Skip to content

Thermodynamic calculation corrections #559

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Paulocracy merged 1 commit into from
Apr 2, 2026
Merged

Thermodynamic calculation corrections #559

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
204 changes: 104 additions & 100 deletions cnapy/gui_elements/thermodynamics_dialog.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -181,114 +181,118 @@ def get_solution_from_thread(self, solution: dict[str, float]) -> None:
def compute_optmdf(self):
self.setCursor(Qt.BusyCursor)

with self.appdata.project.cobra_py_model as model:
self.appdata.project.load_scenario_into_model(model)

extra_linear_constraints: list[ExtraLinearConstraint] = []
for constraint in self.appdata.project.scen_values.constraints:
# e.g., [({'EDD': 1.0}, '>=', 1.0)]
extra_linear_constraint = ExtraLinearConstraint(
stoichiometries={key: value for key, value in constraint[0].items()},
)

direction = constraint[1]
rhs = constraint[2]
if direction == ">=":
extra_linear_constraint.lower_value = rhs
elif direction == "<=":
extra_linear_constraint.upper_value = rhs
else: # == "="
extra_linear_constraint.lower_value = rhs
extra_linear_constraint.upper_value = rhs
# Decouple models ("with" and "deepcopy" do not work) so that no
# extra COBRA-k annotation spills into the original model
modelstr = cobra.io.to_json(self.appdata.project.cobra_py_model)
model = cobra.io.from_json(modelstr)

self.appdata.project.load_scenario_into_model(model)

extra_linear_constraints: list[ExtraLinearConstraint] = []
for constraint in self.appdata.project.scen_values.constraints:
# e.g., [({'EDD': 1.0}, '>=', 1.0)]
extra_linear_constraint = ExtraLinearConstraint(
stoichiometries={key: value for key, value in constraint[0].items()},
)

extra_linear_constraints.append(extra_linear_constraint)
direction = constraint[1]
rhs = constraint[2]
if direction == ">=":
extra_linear_constraint.lower_value = rhs
elif direction == "<=":
extra_linear_constraint.upper_value = rhs
else: # == "="
extra_linear_constraint.lower_value = rhs
extra_linear_constraint.upper_value = rhs

solver_name = self.solver_buttons["group"].checkedButton().property("cobrak_name")
extra_linear_constraints.append(extra_linear_constraint)

if self.analysis_type == ThermodynamicAnalysisTypes.OPTMDFPATHWAY:
min_mdf = -float("inf")
else:
try:
min_mdf = float(self.min_mdf.text())
except ValueError:
QMessageBox.warning(
self,
"Invalid minimal OptMDF",
"The given minimal OptMDF could not be converted into a valid number (such as, e.g., 1.231)."
"Aborting calculation...",
)
return

match self.analysis_type:
case ThermodynamicAnalysisTypes.OPTMDFPATHWAY:
objective = {MDF_VAR_ID: 1}
direction = +1
case ThermodynamicAnalysisTypes.BOTTLENECK_ANALYSIS:
objective = {"bottleneck_z_sum": 1}
direction = -1
case ThermodynamicAnalysisTypes.THERMODYNAMIC_FBA:
objective = {}
for (
reaction,
coefficient,
) in cobra.util.solver.linear_reaction_coefficients(model).items():
if reaction.reversibility:
objective[reaction.id + self.FWDID] = coefficient
objective[reaction.id + self.REVID] = -coefficient
else:
objective[reaction.id] = coefficient
direction = +1

cobrak_model = load_annotated_cobrapy_model_as_cobrak_model(
get_fullsplit_cobra_model(
model,
fwd_suffix=self.FWDID,
rev_suffix=self.REVID,
add_cobrak_sbml_annotation=True,
cobrak_default_min_conc=float(self.min_default_conc.text()),
cobrak_default_max_conc=float(self.max_default_conc.text()),
cobrak_extra_linear_constraints=extra_linear_constraints,
cobrak_kinetic_ignored_metabolites=[],
cobrak_no_extra_versions=True,
reac_lb_ub_cap=1_000.0,
)
)
solver_name = self.solver_buttons["group"].checkedButton().property("cobrak_name")

