From c841ffaa00666e51dc56ef9a3e571c4f6523dd2a Mon Sep 17 00:00:00 2001 From: Andrew Freiburger Date: Fri, 22 Dec 2023 13:10:42 -0600 Subject: [PATCH] minimal_media content from ProjectNotebooks --- .../CMM_iAH991V2_iML1515.kb_media.json | 4317 ++++++++++++++++ examples/minimal_media/minimal_media.py | 241 + .../minimal_media/minimal_media_warning.JPG | Bin 0 -> 21673 bytes examples/minimal_media/troubleshooting.ipynb | 4589 +++++++++++++++++ 4 files changed, 9147 insertions(+) create mode 100644 examples/minimal_media/CMM_iAH991V2_iML1515.kb_media.json create mode 100644 examples/minimal_media/minimal_media.py create mode 100644 examples/minimal_media/minimal_media_warning.JPG create mode 100644 examples/minimal_media/troubleshooting.ipynb diff --git a/examples/minimal_media/CMM_iAH991V2_iML1515.kb_media.json b/examples/minimal_media/CMM_iAH991V2_iML1515.kb_media.json new file mode 100644 index 00000000..14c9b658 --- /dev/null +++ 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Zero + +from .boundary_types import find_boundary_types + +logger = logging.getLogger(__name__) + +class MinMedia: + + @staticmethod + def _add_linear_obj(model: "Model") -> None: + r"""Add a linear version of a minimal medium to the model solver. + + Changes the optimization objective to finding the growth medium + requiring the smallest total import flux: + + ..math:: minimize \sum_{r_i in import_reactions} |r_i| + + Parameters + ---------- + model : cobra.Model + The cobra model to modify. + + """ + coefs = {} + for rxn in find_boundary_types(model, "exchange"): + export = len(rxn.reactants) == 1 + if export: + coefs[rxn.reverse_variable] = 1 + else: + coefs[rxn.forward_variable] = 1 + model.objective.set_linear_coefficients(coefs) + model.objective.direction = "min" + + @staticmethod + def _add_mip_obj(model: "Model") -> None: + """Add a mixed-integer version of a minimal medium to the model. + + Changes the optimization objective to finding the medium with the least + components: + + minimize size(R) where R part of import_reactions + + Arguments + --------- + model : cobra.model + The model to modify. + + """ + if len(model.variables) > 1e4: + logger.warning( + "The MIP version of minimal media is extremely slow for " + "models that large :(" + ) + exchange_rxns = find_boundary_types(model, "exchange") + big_m = max(abs(b) for r in exchange_rxns for b in r.bounds) + prob = model.problem + coefs = {} + to_add = [] + for rxn in exchange_rxns: + export = len(rxn.reactants) == 1 + indicator = prob.Variable("ind_" + rxn.id, lb=0, ub=1, type="binary") + if export: + vrv = rxn.reverse_variable + indicator_const = prob.Constraint( + vrv - indicator * big_m, ub=0, name="ind_constraint_" + rxn.id + ) + else: + vfw = rxn.forward_variable + indicator_const = prob.Constraint( + vfw - indicator * big_m, ub=0, name="ind_constraint_" + rxn.id + ) + to_add.extend([indicator, indicator_const]) + coefs[indicator] = 1 + model.add_cons_vars(to_add) + model.solver.update() + model.objective.set_linear_coefficients(coefs) + model.objective.direction = "min" + + @staticmethod + def _as_medium( + exchanges: Iterable["Reaction"], tolerance: float = 1e-6, exports: bool = False + ) -> pd.Series: + """Convert a solution to medium. + + Parameters + ---------- + exchanges : list of cobra.reaction + The exchange reactions to consider. + tolerance : float > 0, optional + The absolute tolerance for fluxes. Fluxes with an absolute value + smaller than this number will be ignored (default 1e-6). + exports : bool, optional + Whether to return export fluxes as well (default False). + """ + logger.debug("Formatting medium.") + medium = pd.Series() + for rxn in exchanges: + export = len(rxn.reactants) == 1 + flux = rxn.flux + if abs(flux) < tolerance: + continue + if export: + medium[rxn.id] = -flux + elif not export: + medium[rxn.id] = flux + if not exports: + medium = medium[medium > 0] + + return medium + + @staticmethod + def minimal_medium( + model: "Model", + min_objective_value: float = 0.1, + exports: bool = False, + minimize_components: Union[bool, int] = False, + open_exchanges: bool = False, + ) -> Union[pd.Series, pd.DataFrame, None]: + """Find the minimal growth medium for the `model`. + + Finds the minimal growth medium for the `model` which allows for + model as well as individual growth. Here, a minimal medium can either + be the medium requiring the smallest total import flux or the medium + requiring the least components (ergo ingredients), which will be much + slower due to being a mixed integer problem (MIP). + + Parameters + ---------- + model : cobra.model + The model to modify. + min_objective_value : float > 0 or array-like object, optional + The minimum growth rate (objective) that has to be achieved + (default 0.1). + exports : bool, optional + Whether to include export fluxes in the returned medium. + Defaults to False which will only return import fluxes + (default False). + minimize_components : bool or int > 0, optional + Whether to minimize the number of components instead of the total + import flux. Might be more intuitive if set to True, but may also + be slow to calculate for large communities. If set to a number `n` + will return up to `n` alternative solutions all with the same + number of components (default False). + open_exchanges : bool or number, optional + Whether to ignore currently set bounds and make all exchange + reactions in the `model` possible. If set to a `number`, all + exchange reactions will be opened with (-`number`, `number`) as + bounds (default False). + + Notes + ----- + Due to numerical issues, the `minimize_components` option will usually + only minimize the number of "large" import fluxes. Specifically, the + detection limit is given by ``integrality_tolerance * max_bound`` where + ``max_bound`` is the largest bound on an import reaction. Thus, if you + are interested in small import fluxes as well you may have to adjust the + solver tolerance at first with `model.tolerance = 1e-7` for instance. + However, this will be *very* slow for large models especially with GLPK. + + """ + exchange_rxns = find_boundary_types(model, "exchange") + if isinstance(open_exchanges, bool): + open_bound = 1000 + else: + open_bound = open_exchanges + + with model as mod: + if open_exchanges: + logger.debug(f"Opening exchanges for {len(exchange_rxns)} imports.") + for rxn in exchange_rxns: + rxn.bounds = (-open_bound, open_bound) + logger.debug("Applying objective value constraints.") + obj_const = mod.problem.Constraint( + mod.objective.expression, + lb=min_objective_value, + name="medium_obj_constraint", + ) + mod.add_cons_vars([obj_const]) + mod.solver.update() + mod.objective = Zero + logger.debug("Adding new media objective.") + tol = mod.solver.configuration.tolerances.feasibility + + if minimize_components: + _add_mip_obj(mod) + if isinstance(minimize_components, bool): + minimize_components = 1 + seen = set() + best = num_components = mod.slim_optimize() + if mod.solver.status != OPTIMAL: + logger.warning("Minimization of medium was infeasible.") + return None + exclusion = mod.problem.Constraint(Zero, ub=0) + mod.add_cons_vars([exclusion]) + mod.solver.update() + media = [] + + for i in range(minimize_components): + logger.info(f"Finding alternative medium #{(i + 1)}.") + vars = [mod.variables["ind_" + s] for s in seen] + if len(seen) > 0: + exclusion.set_linear_coefficients(dict.fromkeys(vars, 1)) + exclusion.ub = best - 1 + num_components = mod.slim_optimize() + if mod.solver.status != OPTIMAL or num_components > best: + if i == 0: + logger.warning( + "Could not get an optimal solution. " + "This is usually due to numerical instability. " + "Possible remedies are relaoding the model " + "from scratch, switching to a different solver, " + "or decreasing the solver tolerance. Please, " + "carefully read the note on numerical instability " + "in the function documentation." + ) + return None + break + medium = MinMedia._as_medium(exchange_rxns, tol, exports=exports) + media.append(medium) + seen.update(medium[medium > 0].index) + if len(media) > 1: + medium = pd.concat(media, axis=1, sort=True).fillna(0.0) + medium.sort_index(axis=1, inplace=True) + else: + medium = media[0] + else: + MinMedia._add_linear_obj(mod) + mod.slim_optimize() + if mod.solver.status != OPTIMAL: + logger.warning("Minimization of medium was infeasible.") + return None + medium = MinMedia._as_medium(exchange_rxns, tol, exports=exports) + + return medium diff --git a/examples/minimal_media/minimal_media_warning.JPG b/examples/minimal_media/minimal_media_warning.JPG new file mode 100644 index 0000000000000000000000000000000000000000..f2528fca5c0b93a51988f37ef81b73ee651dbf1b GIT binary patch literal 21673 zcmeIY1yo!?wVDyV4M3`@1X2Q^p`igRQGbB@ 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}, + { + "cell_type": "code", + "execution_count": 1, + "id": "25c5ae27", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\requests\\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.9) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version!\n", + " warnings.warn(\"urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported \"\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cobrakbase 0.2.8\n" + ] + } + ], + "source": [ + "from modelseedpy.fbapkg.reactionusepkg import MinimalMedia\n", + "\n", + "# define the environment path \n", + "from pprint import pprint\n", + "from json import dump\n", + "import os\n", + "local_cobrakbase_path = os.path.join('C:', 'Users', 'Andrew Freiburger','Documents','Argonne','cobrakbase')\n", + "os.environ[\"HOME\"] = local_cobrakbase_path\n", + "\n", + "# import the models\n", + "import cobrakbase\n", + "token = 'CKYZK6AZ5V2CT5ILYP7JAXFPW3OLT6VF'\n", + "kbase_api = cobrakbase.KBaseAPI(token)\n", + "model = kbase_api.get_from_ws(\"E_iAH991V2\",40576)\n", + "\n", + "# prevent excessive warnings\n", + "import warnings\n", + "warnings.filterwarnings(action='once')" + ] + }, + { + "cell_type": "markdown", + "id": "88cd097e", + "metadata": {}, + "source": [ + "## Test the recursive logic" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "28dc6a71", + "metadata": {}, + "outputs": [], + "source": [ + "from optlang import Variable, Constraint\n", + "from modelseedpy import FBAHelper\n", + "from optlang.symbolics import Zero\n", + "from deepdiff import DeepDiff\n", + "\n", + "def _var_to_ID(var):\n", + " rxnID = var.name\n", + " if \"_ru\" in rxnID:\n", + " rxnID = rxnID.replace(\"_ru\", \"\")\n", + " return rxnID\n", + "\n", + "def minimize_components(org_model, minimal_growth=None, printing=True):\n", + " \"\"\"minimize the