t1 = numpy.identity(4)
t1[:3,3] = initialConf
negt1 = numpy.identity(4)
for i in range(len(initialConf)):
negt1[i,3] = initialConf[i] * -1
t2 = numpy.identity(4)
t2[:3,3] = [tx, ty, tz]
rot = numpy.identity(4)
r = numpy.array(rotations[ri])
r.shape = (3,3)
rot[0:3,0:3] = r
self.mat = numpy.dot(t2, numpy.dot(t1, numpy.dot(rot,negt1)))
geom = molecule.geomContainer.geoms['master']
geom.SetTransformation(self.mat, transpose=True)
self.outputData(score=score, RMSD=rmsd)
"""
self.setFunction(code)
from Vision.VPE import NodeLibrary
F2Docklib = NodeLibrary('F2Dock', '#663366')
F2Docklib.addNode(RotationFile, 'RotFile', 'Rotations')
F2Docklib.addNode(ReadLog, 'ReadLog', 'Input')
F2Docklib.addNode(BrowseLog, 'BrowseLog', 'Mapper')
def createLib_cb(self, event=None):
classname = self.libclassnametkvar.get()
if classname is None or len(classname)==0:
return
name = self.libnametkvar.get()
if name is None or len(name)==0:
return
libfilename = self.libfiletkvar.get()
if libfilename is None or len(libfilename) == 0:
return
if libfilename[-3:] != ".py":
libfilename = libfilename + ".py"
directory = self.libsGUI.get()
if directory is None or len(directory)==0 or directory==():
return
# libsGUI might return the data packed in a tuple
if type(directory) == types.TupleType:
directory = directory[0]
# build path by joining the directory with the parent path
path = os.path.join(self.editor.userLibsDirs[directory], directory)
# then add the file name
file = os.path.join(path, libfilename)
if os.path.exists(file):
from Dialog import Dialog
d = Dialog(None, {'title': 'File exisits',
'text':
'File "%s" already exists.'
' Do you want to overwrite it ?'%file,
'bitmap': 'warning',
'default': 1,
'strings': ('Yes',
'No')})
if d.num==1: # 'No'
return
from Vision.VPE import NodeLibrary
col = self.colorButton.cget('bg')
newlib = NodeLibrary(name, col, mode='readWrite')
newlib.varName = classname
# write the library header
f = open(file, 'w')
map( f.write, newlib.getHeader())
f.write("%s = NodeLibrary('%s', '%s', mode='readWrite')\n"%(
newlib.varName, name, col))
f.close()
# load the library from the file using same mechanism as saved network
from mglutil.util.packageFilePath import getObjectFromFile
newlib = getObjectFromFile( file, classname)
newlib.varName = classname
modName = directory + "." + libfilename[:-3]
modName = string.replace(modName, "/", ".")
newlib.modName = modName
# we need to __import__ to add this module to sys.modules
# This fixes a problem when trying to add nodes to this new lib before
# we restart and load the new library through 'loadLibrary'
__import__(modName)
self.editor.libraries[ newlib.name] = newlib
self.editor.showLibrary(newlib)
self.hide()
self.inputPortsDescr.append(datatype=None, name='data')
self.inputPortsDescr.append(datatype=None, name='mec')
self.outputPortsDescr.append(datatype=None, name='data')
code = """def doit(self, function, data, mec):
assert callable(function)
result = mec.map(function, data)
self.outputData(data=result)
"""
self.setFunction(code)
from Vision.VPE import NodeLibrary
iplib = NodeLibrary('IPython', 'grey75')
iplib.addNode(IPmec, 'MEC', 'Objects')
iplib.addNode(IPLocalMEC2, 'MEC2local', 'Objects')
iplib.addNode(IPLocalMEC3, 'MEC3local', 'Objects')