if all(cobrak_model.reactions[reac_id].dG0 is None for reac_id in cobrak_model.reactions):
if self.analysis_type == ThermodynamicAnalysisTypes.OPTMDFPATHWAY:
min_mdf = -float("inf")
else:
try:
min_mdf = float(self.min_mdf.text())
except ValueError:
QMessageBox.warning(
self,
"No ΔG'° set",
"To run a thermodynamic calculation, your model needs at least one reaction with a ΔG'° (annotation 'dG0')."
"Check out CNApy's documentation for more",
"Invalid minimal OptMDF",
"The given minimal OptMDF could not be converted into a valid number (such as, e.g., 1.231)."
"Aborting calculation...",
)
self.setCursor(Qt.ArrowCursor)
return
if self.analysis_type in (ThermodynamicAnalysisTypes.OPTMDFPATHWAY, ThermodynamicAnalysisTypes.THERMODYNAMIC_FBA):
solution = perform_lp_optimization(
cobrak_model=cobrak_model,
objective_target=objective,
objective_sense=direction,
with_enzyme_constraints=False,
with_thermodynamic_constraints=True,
with_loop_constraints=False,
min_mdf=min_mdf,
solver=Solver(name=solver_name),
verbose=True,
)
elif self.analysis_type == ThermodynamicAnalysisTypes.BOTTLENECK_ANALYSIS:
bottlenecks, solution = perform_lp_thermodynamic_bottleneck_analysis(
cobrak_model=cobrak_model,
with_enzyme_constraints=False,
min_mdf=min_mdf,
solver=Solver(name=solver_name),
verbose=True,
)
if solution != {}:
solution[ALL_OK_KEY] = True
self.get_solution_from_thread(solution)
# except Exception:
# self.send_solution.emit(pickle.dumps("ERROR"))
# self.finished_computation.emit()

match self.analysis_type:
case ThermodynamicAnalysisTypes.OPTMDFPATHWAY:
objective = {MDF_VAR_ID: 1}
direction = +1
case ThermodynamicAnalysisTypes.BOTTLENECK_ANALYSIS:
objective = {"bottleneck_z_sum": 1}
direction = -1
case ThermodynamicAnalysisTypes.THERMODYNAMIC_FBA:
objective = {}
for (
reaction,
coefficient,
) in cobra.util.solver.linear_reaction_coefficients(model).items():
if reaction.reversibility:
objective[reaction.id + self.FWDID] = coefficient
objective[reaction.id + self.REVID] = -coefficient
else:
objective[reaction.id] = coefficient
direction = +1

cobrak_model = load_annotated_cobrapy_model_as_cobrak_model(
get_fullsplit_cobra_model(
model,
fwd_suffix=self.FWDID,
rev_suffix=self.REVID,
add_cobrak_sbml_annotation=True,
cobrak_default_min_conc=float(self.min_default_conc.text()),
cobrak_default_max_conc=float(self.max_default_conc.text()),
cobrak_extra_linear_constraints=extra_linear_constraints,
cobrak_kinetic_ignored_metabolites=[],
cobrak_no_extra_versions=True,
reac_lb_ub_cap=1_000.0,
)
)

if all(cobrak_model.reactions[reac_id].dG0 is None for reac_id in cobrak_model.reactions):
QMessageBox.warning(
self,
"No ΔG'° set",
"To run a thermodynamic calculation, your model needs at least one reaction with a ΔG'° (annotation 'dG0')."
"Check out CNApy's documentation for more",
)
self.setCursor(Qt.ArrowCursor)
return
if self.analysis_type in (ThermodynamicAnalysisTypes.OPTMDFPATHWAY, ThermodynamicAnalysisTypes.THERMODYNAMIC_FBA):
solution = perform_lp_optimization(
cobrak_model=cobrak_model,
objective_target=objective,
objective_sense=direction,
with_enzyme_constraints=False,
with_thermodynamic_constraints=True,
with_loop_constraints=False,
min_mdf=min_mdf,
solver=Solver(name=solver_name),
verbose=True,
)
elif self.analysis_type == ThermodynamicAnalysisTypes.BOTTLENECK_ANALYSIS:
bottlenecks, solution = perform_lp_thermodynamic_bottleneck_analysis(
cobrak_model=cobrak_model,
with_enzyme_constraints=False,
min_mdf=min_mdf,
solver=Solver(name=solver_name),
verbose=True,
)
if solution != {}:
solution[ALL_OK_KEY] = True
self.get_solution_from_thread(solution)
# except Exception:
# self.send_solution.emit(pickle.dumps("ERROR"))
# self.finished_computation.emit()

def set_boxes(self, solution: dict[str, float]):
# Combine FWD and REV flux solutions
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ dependencies = [
"openpyxl",
"jpype1==1.5.0",
"setuptools",
"cobrak==0.0.2",
"cobrak==0.0.10",
]

[project.scripts]
Expand Down
Loading