def reaction_bounds(model, rxnIds, media):
"""
Extract bounds for each reaction that are present in the SBML file.
Parameters:
model: SBML model
rxnIds: List of reaction IDs from the model
media: Media dictionary of compound IDs and other info. Value is None
if a media file was not given.
"""
# Generate list of external media compounds
if media:
mediaList = [m + "_e0" for m in media.keys()]
rbounds = []
for rIdx in rxnIds:
r = model.getReaction(rIdx)
rk = r.getKineticLaw()
# Check if this is an exchange reaction
# Need to make sure compound is present in media
if "EX" in rIdx and media and rIdx.split("EX_")[-1] not in mediaList:
lb = 0.0
else:
lb = float(rk.getParameter("LOWER_BOUND").getValue())
ub = float(rk.getParameter("UPPER_BOUND").getValue())
rbounds.append((lb, ub))
if verbose:
print "Number of reaction bounds: %d" % len(rbounds)
lp.col_bounds(rbounds)
def reaction_bounds(mdl, rctnids, rmedia):
"""
Extract bounds for each reaction that are present in the SBML file.
Parameters:
mdl: SBML model
rctnids: List of reaction IDs from the model
rmedia: Media dictionary of compound IDs and other info. Value is None
if a media file was not given.
"""
# Generate list of external media compounds
media_list = []
if rmedia:
media_list = [m + "_e0" for m in rmedia.keys()]
rbounds = []
for ridx in rctnids:
r = mdl.getReaction(ridx)
rk = r.getKineticLaw()
# Check if this is an exchange reaction
# Need to make sure compound is present in rmedia
if "EX" in ridx and rmedia and ridx.split("EX_")[-1] not in media_list:
lb = 0.0
else:
lb = float(rk.getParameter("LOWER_BOUND").getValue())
ub = float(rk.getParameter("UPPER_BOUND").getValue())
rbounds.append((lb, ub))
if verbose:
print(f"Number of reaction bounds: {len(rbounds)}")
lp.col_bounds(rbounds)
def test_solve(self):
"""Test the complete linear programing solution, using the
example from the documentation"""
mat = [
[ 1.0, 1.0, 1.0],
[10.0, 4.0, 5.0],
[ 2.0, 2.0, 6.0],
]
lp.load(mat)
lp.objective_coefficients([ 10.0, 6.0, 4.0 ])
lp.row_bounds([(None, 100.0), (None, 600.0), (None, 300.0)])
lp.col_bounds([(0, None), (0, None), (0, None)])
status, result = lp.solve()
r = "%0.3f" % result
self.assertEqual(r, "733.333")
self.assertEqual(status, 'opt')
def test_bound_cols(self):
"""Test adding tuples of boundary conditions for columns"""
mat = [
[1, 2, 3, 4],
[5, 6, 7, 8],
[9, 10, 11, 12]
]
lp.load(mat)
boundsc = []
# test that we don't have enough values
self.assertRaises(ValueError, lp.col_bounds, boundsc)
# a boundary of None should be infiniity!
boundsc = [(None, 1000), (1000, None), (1000, 1000), (None, None)]
lp.col_bounds(boundsc)
def test_primals(self):
"""Test getting the primals back as a list"""
mat = [
[ 1.0, 1.0, 1.0],
[10.0, 4.0, 5.0],
[ 2.0, 2.0, 6.0],
]
rh = ['a', 'b', 'c']
ch = ['x', 'y', 'z']
lp.load(mat, rh, ch)
lp.objective_coefficients([ 10.0, 6.0, 4.0 ])
lp.row_bounds([(None, 100.0), (None, 600.0), (None, 300.0)])
lp.col_bounds([(0, None), (0, None), (0, None)])
status, result = lp.solve()
col_pri = [33.333333333333336, 66.66666666666666, 0.0]
col_res = lp.col_primals()
self.assertEqual(col_pri, col_res)
def reaction_bounds(reactions, reactions_to_run, media, lower=-1000.0, mid=0.0, upper=1000.0, verbose=False):
"""
Set the bounds for each reaction. We set the reactions to run between
either lower/mid, mid/upper, or lower/upper depending on whether the
reaction runs <=, =>, or <=> respectively.
