When I run OptKnock function, I see this error:
Model used: iJO1366
Function: optknock = OptKnock(model, fraction_of_optimum=0.1)
_---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/var/folders/52/sz9nw9797p1cj_mbvfvlmh4c0000gn/T/ipykernel_29273/1164403988.py in
----> 1 optknock = OptKnock(sc_model, fraction_of_optimum=0.1)
~/opt/miniconda3/envs/myCobra/lib/python3.7/site-packages/cameo/strain_design/deterministic/linear_programming.py in init(self, model, exclude_reactions, remove_blocked, fraction_of_optimum, exclude_non_gene_reactions, use_nullspace_simplification, *args, **kwargs)
139 exclude_reactions += [r.id for r in self._model.reactions if not r.genes]
140
--> 141 self._build_problem(exclude_reactions, use_nullspace_simplification)
142
143 def _remove_blocked_reactions(self):
~/opt/miniconda3/envs/myCobra/lib/python3.7/site-packages/cameo/strain_design/deterministic/linear_programming.py in _build_problem(self, exclude_reactions, use_nullspace_simplification)
173 self.reaction_groups = None
174
--> 175 self._make_dual()
176
177 self._combine_primal_and_dual()
~/opt/miniconda3/envs/myCobra/lib/python3.7/site-packages/cameo/strain_design/deterministic/linear_programming.py in _make_dual(self)
209
210 def _make_dual(self):
--> 211 dual_problem = convert_to_dual(self._model.solver)
212 self._dual_problem = dual_problem
213 logger.debug("Dual problem successfully created")
~/opt/miniconda3/envs/myCobra/lib/python3.7/site-packages/cameo/core/model_dual.py in convert_to_dual(model)
43 dual_objective[const_var] = sign * constraint.lb
44 for variable, coef in constraint.expression.as_coefficients_dict().items():
---> 45 coefficients.setdefault(variable.name, {})[const_var] = sign * coef
46 else:
47 if constraint.lb is not None:
AttributeError: 'One' object has no attribute 'name'_
When I run OptKnock function, I see this error:
Model used: iJO1366
Function: optknock = OptKnock(model, fraction_of_optimum=0.1)
_---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/var/folders/52/sz9nw9797p1cj_mbvfvlmh4c0000gn/T/ipykernel_29273/1164403988.py in
----> 1 optknock = OptKnock(sc_model, fraction_of_optimum=0.1)
~/opt/miniconda3/envs/myCobra/lib/python3.7/site-packages/cameo/strain_design/deterministic/linear_programming.py in init(self, model, exclude_reactions, remove_blocked, fraction_of_optimum, exclude_non_gene_reactions, use_nullspace_simplification, *args, **kwargs)
139 exclude_reactions += [r.id for r in self._model.reactions if not r.genes]
140
--> 141 self._build_problem(exclude_reactions, use_nullspace_simplification)
142
143 def _remove_blocked_reactions(self):
~/opt/miniconda3/envs/myCobra/lib/python3.7/site-packages/cameo/strain_design/deterministic/linear_programming.py in _build_problem(self, exclude_reactions, use_nullspace_simplification)
173 self.reaction_groups = None
174
--> 175 self._make_dual()
176
177 self._combine_primal_and_dual()
~/opt/miniconda3/envs/myCobra/lib/python3.7/site-packages/cameo/strain_design/deterministic/linear_programming.py in _make_dual(self)
209
210 def _make_dual(self):
--> 211 dual_problem = convert_to_dual(self._model.solver)
212 self._dual_problem = dual_problem
213 logger.debug("Dual problem successfully created")
~/opt/miniconda3/envs/myCobra/lib/python3.7/site-packages/cameo/core/model_dual.py in convert_to_dual(model)
43 dual_objective[const_var] = sign * constraint.lb
44 for variable, coef in constraint.expression.as_coefficients_dict().items():
---> 45 coefficients.setdefault(variable.name, {})[const_var] = sign * coef
46 else:
47 if constraint.lb is not None:
AttributeError: 'One' object has no attribute 'name'_