コード例 #1
0
    def main( filename ):
        
        anEmlSupport = EmlSupport( filename )
        pathwayProxy = anEmlSupport.createPathwayProxy()

        print 'Jacobian matrix ='
        print getJacobianMatrix( pathwayProxy )
        print 'Jacobian matrix ='
        print getJacobianMatrix2( pathwayProxy )
コード例 #2
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ファイル: Jacobian.py プロジェクト: ecell/spatiocyte
    def main( filename ):
        
        anEmlSupport = EmlSupport( filename )
        pathwayProxy = anEmlSupport.createPathwayProxy()

        print 'Jacobian matrix ='
        print getJacobianMatrix( pathwayProxy )
        print 'Jacobian matrix ='
        print getJacobianMatrix2( pathwayProxy )
コード例 #3
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ファイル: emlsupport.py プロジェクト: t10929jy/Webbs
    def main( aFileName ):
        
        anEmlSupport = EmlSupport( aFileName )

        print anEmlSupport.getAllEntityList( 'System', '/' )
        print anEmlSupport.getVariableList()
        print anEmlSupport.getProcessList()
コード例 #4
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    def main( filename ):

        anEmlSupport = EmlSupport( filename )
        pathwayProxy = anEmlSupport.createPathwayProxy()

        print 'process list ='
        print pathwayProxy.getProcessList()
        print 'related variable list ='
        print pathwayProxy.getVariableList()
        print 'incident matrix ='
        print pathwayProxy.getIncidentMatrix()
        print 'stoichiometry matrix ='
        print pathwayProxy.getStoichiometryMatrix()
        print 'reversibility list ='
        print pathwayProxy.getReversibilityList()
コード例 #5
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ファイル: PathwayProxy.py プロジェクト: ecell/ecell3
    def main( filename ):

        anEmlSupport = EmlSupport( filename )
        pathwayProxy = anEmlSupport.createPathwayProxy()

        print 'process list ='
        print pathwayProxy.getProcessList()
        print 'related variable list ='
        print pathwayProxy.getVariableList()
        print 'incident matrix ='
        print pathwayProxy.getIncidentMatrix()
        print 'stoichiometry matrix ='
        print pathwayProxy.getStoichiometryMatrix()
        print 'reversibility list ='
        print pathwayProxy.getReversibilityList()
コード例 #6
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    def main(fileName):

        anEmlSupport = EmlSupport(fileName)

        print 'system fullID list ='
        print anEmlSupport.getAllEntityList('System', '/')
        print 'variable fullID list ='
        print anEmlSupport.getVariableList()
        print 'process fullID list ='
        print anEmlSupport.getProcessList()
コード例 #7
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    def main(filename):

        anEmlSupport = EmlSupport(filename)
        pathwayProxy = anEmlSupport.createPathwayProxy()

        stoichiometryMatrix = pathwayProxy.getStoichiometryMatrix()

        # print pathwayProxy.getProcessList()
        # print pathwayProxy.getVariableList()

        ##         stoichiometryMatrix = array( [ [ 1., 0., 0., 0., 2. ], [ 0., 0., 1.0, 0., 1. ], [ 1.0, 0.0, 1.0, 0.0, 3.0 ], [ -2.0, 0.0, -2.0, 0.0, -6.0 ] ] )
        ##         stoichiometryMatrix = array( [ [ 1., 2., 3., 4. ], [ 1., 1., 1., 1. ], [ 2., 3., 4., 5. ] ] )
        ##         stoichiometryMatrix = array( [ [ 1., 2., 3. ], [ 0., 2., 10. ], [ 2., 3., 4. ] ] )

        print 'input matrix = '
        print stoichiometryMatrix

        (linkMatrix, kernelMatrix,
         independentList) = generateFullRankMatrix(stoichiometryMatrix)
        reducedMatrix = numpy.take(stoichiometryMatrix, independentList, 0)

        print 'link matrix = '
        print linkMatrix
        print 'kernel matrix = '
        print kernelMatrix
        print 'reduced matrix = '
        print reducedMatrix