quantity of metabolites that are consumed by the model\"\"\"\n", + " model = org_model.copy()\n", + " variables = {\"ru\":{}}\n", + " FBAHelper.add_minimal_objective_cons(\n", + " model, sum([rxn.flux_expression for rxn in model.reactions if \"bio\" in rxn.id]), minimal_growth)\n", + "\n", + " # define the binary variable and constraint\n", + " for ex_rxn in FBAHelper.exchange_reactions(model): # this may need to be relegated to a separate function, depending upon whether additional variables and constraints can be copied with a model \n", + " # define the variable\n", + " variables[\"ru\"][ex_rxn.id] = Variable(ex_rxn.id+\"_ru\", lb=0, ub=1, type=\"binary\")\n", + " model.add_cons_vars(variables[\"ru\"][ex_rxn.id])\n", + " # bin_flux: {rxn_bin}*1000 >= {rxn_rev_flux}\n", + " FBAHelper.create_constraint(model, Constraint(Zero, lb=0, ub=None, name=ex_rxn.id+\"_bin\"),\n", + " coef={variables[\"ru\"][ex_rxn.id]: 1000, ex_rxn.reverse_variable: -1})\n", + " print(\"to objective\", f\"{len(variables['ru'])} variables are defined\")\n", + " FBAHelper.add_objective(model, sum([var for var in variables[\"ru\"].values()]), \"min\")\n", + "\n", + " # determine each solution\n", + " solution_dicts = []\n", + " interdependencies = {}\n", + " sol = model.optimize()\n", + " sol_index = 0\n", + " while sol.status == \"optimal\" and sol_index < 100:\n", + " sol_dict = FBAHelper.solution_to_variables_dict(sol, model)\n", + " solution_dicts.append(sol_dict)\n", + " ## omit the solution from the next search\n", + " FBAHelper.create_constraint(model, Constraint(\n", + " Zero, lb=len(sol_dict)-1, ub=len(sol_dict)-1,name=ex_rxn.id + f\"_exclusion_sol{len(solution_dicts)}\"), sol_dict)\n", + " sol = model.optimize()\n", + " interdependencies[sol_index] = _examine_permutations(model, [rxn for rxn in sol_dict if \"EX_\" in rxn.name], variables, sol_dict, sol_index)\n", + " sol_index += 1\n", + "\n", + "def _knockout(org_model, exID, variables, sol_dict, sol_index):\n", + " # knockout the specified exchange\n", + "# knocked_model = org_model.copy() # !!! This model may need to be copied, and re-constrained with the previous constraints, to prevent \n", + " coef = {variables[\"ru\"][exID]: 0}\n", + " coef.update({variables[\"ru\"][_var_to_ID(exVar2)]: 1\n", + " for exVar2 in sol_dict if exID != _var_to_ID(exVar2) and \"EX_\" in exVar2.name})\n", + " FBAHelper.create_constraint(org_model, Constraint(Zero, lb=0.1, ub=None, name=f\"{exID}-sol{sol_index}\"), coef)\n", + " return org_model.optimize()\n", + "\n", + "def _examine_permutations(model, exchange_ids_to_explore, variables, sol_dict, sol_index):\n", + " interdependencies = {sol_index:{}}\n", + " for ex in exchange_ids_to_explore:\n", + " sol_dict_sans_ex = sol_dict.copy()\n", + " sol_dict_sans_ex.pop(ex)\n", + " exID = _var_to_ID(ex)\n", + " interdependencies[sol_index][exID] = []\n", + "\n", + " ## explore permutations after removing the selected variable\n", + " diff = DeepDiff(sol_dict_sans_ex, FBAHelper.solution_to_dict(\n", + " _knockout(model, exID, variables, sol_dict, sol_index)))\n", + " if diff: # the addition of new exchanges or altered exchange fluxes are detected after the removed exchange\n", + " for key, value in diff.items():\n", + " print(key, value)\n", + " if key == \"dictionary_item_added\":\n", + " new_mets = [re.search(\"(?<=\\[\\')(.+)(?=\\'\\])\", met).group() for met in value.items()]\n", + " # this dictionary should be parsed into a list of substitute metabolites and a list of functionally coupled reactions\n", + " for met in new_mets:\n", + " interdependencies[sol_index][exID].update(met)\n", + " _examine_permutations(model, exchange_ids_to_explore, variables, sol_dict, sol_index)\n", + " # coef = {variables[\"met\"][exID]: 0 for cpd in new_mets.keys()}\n", + " # coef.update({variables[\"met\"][exID]: 1 for exID in sol_dict if exID not in new_mets.keys()})\n", + " cpd_name = \"_\".join(new_mets.keys())\n", + " BaseFBAPkg.build_constraint(self, \"met\", 0.1, None, coef, f\"{cpd_name}-sol{sol_index}\")\n", + " new_sol = self.model.optimize()\n", + " if new_sol.status != \"optimal\":\n", + " return interdependencies\n", + " _examine_permutations(exID, new_sol, sol_index, sol_dict_sans_ex)\n", + " return interdependencies" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "5c664b65", + "metadata": { + "scrolled": true, + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "to objective 281 variables are defined\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\util\\solver.py:554: UserWarning: Solver status is 'infeasible'.\n", + " warn(f\"Solver status is '{status}'.\", UserWarning)\n", + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\util\\solver.py:554: UserWarning: Solver status is 'infeasible'.\n", + " warn(f\"Solver status is '{status}'.\", UserWarning)\n", + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Temp\\ipykernel_43064\\997489651.py:69: DeprecationWarning: invalid escape sequence \\[\n", + " new_mets = [re.search(\"(?<=\\[\\')(.+)(?