iplib.addNode(IPLocalMEC4, 'MEC4local', 'Objects')
iplib.addNode(IPLocalMEC5, 'MEC5local', 'Objects')
iplib.addNode(IPLocalMEC6, 'MEC6local', 'Objects')
iplib.addNode(IPLocalMEC7, 'MEC7local', 'Objects')
iplib.addNode(IPLocalMEC8, 'MEC8local', 'Objects')
iplib.addNode(IPPull, 'Pull', 'Communication')
iplib.addNode(IPPush, 'Push', 'Communication')
#iplib.addNode(IPPushFunction, 'Push Func', 'Communication')
iplib.addNode(IPScatter, 'Scatter', 'Communication')
iplib.addNode(IPGather, 'Gather', 'Communication')
iplib.addNode(IPmap, 'PMap', 'Mapper')
self.inputPortsDescr.append(datatype=None, name='data')
self.inputPortsDescr.append(datatype=None, name='mec')
self.outputPortsDescr.append(datatype=None, name='data')
code = """def doit(self, function, data, mec):
assert callable(function)
result = mec.map(function, data)
self.outputData(data=result)
"""
self.setFunction(code)
from Vision.VPE import NodeLibrary
iplib = NodeLibrary('IPython', 'grey75')
iplib.addNode(IPmec, 'MEC', 'Objects')
iplib.addNode(IPLocalMEC2, 'MEC2local', 'Objects')
iplib.addNode(IPLocalMEC3, 'MEC3local', 'Objects')
iplib.addNode(IPLocalMEC4, 'MEC4local', 'Objects')
iplib.addNode(IPLocalMEC5, 'MEC5local', 'Objects')
iplib.addNode(IPLocalMEC6, 'MEC6local', 'Objects')
iplib.addNode(IPLocalMEC7, 'MEC7local', 'Objects')
iplib.addNode(IPLocalMEC8, 'MEC8local', 'Objects')
iplib.addNode(IPPull, 'Pull', 'Communication')
iplib.addNode(IPPush, 'Push', 'Communication')
#iplib.addNode(IPPushFunction, 'Push Func', 'Communication')
iplib.addNode(IPScatter, 'Scatter', 'Communication')
iplib.addNode(IPGather, 'Gather', 'Communication')
iplib.addNode(IPmap, 'PMap', 'Mapper')
t1 = numpy.identity(4)
t1[:3,3] = initialConf
negt1 = numpy.identity(4)
for i in range(len(initialConf)):
negt1[i,3] = initialConf[i] * -1
t2 = numpy.identity(4)
t2[:3,3] = [tx, ty, tz]
rot = numpy.identity(4)
r = numpy.array(rotations[ri])
r.shape = (3,3)
rot[0:3,0:3] = r
self.mat = numpy.dot(t2, numpy.dot(t1, numpy.dot(rot,negt1)))
geom = molecule.geomContainer.geoms['master']
geom.SetTransformation(self.mat, transpose=True)
self.outputData(score=score, RMSD=rmsd)
"""
self.setFunction(code)
from Vision.VPE import NodeLibrary
F2Docklib = NodeLibrary('F2Dock', '#663366')
F2Docklib.addNode(RotationFile, 'RotFile', 'Rotations')
F2Docklib.addNode(ReadLog, 'ReadLog', 'Input')
F2Docklib.addNode(BrowseLog, 'BrowseLog', 'Mapper')
def createLib_cb(self, event=None):
classname = self.libclassnametkvar.get()
if classname is None or len(classname) == 0:
return
name = self.libnametkvar.get()
if name is None or len(name) == 0:
return
libfilename = self.libfiletkvar.get()
if libfilename is None or len(libfilename) == 0:
return
if libfilename[-3:] != ".py":
libfilename = libfilename + ".py"
directory = self.libsGUI.get()
if directory is None or len(directory) == 0 or directory == ():
return
# libsGUI might return the data packed in a tuple
if type(directory) == types.TupleType:
directory = directory[0]
# build path by joining the directory with the parent path
path = os.path.join(self.editor.userLibsDirs[directory], directory)
# then add the file name
file = os.path.join(path, libfilename)
if os.path.exists(file):
from Dialog import Dialog
d = Dialog(
None, {
'title':
'File exisits',
'text':
'File "%s" already exists.'
