Python NodeLibrary.addNode Examples, Vision.VPE.NodeLibrary.addNode Python Examples

Example #1

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File: F2DockNodes.py Project: MolecularFlipbook/FlipbookApp

    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')

Example #2

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    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')

Example #3

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File: IPythonNodes.py Project: lisarosalina/App

        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')

Example #4

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                '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')

Example #5

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File: IPythonNodes.py Project: MolecularFlipbook/FlipbookApp

        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')

Example #6

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            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'

Example #7

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File: PmvNodes.py Project: jackygrahamez/DrugDiscovery-Home

        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')

Example #8

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File: WebNodes.py Project: MolecularFlipbook/FlipbookApp

            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)

Example #9

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                '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

Example #10

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File: WSNodes.py Project: MolecularFlipbook/FlipbookApp

        
        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')

Example #11

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	    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')

Example #12

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File: PmvNodes.py Project: lisarosalina/App

            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(