2, node4, "radii", "radii")
pause()
# check data
from mslib import MSMS
assert isinstance(node4.outputPorts[0].data, MSMS),\
"Expected %s, got %s"%(MSMS, node4.outputPorts[0].data.__class__)
assert len(node4.outputPorts[0].data.coords) == 327,\
"Expected 327, got %s"%len(node4.outputPorts[0].data.coords)
# just for the fun of it, click the united radii checkbutton a couple times
node2.inputPorts[1].widget.set(1)
node2.inputPorts[1].widget.set(0)
node2.inputPorts[1].widget.set(1)
node2.inputPorts[1].widget.set(0)
def test_05_AtomsProperty():
# test the Extract Atoms property node
net = ed.currentNetwork
net.runOnNewData.value = True
node1 = ReadMolecule(library=molkitlib)
net.addNode(node1, 20, 20)
node1.inputPorts[0].widget.set(os.path.abspath("1crn.pdb"))
node2 = NodeSelector(library=molkitlib)
net.addNode(node2, 30, 100)
net.connectNodes(node1, node2, "MolSets", "nodes")
node3 = AtomsProperty(library=molkitlib)
net.addNode(node3, 90, 170)
net.connectNodes(node2, node3, "nodes", "atoms")
node3.toggleNodeExpand_cb()
pause()
# define a couple of attributes we want to access
# FIXME: ATTRIBUTE "radius" is not working!!??
attrs = [
"_uniqIndex", "atomicNumber", "bondOrderRadius", "covalentRadius",
"element", "name", "number", "organic", "segID", "temperatureFactor",
"vdwRadius"
]
for a in attrs:
node3.inputPorts[1].widget.set(a)
assert len(node3.outputPorts[0].data) == 327,\
"Expected 327, got %s"%len(node3.outputPorts[0].data)
def test_02_NodeSelector():
# test the select 'node' node
net = ed.currentNetwork
net.runOnNewData.value = True
node1 = ReadMolecule(library=molkitlib)
net.addNode(node1, 20, 20)
node1.inputPorts[0].widget.set(os.path.abspath("1crn.pdb"))
node2 = NodeSelector(library=molkitlib)
net.addNode(node2, 30, 100)
net.connectNodes(node1, node2, "MolSets", "nodes")
node2.toggleNodeExpand_cb()
pause()
# because we run(), upon connecting we pass the data and the output of
# node2 should have data
# default node output is AtomSet
from MolKit.molecule import AtomSet
data = node2.outputPorts[0].data
assert isinstance(
data, AtomSet), "Expected %s, got %s" % (AtomSet, data.__class__)
# switch to ResidueSet
from MolKit.protein import ResidueSet
node2.inputPorts[1].widget.set("Residue")
data = node2.outputPorts[0].data
assert isinstance(
data, ResidueSet), "Expected %s, got %s" % (ResidueSet, data.__class__)
# switch to Chain
from MolKit.protein import ChainSet
node2.inputPorts[1].widget.set("Chain")
data = node2.outputPorts[0].data
assert isinstance(
data, ChainSet), "Expected %s, got %s" % (ChainSet, data.__class__)
# switch to Molecule
from MolKit.molecule import MoleculeSet
node2.inputPorts[1].widget.set("Molecule")
data = node2.outputPorts[0].data
assert isinstance(
data,
MoleculeSet), "Expected %s, got %s" % (MoleculeSet, data.__class__)
def test_02_NodeSelector():
# test the select 'node' node
net = ed.currentNetwork
net.runOnNewData.value = True
node1 = ReadMolecule(library=molkitlib)
net.addNode(node1, 20, 20)
node1.inputPorts[0].widget.set(os.path.abspath("1crn.pdb"))
node2 = NodeSelector(library=molkitlib)
net.addNode(node2, 30, 100)
net.connectNodes(node1, node2, "MolSets", "nodes")
node2.toggleNodeExpand_cb()
pause()
# because we run(), upon connecting we pass the data and the output of
# node2 should have data
# default node output is AtomSet
from MolKit.molecule import AtomSet
data = node2.outputPorts[0].data
assert isinstance(data, AtomSet), "Expected %s, got %s"%(
AtomSet, data.__class__)
# switch to ResidueSet
from MolKit.protein import ResidueSet
node2.inputPorts[1].widget.set("Residue")
data = node2.outputPorts[0].data
assert isinstance(data, ResidueSet), "Expected %s, got %s"%(
ResidueSet, data.__class__)
# switch to Chain
from MolKit.protein import ChainSet
node2.inputPorts[1].widget.set("Chain")
data = node2.outputPorts[0].data
assert isinstance(data, ChainSet), "Expected %s, got %s"%(
ChainSet, data.__class__)