' Do you want to overwrite it ?' % file,
'bitmap':
'warning',
'default':
1,
'strings': ('Yes', 'No')
})
if d.num == 1: # 'No'
return
from Vision.VPE import NodeLibrary
col = self.colorButton.cget('bg')
newlib = NodeLibrary(name, col, mode='readWrite')
newlib.varName = classname
# write the library header
f = open(file, 'w')
map(f.write, newlib.getHeader())
f.write("%s = NodeLibrary('%s', '%s', mode='readWrite')\n" %
(newlib.varName, name, col))
f.close()
# load the library from the file using same mechanism as saved network
from mglutil.util.packageFilePath import getObjectFromFile
newlib = getObjectFromFile(file, classname)
newlib.varName = classname
modName = directory + "." + libfilename[:-3]
modName = string.replace(modName, "/", ".")
newlib.modName = modName
# we need to __import__ to add this module to sys.modules
# This fixes a problem when trying to add nodes to this new lib before
# we restart and load the new library through 'loadLibrary'
__import__(modName)
self.editor.libraries[newlib.name] = newlib
self.editor.showLibrary(newlib)
self.hide()
'labelCfg': {
'text': 'URL'
},
}
self.inputPortsDescr.append({'name': 'url', 'datatype': 'string'})
code = """def doit(self, url):
url = self.getInputPortByName('url').data
webbrowser.open(url)
"""
if code:
self.setFunction(code)
from Vision.VPE import NodeLibrary
wslib = NodeLibrary('Web Services', '#d7fdf9')
wslib.addNode(GetWSNode, 'Load WS', 'Generic')
wslib.addNode(DownloadNode, 'Download', 'Generic')
wslib.addNode(DownloadSaveDirNode, 'DownloadSaveDir', 'Generic')
wslib.addNode(DownloadToFileNode, 'DownloadToFile', 'Generic')
wslib.addNode(GetMainURLNode, 'GetMainURL', 'Generic')
wslib.addNode(GetMainURLFromListNode, 'GetMainURLFromList', 'Generic')
wslib.addNode(GetURLFromListNode, 'GetURLFromList', 'Generic')
wslib.addNode(IsURLNode, 'IsURL', 'Generic')
wslib.addNode(ReplaceURLNode, 'ReplaceURL', 'Generic')
wslib.addNode(WebBrowserNode, 'WebBrowser', 'Generic')
#addOpalServerAsCategory('http://ws.nbcr.net/opal2')
#addOpalServerAsCategory('http://krusty.ucsd.edu:8081/opal2')
#addOpalServerAsCategory('http://kryptonite.ucsd.edu/opal2')
try:
else:
obj = Pmv.Mols.get(molecule)
if obj:
self.outputData(molecule=obj)
"""
self.setFunction(code)
def beforeAddingToNetwork(self, net):
# loading library molkitlib
importMolKitLib(net)
from Vision.VPE import NodeLibrary
pmvlib = NodeLibrary('Pmv', '#7A7AFF')
pmvlib.addNode(PmvChooseCommand, 'Choose Cmd', 'Filter',)
pmvlib.addNode(PmvSetCPKRadii, 'Set CPK radii', 'Mapper',)
pmvlib.addNode(PmvSetInstanceMatrices, 'Set Instances', 'Mapper',)
pmvlib.addNode(PmvRunCommand, 'Run Command', 'Output',)
pmvlib.addNode(PmvGetSelection, 'Get Selection', 'Input',)
pmvlib.addNode(PmvMoleculeChooser, 'Choose Molecule', 'Input',)
if msmsFound==1:
pmvlib.addNode(GetMSMSGeom, 'Get MSMS Geom', 'Filter')
#AD4FlexibleDockingPreparation
#prepare_ligand_dict
#ReceptorWriter
#AD4ReceptorWriter
#LigandPreparation
#AD4LigandPreparation
#AutoDock3_AtomTyper
#DockingParameters
#DockingParameterFileMaker
#GridParameters
#GridParameterFileMaker
#??Docking??
