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def Stoichiometry_Init(self,nmatrix):
"""
Stoichiometry_Init(nmatrix,load=0)
Initialize the model stoichiometry. Given a stoichiometric matrix N, this method will return an instantiated PyscesStoich instance and status flag.
and test it's correctness. The status flag indicates 0 = reanalyse stoichiometry or
1 = complete structural analysis preloaded.
Arguments:
nmatrix: The input stoichiometric matrix, N
load [default=0]: try to load a saved stoichiometry (1)
"""
#print 'Instantiating new stoichiometry ...'
stc = PyscesStoich.Stoich(nmatrix)
status = 0
return stc,status
this distribution for specifics.
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
Brett G. Olivier
"""
from __future__ import division, print_function
from __future__ import absolute_import
from __future__ import unicode_literals
from .version import __version__
# Structural Analysis module
from pysces.PyscesStoich import Stoich
from .PyscesCore2 import StructMatrix
class PyscesEnhancedStoich(Stoich):
"""PySCeS stoichiometry class for use with core2"""
N = None
Nr = None
K = None
K0 = None
L = None
L0 = None
Gamma = None
def __init__(self, core):
Stoich.__init__(self, core.stoichiometric_matrix.array)
self.species = core.stoichiometric_matrix.row
self.reactions = core.stoichiometric_matrix.col
def getNullSpaces(self):
self.AnalyseK()
print('\nLzeromatrix:')
sm,bg = self.MatrixValueCompare(self.lzeromatrix)
print('Smallest value: ', abs(sm))
print('Largest value: ', abs(bg))
print('Ratio abs(bg/sm):', abs(bg/sm))
print('\nPlease note: I\'ve found that for larger models the rank calculated by SVD in this test can become unstable and give incorrect results.')
print(' ')
if resultback:
return u,s,vh
if __psyco_active__:
psyco.bind(MathArrayFunc)
psyco.bind(Stoich)
def __init__(self, core):
Stoich.__init__(self, core.stoichiometric_matrix.array)
self.species = core.stoichiometric_matrix.row
self.reactions = core.stoichiometric_matrix.col