:param reactions: The dict of all reactions we know about
:type reactions: dict of metabolism.Reaction
:param reactions_to_run: The sorted list of reactions to run
:type reactions_to_run: set
:param media: The media compounds
:type media: set
:param lower: The default lower bound
:type lower: float
:param mid: The default mid value (typically 0)
:type mid: float
:param upper: The default upper bound
:type upper: float
:return: A dict of the reaction ID and the tuple of bounds
:rtype: dict
"""
rbvals = {}
media_uptake_secretion_count = 0
other_uptake_secretion_count = 0
for r in reactions_to_run:
# if we already know the bounds, eg from an SBML file
if r is not 'BIOMASS_EQN' and reactions[r].lower_bound is not None and reactions[r].upper_bound is not None:
rbvals[r] = (reactions[r].lower_bound, reactions[r].upper_bound)
continue
if r in reactions:
direction = reactions[r].direction
elif r == 'BIOMASS_EQN':
direction = '>'
else:
sys.stderr.write("Did not find {} in reactions\n".format(r))
direction = "="
# this is where we define whether our media has the components
if r != 'BIOMASS_EQN' and (reactions[r].is_uptake_secretion or reactions[r].is_transport):
in_media = False
override = False # if we have external compounds that are not in the media, we don't want to run this as a media reaction
for c in reactions[r].left_compounds:
if c.location == 'e':
if c in media:
in_media = True
else:
override = True
# in this case, we have some external compounds that we should not import.
# for example,
if override:
in_media = False
if in_media:
rbvals[r] = (lower, upper)
media_uptake_secretion_count += 1
else:
rbvals[r] = (0.0, upper)
other_uptake_secretion_count += 1
continue
if direction == "=":
# This is what I think it should be:
rbvals[r] = (lower, upper)
# rbvals[r] = (mid, upper)
elif direction == ">":
# This is what I think it should be:
rbvals[r] = (mid, upper)
# rbvals[r] = (lower, upper)
elif direction == "<":
# This is what I think it should be:
# rbvals[r] = (lower, mid)
rbvals[r] = (lower, upper)
else:
sys.stderr.write("DO NOT UNDERSTAND DIRECTION " + direction + " for " + r + "\n")
rbvals[r] = (mid, upper)
if verbose:
sys.stderr.write("In parsing the bounds we found {} media uptake ".format(media_uptake_secretion_count) +
"and secretion reactions and {} other u/s reactions\n".format(other_uptake_secretion_count))
rbounds = [rbvals[r] for r in reactions_to_run]
lp.col_bounds(rbounds)
return rbvals
def reaction_bounds(reactions,
reactions_to_run,
media,
lower=-1000.0,
mid=0.0,
upper=1000.0,
verbose=False):
"""
Set the bounds for each reaction. We set the reactions to run between
either lower/mid, mid/upper, or lower/upper depending on whether the
reaction runs <=, =>, or <=> respectively.
:param reactions: The dict of all reactions we know about
:type reactions: dict of metabolism.Reaction
:param reactions_to_run: The sorted list of reactions to run
:type reactions_to_run: set
:param media: The media compounds
:type media: set
:param lower: The default lower bound
:type lower: float
:param mid: The default mid value (typically 0)
:type mid: float
:param upper: The default upper bound
:type upper: float
:return: A dict of the reaction ID and the tuple of bounds
:rtype: dict
"""
rbvals = {}
media_uptake_secretion_count = 0
other_uptake_secretion_count = 0
for r in reactions_to_run:
# if we already know the bounds, eg from an SBML file
if r is not 'BIOMASS_EQN' and reactions[
r].lower_bound is not None and reactions[
r].upper_bound is not None:
rbvals[r] = (reactions[r].lower_bound, reactions[r].upper_bound)
continue
if r in reactions:
direction = reactions[r].direction
elif r == 'BIOMASS_EQN':
direction = '>'
else:
sys.stderr.write("Did not find {} in reactions\n".format(r))
direction = "="
# this is where we define whether our media has the components
if r != 'BIOMASS_EQN' and (reactions[r].is_uptake_secretion
or reactions[r].is_transport):
in_media = False
override = False # if we have external compounds that are not in the media, we don't want to run this as a media reaction
for c in reactions[r].left_compounds:
if c.location == 'e':
if c in media:
in_media = True
else:
override = True
# in this case, we have some external compounds that we should not import.
# for example,
if override:
in_media = False
if in_media:
rbvals[r] = (lower, upper)
media_uptake_secretion_count += 1
else:
rbvals[r] = (0.0, upper)
other_uptake_secretion_count += 1
continue
if direction == "=":
# This is what I think it should be:
rbvals[r] = (lower, upper)
# rbvals[r] = (mid, upper)
elif direction == ">":
# This is what I think it should be:
rbvals[r] = (mid, upper)
# rbvals[r] = (lower, upper)
elif direction == "<":
# This is what I think it should be:
# rbvals[r] = (lower, mid)
rbvals[r] = (lower, upper)
else:
sys.stderr.write("DO NOT UNDERSTAND DIRECTION " + direction +
" for " + r + "\n")
rbvals[r] = (mid, upper)
if verbose:
sys.stderr.write("In parsing the bounds we found {} media uptake ".
format(media_uptake_secretion_count) +
"and secretion reactions and {} other u/s reactions\n"
.format(other_uptake_secretion_count))
rbounds = [rbvals[r] for r in reactions_to_run]
lp.col_bounds(rbounds)
return rbvals