from Vision.VPE import NodeLibrary
adtlib = NodeLibrary('adtlib', '#4444FF')
#macros from other files in this directory
#from AutoDockTools.VisionInterface.PrepareAD4Molecule import PrepareAD4Molecule
#adtlib.addNode(PrepareAD4Molecule, 'Prepare AD4Molecule', 'Macro')
#from AutoDockTools.VisionInterface.AD4Ligands import AD4Ligands
#adtlib.addNode(AD4Ligands, 'Prepare AD4 Ligands', 'Macro')
#from AutoDockTools.VisionInterface.Prepare_AD4_Ligands import Prepare_AD4_Ligands
#adtlib.addNode(Prepare_AD4_Ligands, 'Prepare AD4 Ligands', 'Macro')
###from AutoDockTools.VisionInterface.PrepareAD3Ligand import PrepareAD3Ligand
###adtlib.addNode(PrepareAD3Ligand, 'Prepare AD3 Ligand', 'Macro')
###from AutoDockTools.VisionInterface.PrepareAD3Receptor import PrepareAD3Receptor
###adtlib.addNode(PrepareAD3Receptor, 'Prepare AD3Receptor', 'Macro')
###from AutoDockTools.VisionInterface.AD3Gpf import AD3Gpf
###adtlib.addNode(AD3Gpf, 'Prepare AD3 Gpf ', 'Macro')
###from AutoDockTools.VisionInterface.AD3Dpf import AD3Dpf
# this method is defined outside this node
buildCGIWidget(node, form)
self.editor.currentNetwork.addNode(node, posX, posY)
#node.addOutputPort(name='html', datatype='list')
node.CGIFormObj = form
node.CGIFormObj.setURL(url)
self.outputData(forms=forms)\n"""
self.setFunction(code)
from Vision.VPE import NodeLibrary
weblib = NodeLibrary('Web', '#bb4040')
weblib.addNode(ConsurfClientNode, 'Consurf', 'Filter')
#weblib.addNode(WebBrowser, 'Web Browser', 'Output') # not supported any longr
weblib.addNode(GetCGIForms, 'Get CGI Forms', 'Filter')
#weblib.addNode(CGIFormNode, 'CGI Form Node', 'Output')
if __name__ == '__main__':
print 'Creating client Object'
server = ConsurfServer()
print 'submitting job'
server.setArguments(pdb_ID='2plv', chain='1', ALGORITHM="Likelihood")
result = server.run()
print 'get temporary result page'
resultPage = server.getResultPage(result)
print ' wait for completion'
from os import sep, path
from Vision.VPE import NodeLibrary
from Vision.UserLibBuild import userLibBuild, addDirToSysPath, addTypes
dependents = {
} # {'scipy':'0.6.0',} the numbers indicate the highest tested version of the needed packages
libraryColor = '#4444FF'
addDirToSysPath(path.dirname(__file__) + sep + '..')
fileSplit = __file__.split(sep)
if fileSplit[-1] == '__init__.pyc' or fileSplit[-1] == '__init__.py':
libInstanceName = fileSplit[-2]
else:
libInstanceName = path.splitext(fileSplit[-1])[0]
try:
from Vision import ed
except:
ed = None
if ed is not None and ed.libraries.has_key(libInstanceName):
locals()[libInstanceName] = ed.libraries[libInstanceName]
else:
locals()[libInstanceName] = NodeLibrary(libInstanceName,
libraryColor,
mode='readWrite')
success = userLibBuild(eval(libInstanceName), __file__, dependents=dependents)
if success is False:
locals().pop(libInstanceName)
elif path.isfile(path.dirname(__file__) + sep + 'libTypes.py'):
addTypes(locals()[libInstanceName], libInstanceName + '.libTypes')
# this method is defined outside this node
buildCGIWidget(node, form)
self.editor.currentNetwork.addNode(node, posX, posY)
#node.addOutputPort(name='html', datatype='list')
node.CGIFormObj = form
node.CGIFormObj.setURL(url)
self.outputData(forms=forms)\n"""
self.setFunction(code)
from Vision.VPE import NodeLibrary
weblib = NodeLibrary('Web', '#bb4040')
weblib.addNode(ConsurfClientNode, 'Consurf', 'Filter')
#weblib.addNode(WebBrowser, 'Web Browser', 'Output') # not supported any longr
weblib.addNode(GetCGIForms, 'Get CGI Forms', 'Filter')
#weblib.addNode(CGIFormNode, 'CGI Form Node', 'Output')
if __name__ == '__main__':
print 'Creating client Object'