=\\'\\])\", met).group() for met in value.items()]\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "dictionary_item_added [root['12ETHDt_c0'], root['12PPDRt_c0'], root['12PPDt_c0'], root['23PDE2_c0'], root['23PDE4_c0'], root['23PDE7_c0'], root['23PDE9_c0'], root['26DAPLLATi_c0'], root['2AMEPHPAT_c0'], root['2FUCLAC__DASH__FUCASEe_c0'], root['2MBCOATA_c0'], root['2MMALD_c0'], root['2MMALD2_c0'], root['3DSPHR_c0'], root['3FUCLAC__DASH__FUCASEe_c0'], root['3HACPR1_c0'], root['3HACPR2_c0'], root['3HAD100_c0'], root['3HAD10M11_c0'], root['3HAD10M12_c0'], root['3HAD11M12_c0'], root['3HAD120_c0'], root['3HAD121_c0'], root['3HAD12M13_c0'], root['3HAD12M14_c0'], root['3HAD13M14_c0'], root['3HAD140_c0'], root['3HAD141_c0'], root['3HAD14M15_c0'], root['3HAD14M16_c0'], 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root['EX_cpd00041_e0'], root['EX_levan1000_e0'], root['EX_cpd00028_e0'], root['EX_cpd00311_e0'], root['EX_unsdigalur_e0'], root['EX_cpd00154_e0'], root['EX_hspg_degr_4_e0'], root['EX_3fuclac_e0'], root['EX_mqn10_e0'], root['EX_cspg_c_degr_e0'], root['EX_cpd00428_e0'], root['EX_cpd10515_e0'], root['EX_hspg_degr_3_e0'], root['SK_cpd02701_c0'], root['SK_cpd11416_c0']]\n" + ] + }, + { + "ename": "TypeError", + "evalue": "'list' object is not callable", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mTypeError\u001b[0m Traceback (most recent call last)", + "Input \u001b[1;32mIn [13]\u001b[0m, in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[0m \u001b[43mminimize_components\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodel\u001b[49m\u001b[43m)\u001b[49m\n", + "Input \u001b[1;32mIn [12]\u001b[0m, in \u001b[0;36mminimize_components\u001b[1;34m(org_model, minimal_growth, printing)\u001b[0m\n\u001b[0;32m 39\u001b[0m FBAHelper\u001b[38;5;241m.\u001b[39mcreate_constraint(model, Constraint(\n\u001b[0;32m 40\u001b[0m Zero, lb\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mlen\u001b[39m(sol_dict)\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, ub\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mlen\u001b[39m(sol_dict)\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m,name\u001b[38;5;241m=\u001b[39mex_rxn\u001b[38;5;241m.\u001b[39mid \u001b[38;5;241m+\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_exclusion_sol\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mlen\u001b[39m(solution_dicts)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m), sol_dict)\n\u001b[0;32m 41\u001b[0m sol \u001b[38;5;241m=\u001b[39m model\u001b[38;5;241m.\u001b[39moptimize()\n\u001b[1;32m---> 42\u001b[0m interdependencies[sol_index] \u001b[38;5;241m=\u001b[39m \u001b[43m_examine_permutations\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodel\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[43mrxn\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mfor\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mrxn\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01min\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43msol_dict\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mEX_\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01min\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mrxn\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mvariables\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msol_dict\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msol_index\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 43\u001b[0m sol_index \u001b[38;5;241m+\u001b[39m\u001b[38;5;241m=\u001b[39m \u001b[38;5;241m1\u001b[39m\n", + "Input \u001b[1;32mIn [12]\u001b[0m, in \u001b[0;36m_examine_permutations\u001b[1;34m(model, exchange_ids_to_explore, variables, sol_dict, sol_index)\u001b[0m\n\u001b[0;32m 67\u001b[0m \u001b[38;5;28mprint\u001b[39m(key, value)\n\u001b[0;32m 68\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m key \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdictionary_item_added\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[1;32m---> 69\u001b[0m new_mets \u001b[38;5;241m=\u001b[39m [re\u001b[38;5;241m.\u001b[39msearch(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m(?<=\u001b[39m\u001b[38;5;124m\\\u001b[39m\u001b[38;5;124m[\u001b[39m\u001b[38;5;130;01m\\'\u001b[39;00m\u001b[38;5;124m)(.+)(?=\u001b[39m\u001b[38;5;130;01m\\'\u001b[39;00m\u001b[38;5;124m\\\u001b[39m\u001b[38;5;124m])\u001b[39m\u001b[38;5;124m\"\u001b[39m, met)\u001b[38;5;241m.\u001b[39mgroup() \u001b[38;5;28;01mfor\u001b[39;00m met \u001b[38;5;129;01min\u001b[39;00m \u001b[43mvalue\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mitems\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m]\n\u001b[0;32m 70\u001b[0m \u001b[38;5;66;03m# this dictionary should be parsed into a list of substitute metabolites and a list of functionally coupled reactions\u001b[39;00m\n\u001b[0;32m 71\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m met \u001b[38;5;129;01min\u001b[39;00m new_mets:\n", + "\u001b[1;31mTypeError\u001b[0m: 'list' object is not callable" + ] + } + ], + "source": [ + "minimize_components(model)" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "id": "71a3634d", + "metadata": {}, + "outputs": [ + { + "ename": "NameError", + "evalue": "name 'solution_dicts' is not defined", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0msolution_dicts\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;31mNameError\u001b[0m: name 'solution_dicts' is not defined" + ] + } + ], + "source": [ + "solution_dicts" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "cfa957b0", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "first Bacteroides_thetaiotaomicron_VPI-5482.fbamdl.23\n", + "Bacteroides_thetaiotaomicron_VPI-5482.fbamdl.23\n", + "Bacteroides_thetaiotaomicron_VPI-5482.fbamdl.23\n", + "min_growth: 0.1 <= 1.0*bio1 - 1.0*bio1_reverse_b18f7\n" + ] + } + ], + "source": [ + "from optlang import Variable, Constraint\n", + "from modelseedpy.core.fbahelper import FBAHelper\n", + "from optlang.symbolics import Zero\n", + "\n", + "def _load_model(org_model, var_types=None):\n", + " print(\"first\", org_model.id)\n", + " model = org_model.copy()\n", + " print(model.id)\n", + " var_types = var_types or [\"ru\"]\n", + " variables = {var_type:{} for var_type in var_types}\n", + " return model, variables\n", + "\n", + "def _add_constraint(model, constraint, coef=None):\n", + " model.add_cons_vars(constraint)\n", + " if coef:\n", + " constraint.set_linear_coefficients(coef)\n", + " print(constraint)\n", + " model.solver.update()\n", + "\n", + "def minimize_components(org_model):\n", + " \"\"\"minimize the quantity of metabolites that are consumed by the model\"\"\"\n", + " model, variables = _load_model(org_model)\n", + " print(model.id)\n", + " # add a constraint of minimal growth\n", + " _add_constraint(model, Constraint(sum([rxn.flux_expression for rxn in model.reactions if \"bio\" in rxn.id]),\n", + " lb=0.1, ub=None, name=\"min_growth\"))\n", + "\n", + " # define the binary variable and constraint\n", + " for ex_rxn in FBAHelper.exchange_reactions(model):\n", + " # define the variable\n", + " variables[\"ru\"][ex_rxn.id] = Variable(ex_rxn.id+\"_ru\", lb=0, ub=1, type=\"binary\")\n", + " model.add_cons_vars(variables[\"ru\"][ex_rxn.id])\n", + " \n", + " # bin_flux: {rxn_bin}*1000 >= {rxn_rev_flux}\n", + " # _add_constraint(model, Constraint(Zero, lb=0, ub=None, name=ex_rxn.id+\"_bin\"),\n", + " # coef={variables[\"ru\"][ex_rxn.id]: 1000, ex_rxn.reverse_variable: -1})\n", + " # print(\"to objective\")\n", + " # FBAHelper.add_objective(model, sum([var for var in variables[\"ru\"].values()]), \"min\")\n", + " \n", + "minimize_components(model)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "01ce3946", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "bb24e0c0", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "e3bb91fd", + "metadata": { + "scrolled": true, + "tags": [] + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\util\\solver.py:554: UserWarning: Solver status is 'infeasible'.\n", + " warn(f\"Solver status is '{status}'.\", UserWarning)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[0 <= EX_hspg_degr_6_e0 <= 1000, 0 <= EX_hspg_degr_5_e0 <= 1000, 0 <= EX_cpd00428_e0 <= 1000, 0 <= EX_core2_e0 <= 1000, 0 <= EX_leugly_e0 <= 1000, 0 <= EX_cpd00143_e0 <= 1000, 0 <= EX_s2l2n2m2m_e0 <= 1000, 0 <= EX_cpd00035_e0 <= 1000, 0 <= EX_lacnnttr_e0 <= 1000, 0 <= EX_cpd00029_e0 <= 1000, 0 <= EX_ha_e0 <= 1000, 0 <= EX_cpd00832_e0 <= 1000, 0 <= EX_cpd00082_e0 <= 1000, 0 <= EX_arabttr_e0 <= 1000, 0 <= EX_cpd00184_e0 <= 1000, 0 <= EX_3fuclac_e0 <= 1000, 0 <= EX_chtbs_e0 <= 1000, 0 <= EX_starch1200_e0 <= 1000, 0 <= EX_cpd00084_e0 <= 1000, 0 <= EX_cpd00039_e0 <= 1000, 0 <= EX_idour_e0 <= 1000, 0 <= EX_cspg_c_rest_e0 <= 1000, 0 <= EX_cpd00382_e0 <= 1000, 0 <= EX_cpd00281_e0 <= 1000, 0 <= EX_cpd00249_e0 <= 1000, 0 <= EX_metala_e0 <= 1000, 0 <= EX_amannan140_e0 <= 1000, 0 <= EX_cpd00154_e0 <= 1000, 0 <= EX_cpd01329_e0 <= 1000, 0 <= EX_cpd03105_e0 <= 1000, 0 <= EX_cpd00208_e0 <= 1000, 0 <= EX_cpd00971_e0 <= 1000, 0 <= EX_alathr_e0 <= 1000, 0 <= EX_cpd00054_e0 <= 1000, 0 <= EX_hspg_degr_9_e0 <= 1000, 0 <= EX_cpd00107_e0 <= 1000, 0 <= EX_neulacnttr_e0 <= 1000, 0 <= EX_cpd10516_e0 <= 1000, 0 <= EX_cpd00280_e0 <= 1000, 0 <= EX_cpd00092_e0 <= 1000, 0 <= EX_cpd00098_e0 <= 1000, 0 <= EX_12ethd_e0 <= 1000, 0 <= EX_2omxyl_e0 <= 1000, 0 <= EX_ha_pre1_e0 <= 1000, 0 <= EX_alaglu_e0 <= 1000, 0 <= EX_Ser_Thr_e0 <= 1000, 0 <= EX_mantr_e0 <= 1000, 0 <= EX_cpd15605_e0 <= 1000, 0 <= EX_cpd00731_e0 <= 1000, 0 <= EX_cpd00063_e0 <= 1000, 0 <= EX_hspg_degr_13_e0 <= 1000, 0 <= EX_gncore1_e0 <= 1000, 0 <= EX_levantttr_e0 <= 1000, 0 <= EX_cpd00153_e0 <= 1000, 0 <= EX_alaasp_e0 <= 1000, 0 <= EX_cpd15495_e0 <= 1000, 0 <= EX_cpd00034_e0 <= 1000, 0 <= EX_cpd00311_e0 <= 1000, 0 <= EX_cpd00220_e0 <= 1000, 0 <= EX_amylose300_e0 <= 1000, 0 <= EX_acgalglcur_e0 <= 1000, 0 <= EX_cpd15551_e0 <= 1000, 0 <= EX_cpd00011_e0 <= 1000, 0 <= EX_cpd00161_e0 <= 1000, 0 <= EX_f1a_e0 <= 1000, 0 <= EX_lmn2_e0 <= 1000, 0 <= EX_stys_e0 <= 1000, 0 <= EX_plac_e0 <= 1000, 0 <= EX_pe_cer1_bt_e0 <= 1000, 0 <= EX_phppa_e0 <= 1000, 0 <= EX_cpd00030_e0 <= 1000, 0 <= EX_Tn_antigen_e0 <= 1000, 0 <= EX_cpd05228_e0 <= 1000, 0 <= EX_cpd00156_e0 <= 1000, 0 <= EX_7ocholate_e0 <= 1000, 0 <= EX_isobut_e0 <= 1000, 0 <= EX_cpd11584_e0 <= 1000, 0 <= EX_cpd00159_e0 <= 1000, 0 <= EX_fucneulacnhx_e0 <= 1000, 0 <= EX_cpd00305_e0 <= 1000, 0 <= EX_argarg_e0 <= 1000, 0 <= EX_cpd00013_e0 <= 1000, 0 <= EX_core8_e0 <= 1000, 0 <= EX_glyasn_e0 <= 1000, 0 <= EX_cpd00099_e0 <= 1000, 0 <= EX_n2m2mn_e0 <= 1000, 0 <= EX_ha_deg1_e0 <= 1000, 0 <= EX_oligofru4_e0 <= 1000, 0 <= EX_levanttr_e0 <= 1000, 0 <= EX_pect_e0 <= 1000, 0 <= EX_cpd00141_e0 <= 1000, 0 <= EX_cpd00036_e0 <= 1000, 0 <= EX_gncore2_e0 <= 1000, 0 <= EX_cpd03047_e0 <= 1000, 0 <= EX_cpd00232_e0 <= 1000, 0 <= EX_s2l2fn2m2masn_e0 <= 1000, 0 <= EX_cpd00149_e0 <= 1000, 0 <= EX_cpd08305_e0 <= 1000, 0 <= EX_cspg_a_degr_e0 <= 1000, 0 <= EX_cpd00412_e0 <= 1000, 0 <= EX_cpd00104_e0 <= 1000, 0 <= EX_hspg_degr_11_e0 <= 1000, 0 <= EX_cpd15606_e0 <= 1000, 0 <= EX_cpd00041_e0 <= 1000, 0 <= EX_galam_e0 <= 1000, 0 <= EX_glycogen1500_e0 <= 1000, 0 <= EX_dsT_antigen_e0 <= 1000, 0 <= EX_cpd00703_e0 <= 1000, 0 <= EX_hspg_degr_1_e0 <= 1000, 0 <= EX_hspg_degr_3_e0 <= 1000, 0 <= EX_cpd00023_e0 <= 1000, 0 <= EX_cpd00118_e0 <= 1000, 0 <= EX_glyglu_e0 <= 1000, 0 <= EX_hspg_rest_e0 <= 1000, 0 <= EX_cpd00367_e0 <= 1000, 0 <= EX_cpd01399_e0 <= 1000, 0 <= EX_pecticgal_e0 <= 1000, 0 <= EX_mbenz_e0 <= 1000, 0 <= EX_cpd00794_e0 <= 1000, 0 <= EX_manttr_e0 <= 1000, 0 <= EX_cpd03198_e0 <= 1000, 0 <= EX_cpd00224_e0 <= 1000, 0 <= EX_3ddlhept_e0 <= 1000, 0 <= EX_cpd00076_e0 <= 1000, 0 <= EX_glypro_e0 <= 1000, 0 <= EX_cpd11658_e0 <= 1000, 0 <= EX_cpd00027_e0 <= 1000, 0 <= EX_isocapr_e0 <= 1000, 0 <= EX_cpd00048_e0 <= 1000, 0 <= EX_cpd00393_e0 <= 1000, 0 <= EX_cpd00058_e0 <= 1000, 0 <= EX_core4_e0 <= 1000, 0 <= EX_cpd00210_e0 <= 1000, 0 <= EX_hspg_degr_8_e0 <= 1000, 0 <= EX_cpd01017_e0 <= 1000, 0 <= EX_gchola_e0 <= 1000, 0 <= EX_cpd00309_e0 <= 1000, 0 <= EX_m2mn_e0 <= 1000, 0 <= EX_cpd00106_e0 <= 1000, 0 <= EX_cpd00047_e0 <= 1000, 0 <= EX_cpd00136_e0 <= 1000, 0 <= EX_cpd00246_e0 <= 1000, 0 <= EX_cpd00028_e0 <= 1000, 0 <= EX_lps_bt_e0 <= 1000, 0 <= EX_cpd00322_e0 <= 1000, 0 <= EX_cpd00751_e0 <= 1000, 0 <= EX_cspg_c_e0 <= 1000, 0 <= EX_manpt_e0 <= 1000, 0 <= EX_cpd00007_e0 <= 1000, 0 <= EX_cspg_b_e0 <= 1000, 0 <= EX_cpd00001_e0 <= 1000, 0 <= EX_cpd00182_e0 <= 1000, 0 <= EX_cpd00635_e0 <= 1000, 0 <= EX_lacdfucttr_e0 <= 1000, 0 <= EX_cpd00122_e0 <= 1000, 0 <= EX_cpd00264_e0 <= 1000, 0 <= EX_core6_e0 <= 1000, 0 <= EX_cpd00276_e0 <= 1000, 0 <= EX_cpd00453_e0 <= 1000, 0 <= EX_cpd11591_e0 <= 1000, 0 <= EX_cpd00205_e0 <= 1000, 0 <= EX_kestottr_e0 <= 1000, 0 <= EX_cpd00396_e0 <= 1000, 0 <= EX_lacnttr_e0 <= 1000, 0 <= EX_glyasp_e0 <= 1000, 0 <= EX_mqn10_e0 <= 1000, 0 <= EX_cpd00263_e0 <= 1000, 0 <= EX_cpd00254_e0 <= 1000, 0 <= EX_cpd00108_e0 <= 1000, 0 <= EX_cpd00064_e0 <= 1000, 0 <= EX_s2l2n2m2mn_e0 <= 1000, 0 <= EX_cpd01861_e0 <= 1000, 0 <= EX_cpd00489_e0 <= 1000, 0 <= EX_cpd15836_e0 <= 1000, 0 <= EX_hspg_degr_15_e0 <= 1000, 0 <= EX_lacnfucpt_e0 <= 1000, 0 <= EX_core3_e0 <= 1000, 0 <= EX_cpd04097_e0 <= 1000, 0 <= EX_sT_antigen_e0 <= 1000, 0 <= EX_s2l2n2m2masn_e0 <= 1000, 0 <= EX_cpd11602_e0 <= 1000, 0 <= EX_cpd00065_e0 <= 1000, 0 <= EX_cpd00654_e0 <= 1000, 0 <= EX_core7_e0 <= 1000, 0 <= EX_rhamnogalurI_e0 <= 1000, 0 <= EX_cpd01391_e0 <= 1000, 0 <= EX_cpd00069_e0 <= 1000, 0 <= EX_leuleu_e0 <= 1000, 0 <= EX_cpd00129_e0 <= 1000, 0 <= EX_arabinan101_e0 <= 1000, 0 <= EX_cpd03725_e0 <= 1000, 0 <= EX_cpd00875_e0 <= 1000, 0 <= EX_cpd00116_e0 <= 1000, 0 <= EX_cpd00138_e0 <= 1000, 0 <= EX_mqn9_e0 <= 1000, 0 <= EX_cpd15500_e0 <= 1000, 0 <= EX_cpd00363_e0 <= 1000, 0 <= EX_homogal_e0 <= 1000, 0 <= EX_hspg_degr_14_e0 <= 1000, 0 <= EX_cpd15604_e0 <= 1000, 0 <= EX_kestopt_e0 <= 1000, 0 <= EX_levan1000_e0 <= 1000, 0 <= EX_cpd00073_e0 <= 1000, 0 <= EX_cpd00105_e0 <= 1000, 0 <= EX_arabinogal_e0 <= 1000, 0 <= EX_cpd00355_e0 <= 1000, 0 <= EX_cpd15494_e0 <= 1000, 0 <= EX_cpd00179_e0 <= 1000, 0 <= EX_cpd03279_e0 <= 1000, 0 <= EX_hspg_degr_7_e0 <= 1000, 0 <= EX_strch2_e0 <= 1000, 0 <= EX_cpd00531_e0 <= 1000, 0 <= EX_cpd00066_e0 <= 1000, 0 <= EX_mqn11_e0 <= 1000, 0 <= EX_cpd11640_e0 <= 1000, 0 <= EX_cpd01262_e0 <= 1000, 0 <= EX_cpd00060_e0 <= 1000, 0 <= EX_alagly_e0 <= 1000, 0 <= EX_cspg_a_e0 <= 1000, 0 <= EX_lmn30_e0 <= 1000, 0 <= EX_apio_D_e0 <= 1000, 0 <= EX_cpd00009_e0 <= 1000, 0 <= EX_cpd00020_e0 <= 1000, 0 <= EX_hspg_degr_12_e0 <= 1000, 0 <= EX_cpd00053_e0 <= 1000, 0 <= EX_l2n2m2mn_e0 <= 1000, 0 <= EX_hspg_degr_4_e0 <= 1000, 0 <= EX_cpd00644_e0 <= 1000, 0 <= EX_cspg_b_degr_e0 <= 1000, 0 <= EX_cpd00166_e0 <= 1000, 0 <= EX_cpd00117_e0 <= 1000, 0 <= EX_cpd00221_e0 <= 1000, 0 <= EX_acgalidour_e0 <= 1000, 0 <= EX_cpd11606_e0 <= 1000, 0 <= EX_indlac_e0 <= 1000, 0 <= EX_cpd00033_e0 <= 1000, 0 <= EX_cpd00051_e0 <= 1000, 0 <= EX_cpd00277_e0 <= 1000, 0 <= EX_hspg_degr_2_e0 <= 1000, 0 <= EX_isoval_e0 <= 1000, 0 <= EX_pullulan1200_e0 <= 1000, 0 <= EX_acerA_e0 <= 1000, 0 <= EX_cpd00075_e0 <= 1000, 0 <= EX_cpd00430_e0 <= 1000, 0 <= EX_hspg_degr_10_e0 <= 1000, 0 <= EX_kesto_e0 <= 1000, 0 <= EX_2fuclac_e0 <= 1000, 0 <= EX_cspg_c_degr_e0 <= 1000, 0 <= EX_cpd00438_e0 <= 1000, 0 <= EX_cpd01012_e0 <= 1000, 0 <= EX_rhamnogalurII_e0 <= 1000, 0 <= EX_strch1_e0 <= 1000, 0 <= EX_mn_e0 <= 1000, 0 <= EX_unsdigalur_e0 <= 1000, 0 <= EX_cpd10515_e0 <= 1000, 0 <= EX_cpd00239_e0 <= 1000, 0 <= EX_cpd00132_e0 <= 1000, 0 <= EX_hspg_e0 <= 1000, 0 <= EX_cpd00218_e0 <= 1000, 0 <= EX_sphmyln_bt_e0 <= 1000, 0 <= EX_cspg_ab_rest_e0 <= 1000, 0 <= EX_acgalidour2s_e0 <= 1000, 0 <= EX_core5_e0 <= 1000, 0 <= EX_cpd11583_e0 <= 1000, 0 <= EX_cpd11580_e0 <= 1000, 0 <= EX_cpd00164_e0 <= 1000, 0 <= EX_cpd00137_e0 <= 1000, 0 <= EX_manb_e0 <= 1000, 0 <= EX_cpd00119_e0 <= 1000, 0 <= EX_cps_bt_e0 <= 1000, 0 <= EX_2omfuc_e0 <= 1000, 0 <= EX_sTn_antigen_e0 <= 1000, 0 <= EX_cpd11587_e0 <= 1000, 0 <= EX_phearg_e0 <= 1000, 0 <= EX_T_antigen_e0 <= 1000, 0 <= EX_levanb_e0 <= 1000, 0 <= EX_dt5hsu_e0 <= 1000, 0 <= EX_cpd00067_e0 <= 1000, 0 <= EX_cpd00540_e0 <= 1000, 0 <= EX_lacndfuchx_e0 <= 1000, 0 <= EX_gam26s_e0 <= 1000]\n" + ] + }, + { + "ename": "KeyError", + "evalue": "'EX_hspg_degr_6'", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mKeyError\u001b[0m Traceback (most recent call last)", + "Input \u001b[1;32mIn [16]\u001b[0m, in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[0;32m 1\u001b[0m get_ipython()\u001b[38;5;241m.