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')
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')
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')
iplib.addNode(IPRunFunction, 'PRunFunc', 'Mapper')
iplib.addNode(FractalDemo, 'Fractal Demo', 'Demo')
'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:
UserLibBuild.addTypes(wslib, 'MolKit.VisionInterface.MolKitTypes')
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')
iplib.addNode(IPRunFunction, 'PRunFunc', 'Mapper')
iplib.addNode(FractalDemo, 'Fractal Demo', 'Demo')
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'
resultUrl = server.checkForCompletion(resultPage)
print ' COMPLETED'
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')
UserLibBuild.addTypes(pmvlib, 'Pmv.VisionInterface.PmvTypes')
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'
resultUrl = server.checkForCompletion(resultPage)
'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:
pass
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:
UserLibBuild.addTypes(wslib, 'MolKit.VisionInterface.MolKitTypes')
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=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(