def main( filename ):
anEmlSupport = EmlSupport( filename )
pathwayProxy = anEmlSupport.createPathwayProxy()
print 'Jacobian matrix ='
print getJacobianMatrix( pathwayProxy )
print 'Jacobian matrix ='
print getJacobianMatrix2( pathwayProxy )
def main( filename ):
anEmlSupport = EmlSupport( filename )
pathwayProxy = anEmlSupport.createPathwayProxy()
print 'Jacobian matrix ='
print getJacobianMatrix( pathwayProxy )
print 'Jacobian matrix ='
print getJacobianMatrix2( pathwayProxy )
def main( aFileName ):
anEmlSupport = EmlSupport( aFileName )
print anEmlSupport.getAllEntityList( 'System', '/' )
print anEmlSupport.getVariableList()
print anEmlSupport.getProcessList()
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()
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()
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()
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)
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
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
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 )
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)
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 )
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()