def get_kernel_GJE(self, reactions=None):
""" Return the kernel K from GJE routine.
Notes
-----
The steady state solution is given by ``reactions = K * indep_variables``
where ``indep_variables = reactions[-K.shape[1]:]``
Parameters
----------
reactions : list
When specified then the reaction list defines the order of flux rows.
Otherwise the rows are order by the sparsity.
Returns
-------
fluxes, indep_fluxes, kernel : list, list, Matrix
"""
from sympycore.matrices.linalg import get_rc_map
self.compute_kernel_GJE(use_cache=True)
gj, row_operations, leading_rows, leading_cols, zero_rows = self.compute_kernel_GJE_data
if reactions is None:
reactions = self.get_sorted_reactions()
start = time.time()
kernel = Matrix(len(reactions), len(reactions) - len(leading_cols))
indep_vars = [r for r in reactions if r in self.independent_variables]
n = len(indep_vars)
rows = get_rc_map(gj.data)
def indep_index(r):
try:
return indep_vars.index(r)
except ValueError:
pass
indep_indices = []
indices = []
for r in self.reactions:
indices.append(reactions.index(r))
indep_indices.append(indep_index(r))
for i0, j0 in zip(leading_rows, leading_cols):
i = indices[j0]
for j1 in rows[i0]:
if j1 != j0:
j = indep_indices[j1]
kernel[i, j] = -gj.data[(i0, j1)]
for j0 in range(len(self.reactions)):
if j0 not in leading_cols:
i = indices[j0]
j = indep_indices[j0]
kernel[i, j] = 1
end = time.time()
self.get_kernel_GJE_elapsed = end - start
return reactions, indep_vars, kernel
def get_kernel_GJE(self, reactions=None):
""" Return the kernel K from GJE routine.
Notes
-----
The steady state solution is given by ``reactions = K * indep_variables``
where ``indep_variables = reactions[-K.shape[1]:]``
Parameters
----------
reactions : list
When specified then the reaction list defines the order of flux rows.
Otherwise the rows are order by the sparsity.
Returns
-------
fluxes, indep_fluxes, kernel : list, list, Matrix
"""
from sympycore.matrices.linalg import get_rc_map
self.compute_kernel_GJE(use_cache=True)
gj, row_operations, leading_rows, leading_cols, zero_rows = self.compute_kernel_GJE_data
if reactions is None:
reactions = self.get_sorted_reactions()
start = time.time ()
kernel = Matrix(len(reactions), len(reactions)-len(leading_cols))
indep_vars = [r for r in reactions if r in self.independent_variables]
n = len (indep_vars)
rows = get_rc_map(gj.data)
def indep_index (r):
try: return indep_vars.index (r)
except ValueError: pass
indep_indices = []
indices = []
for r in self.reactions:
indices.append(reactions.index(r))
indep_indices.append(indep_index (r))
for i0,j0 in zip(leading_rows, leading_cols):
i = indices[j0]
for j1 in rows[i0]:
if j1!=j0:
j = indep_indices[j1]
kernel[i,j] = -gj.data[(i0,j1)]
for j0 in range (len (self.reactions)):
if j0 not in leading_cols:
i = indices[j0]
j = indep_indices[j0]
kernel[i,j] = 1
end = time.time()
self.get_kernel_GJE_elapsed = end-start
return reactions, indep_vars, kernel
def get_sorted_reactions(self):
from sympycore.matrices.linalg import get_rc_map
self.compute_kernel_GJE(use_cache=True)
start = time.time ()
gj, row_operations, leading_rows, leading_cols, zero_rows = self.compute_kernel_GJE_data
l = []
rows = get_rc_map(gj.data)
for i0,j0 in zip (leading_rows, leading_cols):
row = rows[i0]
row.remove (j0)
if row:
l.append ((len(row),-min(row), self.reactions[j0]))
else:
l.append ((len(row),0, self.reactions[j0]))
reactions = [s for i,i1,s in sorted(l, reverse=True)]
reactions += [s for s in self.reactions if s not in reactions]
end = time.time ()
self.get_sorted_reactions_elapsed = end-start
return reactions
def get_sorted_reactions(self):
from sympycore.matrices.linalg import get_rc_map
self.compute_kernel_GJE(use_cache=True)
start = time.time()
gj, row_operations, leading_rows, leading_cols, zero_rows = self.compute_kernel_GJE_data
l = []
rows = get_rc_map(gj.data)
for i0, j0 in zip(leading_rows, leading_cols):
row = rows[i0]
row.remove(j0)
if row:
l.append((len(row), -min(row), self.reactions[j0]))
else:
l.append((len(row), 0, self.reactions[j0]))
reactions = [s for i, i1, s in sorted(l, reverse=True)]
reactions += [s for s in self.reactions if s not in reactions]
end = time.time()
self.get_sorted_reactions_elapsed = end - start
return reactions