        # print 'reconstructed input matrix = '
        # print numpy.dot( linkMatrix, reducedMatrix )
        # print 'null space = '
        # print numpy.dot( stoichiometryMatrix, kernelMatrix )

        reversibilityList = pathwayProxy.getReversibilityList()

        ##         stoichiometryMatrix = numpy.transpose( array( [ [ 0, 0, 1, 0, 0 ], [ 0, -1, 0, 2, 0 ], [ -1, 0, 0, 0, 1 ], [ -2, 0, 2, 1, -1 ], [ 0, 0, 0, -1, 0 ], [ 1, 0, 0, 0, 0 ], [ 0, 1, -1, 0, 0 ], [ 0, -1, 1, 0, 0 ], [ 0, 0, 0, 0, -1 ] ], float ) )
        ##         reversibilityList = [ 1, 1, 1, 1, 0, 0, 0, 0, 0 ]

        print 'input list ='
        print reversibilityList

        print 'elementary flux mode list ='
        print generateElementaryFluxMode(stoichiometryMatrix,
                                         reversibilityList)
コード例 #8
0
ファイル: ControlCoefficient.py プロジェクト: ktnyt/ecell3
    def main( filename ):
        
        anEmlSupport = EmlSupport( filename )
        pathwayProxy = anEmlSupport.createPathwayProxy()

        ( unscaledCCCMatrix, unscaledFCCMatrix ) = calculateControlCoefficient( pathwayProxy )

        print 'unscaled concentration control coefficients ='
        print unscaledCCCMatrix
        print 'unscaled flux control coefficients ='
        print unscaledFCCMatrix

        ( scaledCCCMatrix, scaledFCCMatrix ) = scaleControlCoefficient( pathwayProxy, unscaledCCCMatrix, unscaledFCCMatrix )
        # ( scaledCCCMatrix, scaledFCCMatrix ) = calculateControlCoefficient( pathwayProxy, 1 )

        print 'scaled concentration control coefficients ='
        print scaledCCCMatrix
        print 'scaled flux control coefficients ='
        print scaledFCCMatrix
コード例 #9
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ファイル: ControlCoefficient.py プロジェクト: ecell/ecell3
    def main( filename ):
        
        anEmlSupport = EmlSupport( filename )
        pathwayProxy = anEmlSupport.createPathwayProxy()

        ( unscaledCCCMatrix, unscaledFCCMatrix ) = calculateControlCoefficient( pathwayProxy )

        print 'unscaled concentration control coefficients ='
        print unscaledCCCMatrix
        print 'unscaled flux control coefficients ='
        print unscaledFCCMatrix

        ( scaledCCCMatrix, scaledFCCMatrix ) = scaleControlCoefficient( pathwayProxy, unscaledCCCMatrix, unscaledFCCMatrix )
        # ( scaledCCCMatrix, scaledFCCMatrix ) = calculateControlCoefficient( pathwayProxy, 1 )

        print 'scaled concentration control coefficients ='
        print scaledCCCMatrix
        print 'scaled flux control coefficients ='
        print scaledFCCMatrix
コード例 #10
0
ファイル: Structure.py プロジェクト: ecell/spatiocyte
    def main( filename ):
        
        anEmlSupport = EmlSupport( filename )
        pathwayProxy = anEmlSupport.createPathwayProxy()
        
        stoichiometryMatrix = pathwayProxy.getStoichiometryMatrix()

        # print pathwayProxy.getProcessList()        
        # print pathwayProxy.getVariableList()

##         stoichiometryMatrix = array( [ [ 1., 0., 0., 0., 2. ], [ 0., 0., 1.0, 0., 1. ], [ 1.0, 0.0, 1.0, 0.0, 3.0 ], [ -2.0, 0.0, -2.0, 0.0, -6.0 ] ] )
##         stoichiometryMatrix = array( [ [ 1., 2., 3., 4. ], [ 1., 1., 1., 1. ], [ 2., 3., 4., 5. ] ] )
##         stoichiometryMatrix = array( [ [ 1., 2., 3. ], [ 0., 2., 10. ], [ 2., 3., 4. ] ] )

        print 'input matrix = '
        print stoichiometryMatrix

        ( linkMatrix, kernelMatrix, independentList ) = generateFullRankMatrix( stoichiometryMatrix )
        reducedMatrix = numpy.take( stoichiometryMatrix, independentList, 0 )

        print 'link matrix = '
        print linkMatrix
        print 'kernel matrix = '
        print kernelMatrix
        print 'reduced matrix = '
        print reducedMatrix