\u001b[39mrun_line_magic(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrun\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m../../modelseedpy/modelseedpy/core/minimalmediapkg.py\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m----> 2\u001b[0m \u001b[43mMinimalMediaPkg\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mminimize_components\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodel\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[1;32m~\\Documents\\Argonne\\ModelSEEDpy\\modelseedpy\\core\\minimalmediapkg.py:98\u001b[0m, in \u001b[0;36mMinimalMediaPkg.minimize_components\u001b[1;34m(org_model)\u001b[0m\n\u001b[0;32m 96\u001b[0m sol_exchanges \u001b[38;5;241m=\u001b[39m [rxn \u001b[38;5;28;01mfor\u001b[39;00m rxn \u001b[38;5;129;01min\u001b[39;00m sol_dict \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mEX_\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m rxn\u001b[38;5;241m.\u001b[39mname]\n\u001b[0;32m 97\u001b[0m \u001b[38;5;28mprint\u001b[39m(sol_exchanges)\n\u001b[1;32m---> 98\u001b[0m interdependencies[sol_index] \u001b[38;5;241m=\u001b[39m \u001b[43mMinimalMediaPkg\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_examine_permutations\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodel\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msol_exchanges\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mvariables\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msol_dict\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msol_index\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[1;32m~\\Documents\\Argonne\\ModelSEEDpy\\modelseedpy\\core\\minimalmediapkg.py:111\u001b[0m, in \u001b[0;36mMinimalMediaPkg._examine_permutations\u001b[1;34m(model, exchange_ids_to_explore, variables, sol_dict, sol_index)\u001b[0m\n\u001b[0;32m 108\u001b[0m interdependencies \u001b[38;5;241m=\u001b[39m {}\n\u001b[0;32m 109\u001b[0m \u001b[38;5;66;03m## explore permutations after removing the selected variable\u001b[39;00m\n\u001b[0;32m 110\u001b[0m diff \u001b[38;5;241m=\u001b[39m DeepDiff(sol_dict_sans_ex,\n\u001b[1;32m--> 111\u001b[0m FBAHelper\u001b[38;5;241m.\u001b[39msolution_to_dict(\u001b[43mMinimalMediaPkg\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_knockout\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodel\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mexID\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mvariables\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msol_dict\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msol_index\u001b[49m\u001b[43m)\u001b[49m))\n\u001b[0;32m 112\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m diff: \u001b[38;5;66;03m# the addition of new exchanges or altered exchange fluxes are detected after the removed exchange\u001b[39;00m\n\u001b[0;32m 113\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m key, value \u001b[38;5;129;01min\u001b[39;00m diff\u001b[38;5;241m.\u001b[39mitems():\n", + "File \u001b[1;32m~\\Documents\\Argonne\\ModelSEEDpy\\modelseedpy\\core\\minimalmediapkg.py:55\u001b[0m, in \u001b[0;36mMinimalMediaPkg._knockout\u001b[1;34m(org_model, exVar, variables, sol_dict, sol_index)\u001b[0m\n\u001b[0;32m 53\u001b[0m knocked_model \u001b[38;5;241m=\u001b[39m org_model\u001b[38;5;241m.\u001b[39mcopy()\n\u001b[0;32m 54\u001b[0m exID \u001b[38;5;241m=\u001b[39m MinimalMediaPkg\u001b[38;5;241m.\u001b[39m_varName_to_ID(exVar\u001b[38;5;241m.\u001b[39mname)\n\u001b[1;32m---> 55\u001b[0m coef \u001b[38;5;241m=\u001b[39m {\u001b[43mvariables\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mru\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m[\u001b[49m\u001b[43mexID\u001b[49m\u001b[43m]\u001b[49m: \u001b[38;5;241m0\u001b[39m}\n\u001b[0;32m 56\u001b[0m coef\u001b[38;5;241m.\u001b[39mupdate({variables[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mru\u001b[39m\u001b[38;5;124m\"\u001b[39m][MinimalMediaPkg\u001b[38;5;241m.\u001b[39m_varName_to_ID(exVar2\u001b[38;5;241m.\u001b[39mname)]: \u001b[38;5;241m1\u001b[39m\n\u001b[0;32m 57\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m exVar2 \u001b[38;5;129;01min\u001b[39;00m sol_dict \u001b[38;5;28;01mif\u001b[39;00m exVar \u001b[38;5;241m!=\u001b[39m exVar2 \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mEX_\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m exVar2\u001b[38;5;241m.\u001b[39mname})\n\u001b[0;32m 58\u001b[0m MinimalMediaPkg\u001b[38;5;241m.\u001b[39m_add_constraint(knocked_model, Constraint(Zero, lb\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0.1\u001b[39m, ub\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mexVar\u001b[38;5;241m.