server = ConsurfServer()
print 'submitting job'
server.setArguments( pdb_ID='2plv', chain='1', ALGORITHM="Likelihood")
result = server.run()
print 'get temporary result page'
resultPage = server.getResultPage(result)
},
'master': 'node',
'widgetGridCfg': {
'labelSide': 'left'
}, #, 'column': 1, 'row': 1},
'labelCfg': {
'text': 'MPEG player pgm'
},
'class': 'NEEntryWithFileBrowser'
}
except ImportError:
print 'Failed to import pymedia.video.vcodec'
from Vision.VPE import NodeLibrary
imagelib = NodeLibrary('Imaging', '#995699')
imagelib.addNode(ImageFromArray, 'Image from array', 'Input')
imagelib.addNode(ReadImage, 'Read Image', 'Input')
imagelib.addNode(GetFrontBuffer, 'Grab Image', 'Input')
#imagelib.addNode(GetZBuffer, 'RecordMPEGmovie', 'Input')
imagelib.addNode(ShowImage, 'Show Image', 'Output')
imagelib.addNode(ImageStat, 'Image Stat', 'Output')
imagelib.addNode(SaveImage, 'Save Image', 'Output')
try:
import pymedia.video.vcodec as vcodec
imagelib.addNode(RecordMPEGmovie, 'Record MPEG movie', 'Output')
imagelib.addNode(PlayMPEG, 'Play MPEG', 'Output')
except ImportError:
apply( NetworkNode.__init__, (self,), kw )
self.widgetDescr['url'] = {'class':'NEEntry', 'master':'node',
'labelCfg':{'text':'URL'},
}
self.inputPortsDescr.append( {'name':'url', 'datatype':'string'} )
code = """def doit(self, url):
url = self.getInputPortByName('url').data
webbrowser.open(url)
"""
if code:
self.setFunction(code)
from Vision.VPE import NodeLibrary
wslib = NodeLibrary('Web Services', '#d7fdf9')
wslib.addNode(GetWSNode, 'Load WS', 'Generic')
wslib.addNode(DownloadNode, 'Download', 'Generic')
wslib.addNode(DownloadSaveDirNode, 'DownloadSaveDir', 'Generic')
wslib.addNode(DownloadToFileNode, 'DownloadToFile', 'Generic')
wslib.addNode(GetMainURLNode, 'GetMainURL', 'Generic')
wslib.addNode(GetMainURLFromListNode, 'GetMainURLFromList', 'Generic')
wslib.addNode(GetURLFromListNode, 'GetURLFromList', 'Generic')
wslib.addNode(IsURLNode, 'IsURL', 'Generic')
wslib.addNode(ReplaceURLNode, 'ReplaceURL', 'Generic')
wslib.addNode(WebBrowserNode, 'WebBrowser', 'Generic')
#addOpalServerAsCategory('http://ws.nbcr.net/opal2')
#addOpalServerAsCategory('http://krusty.ucsd.edu:8081/opal2')
#addOpalServerAsCategory('http://kryptonite.ucsd.edu/opal2')
try:
c[p] = col
i = i + 1
self.outputData(out1=c)\n"""
if code: self.setFunction(code)
self.inputPortsDescr.append({'name': 'in1', 'datatype': 'None'})
self.outputPortsDescr.append({'name': 'out1', 'datatype': 'None'})
class DefaultIndices(NetworkNode):
def __init__(self, name='default indices', **kw):
apply(NetworkNode.__init__, (self, ), kw)
code = """def doit(self, in1):
self.outputData(out1=[range(in1[0])])\n"""
if code: self.setFunction(code)
self.inputPortsDescr.append({'name': 'length', 'datatype': 'int'})
self.outputPortsDescr.append({'name': 'out1', 'datatype': 'None'})
from Vision.VPE import NodeLibrary
flexlib = NodeLibrary('Flex', '#AA66AA')
flexlib.addNode(DistanceMatrix, 'DM', 'Input')
flexlib.addNode(DDM, 'DDM', 'Input')
flexlib.addNode(Cluster, 'Cluster', 'Input')
flexlib.addNode(ColorCluster, 'Color Cluster', 'Input')
flexlib.addNode(DefaultIndices, 'indices', 'Input')
self.outputData(molecule=None)
else:
obj = Pmv.Mols.get(molecule)
if obj:
self.outputData(molecule=obj)
"""
self.setFunction(code)
def beforeAddingToNetwork(self, net):
# loading library molkitlib
importMolKitLib(net)
from Vision.VPE import NodeLibrary
pmvlib = NodeLibrary('Pmv', '#7A7AFF')
pmvlib.addNode(
PmvChooseCommand,
'Choose Cmd',
'Filter',
)
pmvlib.addNode(
PmvSetCPKRadii,
'Set CPK radii',
'Mapper',
)
pmvlib.addNode(
PmvSetInstanceMatrices,
'Set Instances',