        # print 'reconstructed input matrix = '
        # print numpy.dot( linkMatrix, reducedMatrix )
        # print 'null space = '
        # print numpy.dot( stoichiometryMatrix, kernelMatrix )

        reversibilityList = pathwayProxy.getReversibilityList()
        
##         stoichiometryMatrix = numpy.transpose( array( [ [ 0, 0, 1, 0, 0 ], [ 0, -1, 0, 2, 0 ], [ -1, 0, 0, 0, 1 ], [ -2, 0, 2, 1, -1 ], [ 0, 0, 0, -1, 0 ], [ 1, 0, 0, 0, 0 ], [ 0, 1, -1, 0, 0 ], [ 0, -1, 1, 0, 0 ], [ 0, 0, 0, 0, -1 ] ], float ) )
##         reversibilityList = [ 1, 1, 1, 1, 0, 0, 0, 0, 0 ]

        print 'input list ='
        print reversibilityList

        print 'elementary flux mode list ='
        print generateElementaryFluxMode( stoichiometryMatrix, reversibilityList )
コード例 #11
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ファイル: Elasticity.py プロジェクト: ecell/ecell3
    def main(fileName, fullPN=None):

        anEmlSupport = EmlSupport(fileName)
        pathwayProxy = anEmlSupport.createPathwayProxy()

        if fullPN != None:

            print "elasticity array for '%s' =" % (fullPN)
            print getElasticityArray(pathwayProxy, fullPN)
            print "acculate elasticity array for '%s' =" % (fullPN)
            print getAcculateElasticityArray(pathwayProxy, fullPN)
            print "scaled elasticity array for '%s' =" % (fullPN)
            print getScaledElasticity(pathwayProxy, fullPN)

        print "epsilon elasticity matrix ="
        print getEpsilonElasticityMatrix(pathwayProxy)
        print "scaled epsilon elasticity matrix ="
        print getScaledEpsilonElasticityMatrix(pathwayProxy)
        print "epsilon elasticity matrix ="
        print getEpsilonElasticityMatrix2(pathwayProxy)
コード例 #12
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ファイル: Elasticity.py プロジェクト: ktnyt/ecell3
    def main( fileName, fullPN=None ):
        
        anEmlSupport = EmlSupport( fileName )
        pathwayProxy = anEmlSupport.createPathwayProxy()

        if fullPN != None:

            print 'elasticity array for \'%s\' =' % ( fullPN )
            print getElasticityArray( pathwayProxy, fullPN )
            print 'acculate elasticity array for \'%s\' =' % ( fullPN )
            print getAcculateElasticityArray( pathwayProxy, fullPN )
            print 'scaled elasticity array for \'%s\' =' % ( fullPN )
            print getScaledElasticity( pathwayProxy, fullPN )

        print 'epsilon elasticity matrix ='
        print getEpsilonElasticityMatrix( pathwayProxy )
        print 'scaled epsilon elasticity matrix ='
        print getScaledEpsilonElasticityMatrix( pathwayProxy )
        print 'epsilon elasticity matrix ='
        print getEpsilonElasticityMatrix2( pathwayProxy )
コード例 #13
0
ファイル: emlsupport.py プロジェクト: ecell/ecell3
    def main( fileName ):
        
        anEmlSupport = EmlSupport( fileName )

        print 'system fullID list ='
        print anEmlSupport.getAllEntityList( 'System', '/' )
        print 'variable fullID list ='
        print anEmlSupport.getVariableList()
        print 'process fullID list ='
        print anEmlSupport.getProcessList()