# switch to Molecule
from MolKit.molecule import MoleculeSet
node2.inputPorts[1].widget.set("Molecule")
data = node2.outputPorts[0].data
assert isinstance(data, MoleculeSet), "Expected %s, got %s"%(
MoleculeSet, data.__class__)
def test_07_MSMSWithAtomSubset():
# test if we can pass an atom set (C,CA,N) to compute an MSMS
masterNet = ed.currentNetwork
## saving node Read Molecule ##
node0 = ReadMolecule(library=molkitlib)
masterNet.addNode(node0, 20, 20)
node0.inputPorts[0].widget.set(os.path.abspath("1crn.pdb"),
0) # do not run yet
## saving node MSMS ##
node2 = AtomsAsMSMS(library=molkitlib)
masterNet.addNode(node2, 250, 275)
## saving node Select Nodes ##
node4 = NodeSelector(library=molkitlib)
masterNet.addNode(node4, 14, 153)
node4.inputPorts[2].widget.set("C,CA,N")
apply(node4.configure, (), {'expanded': True})
## saving node Assign Radii ##
node5 = AssignRadii(library=molkitlib)
masterNet.addNode(node5, 275, 62)
apply(node5.configure, (), {'expanded': True})
## saving node Extract Atom Property ##
node7 = AtomsProperty(library=molkitlib)
masterNet.addNode(node7, 302, 169)
node7.inputPorts[1].widget.set("radius")
apply(node7.configure, (), {'expanded': True})
## saving connections for network Network 0 ##
masterNet.connectNodes(node0, node5, "MolSets", "molecules")
masterNet.connectNodes(node5, node4, "molecules", "nodes")
masterNet.connectNodes(node4, node2, "nodes", "atoms")
masterNet.connectNodes(node4, node7, "nodes", "atoms")
masterNet.connectNodes(node7, node2, "propertyValues", "radii")
pause()
masterNet.run()
# check if the data is correct
# (compare to above: the entire AtomSet would be 237)
assert node2.outputPorts[0].data is not None,\
"Expected data, got %s"%node2.outputPorts[0].data
assert len(node2.outputPorts[0].data.coords) == 138,\
"Expected 128, got %s"%len(node2.outputPorts[0].data.coords)
## saving node Assign Radii ##
from MolKit.VisionInterface.MolKitNodes import AssignRadii
node1 = AssignRadii(constrkw={}, name='Assign Radii', library=molkitlib)
masterNet.addNode(node1, 86, 114)
widget = node1.inputPorts[1].widget
widget.set(0, 0)
except:
print "WARNING: failed to restore node AssignRadii called Assign Radii in network masterNet"
print_exc()
node1 = None
try:
## saving node Select Nodes ##
from MolKit.VisionInterface.MolKitNodes import NodeSelector
node2 = NodeSelector(constrkw={}, name='Select Nodes', library=molkitlib)
masterNet.addNode(node2, 89, 177)
widget = node2.inputPorts[1].widget
widget.set("Atom", 0)
widget = node2.inputPorts[2].widget
widget.set("", 0)
except:
print "WARNING: failed to restore node NodeSelector called Select Nodes in network masterNet"
print_exc()
node2 = None
try:
## saving node CPK ##
from MolKit.VisionInterface.MolKitNodes import AtomsAsCPK
node3 = AtomsAsCPK(constrkw={}, name='CPK', library=molkitlib)
masterNet.addNode(node3, 85, 250)
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()
from MolKit.VisionInterface.MolKitNodes import molkitlib
masterNet.getEditor().addLibraryInstance(molkitlib,
"MolKit.VisionInterface.MolKitNodes",
"molkitlib")
from DejaVu.VisionInterface.DejaVuNodes import vizlib
masterNet.getEditor().addLibraryInstance(vizlib,
"DejaVu.VisionInterface.DejaVuNodes",
"vizlib")
try:
## saving node Select MolFrag ##
from MolKit.VisionInterface.MolKitNodes import NodeSelector
Select_MolFrag_0 = NodeSelector(constrkw={},
name='Select MolFrag',
library=molkitlib)
masterNet.addNode(Select_MolFrag_0, 201, 156)
Select_MolFrag_0.inputPortByName['selectionString'].widget.set("CA",
run=False)
except:
print "WARNING: failed to restore NodeSelector named Select MolFrag in network masterNet"
print_exc()
Select_MolFrag_0 = None
try:
## saving node Extract Atom Property ##
from MolKit.VisionInterface.MolKitNodes import AtomsProperty
Extract_Atom_Property_1 = AtomsProperty(constrkw={},
name='Extract Atom Property',
library=molkitlib)
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()