\u001b[39mname\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m-sol\u001b[39m\u001b[38;5;132;01m{\u001b[39;00msol_index\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m), coef)\n", + "\u001b[1;31mKeyError\u001b[0m: 'EX_hspg_degr_6'" + ] + } + ], + "source": [ + "%run ../../modelseedpy/modelseedpy/core/minimalmediapkg.py\n", + "MinimalMediaPkg.minimize_components(model)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ae614f77", + "metadata": {}, + "outputs": [], + "source": [ + "from optlang.symbolics import Zero\n", + "from modelseedpy import FBAHelper\n", + "\n", + "# add a constraint of minimal growth\n", + "cons = model.problem.Constraint(sum([rxn.flux_expression for rxn in model.reactions if \"bio\" in rxn.id]), lb=0.1, ub=None, name=\"min_growth\")\n", + "model.add_cons_vars(cons)\n", + "model.solver.update()\n", + "\n", + "# define the exchange variables and constraints\n", + "variables = {}\n", + "for ex_rxn in FBAHelper.exchange_reactions(model):\n", + " if ex_rxn.lower_bound >= 0:\n", + " print(ex_rxn.bounds)\n", + " \n", + " variables[ex_rxn.id] = model.problem.Variable(ex_rxn.id+\"_bin\", lb=0, ub=1, type=\"binary\")\n", + " model.add_cons_vars(variables[ex_rxn.id])\n", + " \n", + " # bin_flux: {rxn_bin}*1000 >= {rxn_rev_flux}\n", + " cons = model.problem.Constraint(Zero, lb=0, ub=None, name=ex_rxn.id+\"_bin\")\n", + " model.add_cons_vars(cons)\n", + " cons.set_linear_coefficients({variables[ex_rxn.id]:1000, ex_rxn.reverse_variable:-1})\n", + " model.solver.update()\n", + "FBAHelper.add_objective(model, sum([var for var in variables.values()]), \"min\")\n", + "\n", + "solutions = []\n", + "sol = model.optimize()\n", + "while sol.status == \"optimal\":\n", + " solutions.append(sol)\n", + " sol_dict = FBAHelper.solution_to_variables_dict(sol, model)\n", + " \n", + " ## omit the solution from the next search\n", + " cons = model.problem.Constraint(Zero, lb=len(sol_dict)-1, ub=len(sol_dict)-1, name=ex_rxn.id+f\"_exclusion_sol{len(solutions)}\")\n", + " model.add_cons_vars(cons)\n", + " model.solver.update()\n", + " cons.set_linear_coefficients(sol_dict)\n", + " \n", + " sol = model.optimize()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "178e2380", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "0f0f739c", + "metadata": { + "collapsed": true, + "jupyter": { + "outputs_hidden": true + }, + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1530\n", + "12ETHDt_c0 -0.0018671999998142452\n", + "12PPDRt_c0 0.0\n", + "12PPDt_c0 0.0\n", + "23PDE2_c0 0.0\n", + "23PDE4_c0 0.0\n", + "23PDE7_c0 0.0\n", + "23PDE9_c0 0.0\n", + "26DAPLLATi_c0 -0.04260259999973472\n", + "2AMEPHPAT_c0 -0.00046680000000000007\n", + "2FUCLAC__DASH__FUCASEe_c0 0.0\n", + "2MBCOATA_c0 0.0149072\n", + "2MMALD_c0 0.043162200000000005\n", + "2MMALD2_c0 0.043162200000000005\n", + "3DSPHR_c0 -0.00046679999991038594\n", + "3FUCLAC__DASH__FUCASEe_c0 0.0\n", + "3HACPR1_c0 0.00046680000000000007\n", + "3HACPR2_c0 0.00046680000000000007\n", + "3HAD100_c0 0.04037539999991034\n", + "3HAD10M11_c0 0.0127776\n", + "3HAD10M12_c0 0.0149072\n", + "3HAD11M12_c0 0.019263999999910388\n", + "3HAD120_c0 0.03611619999991034\n", + "3HAD121_c0 0.0042592\n", + "3HAD12M13_c0 0.0127776\n", + "3HAD12M14_c0 0.0149072\n", + "3HAD13M14_c0 0.019263999999910388\n", + "3HAD140_c0 0.029911999999910337\n", + "3HAD141_c0 0.0042592\n", + "3HAD14M15_c0 0.0063888\n", + "3HAD14M16_c0 0.0085184\n", + "3HAD15M16_c0 0.008985199999910386\n", + "3HAD160_c0 0.01750359999991039\n", + "3HAD161_c0 0.0042592\n", + "3HAD180_c0 0.0085184\n", + "3HAD181_c0 0.0042592\n", + "3HAD40_c0 0.04037539999991034\n", + "3HAD4M5_c0 0.0127776\n", + "3HAD4M6_c0 0.0149072\n", + "3HAD5M6_c0 0.019263999999910388\n", + "3HAD60_c0 0.04037539999991034\n", + "3HAD6M7_c0 0.0127776\n", + "3HAD6M8_c0 0.0149072\n", + "3HAD7M8_c0 0.019263999999910388\n", + "3HAD80_c0 0.04037539999991034\n", + "3HAD8M10_c0 0.0149072\n", + "3HAD8M9_c0 0.0127776\n", + "3HAD9M10_c0 0.019263999999910388\n", + "3OAACPR1_c0 0.00046680000000000007\n", + "3OAACPR2_c0 0.00046680000000000007\n", + "3OAR100_c0 -0.04037539999991034\n", + "3OAR10M11_c0 0.0127776\n", + "3OAR10M12_c0 0.0149072\n", + "3OAR11M12_c0 0.019263999999910388\n", + "3OAR120_c0 -0.03611619999991034\n", + "3OAR121_c0 0.0042592\n", + "3OAR12M13_c0 0.0127776\n", + "3OAR12M14_c0 0.0149072\n", + "3OAR13M14_c0 0.019263999999910388\n", + "3OAR140_c0 -0.029911999999910337\n", + "3OAR141_c0 0.0042592\n", + "3OAR14M15_c0 0.0063888\n", + "3OAR14M16_c0 0.0085184\n", + "3OAR15M16_c0 0.012875199999910386\n", + "3OAR160_c0 -0.021393599999910334\n", + "3OAR161_c0 0.0042592\n", + "3OAR180_c0 0.0085184\n", + "3OAR181_c0 0.0042592\n", + "3OAR40_c0 0.04037539999991034\n", + "3OAR4M5_c0 0.0127776\n", + "3OAR4M6_c0 0.0149072\n", + "3OAR5M6_c0 0.019263999999910388\n", + "3OAR60_c0 -0.04037539999991034\n", + "3OAR6M7_c0 0.0127776\n", + "3OAR6M8_c0 0.0149072\n", + "3OAR7M8_c0 0.019263999999910388\n", + "3OAR80_c0 -0.04037539999991034\n", + "3OAR8M10_c0 0.0149072\n", + "3OAR8M9_c0 0.0127776\n", + "3OAR9M10_c0 0.019263999999910388\n", + "3OAS100_c0 0.04037539999991034\n", + "3OAS10M11_c0 0.0127776\n", + "3OAS10M12_c0 0.0149072\n", + "3OAS11M12_c0 0.019263999999910388\n", + "3OAS120_c0 0.03611619999991034\n", + "3OAS121_c0 0.0042592\n", + "3OAS12M13_c0 0.0063888\n", + "3OAS12M14_c0 0.0085184\n", + "3OAS13M14_c0 0.012875199999910386\n", + "3OAS140_c0 0.029911999999910337\n", + "3OAS141_c0 0.0042592\n", + "3OAS160_c0 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"EX_alagly_e0 -0.0\n", + "EX_m2mn_e0 -0.0\n", + "EX_cpd15604_e0 -1.665334536937738e-16\n", + "EX_T_antigen_e0 -0.0\n", + "EX_core4_e0 -0.0\n", + "EX_cpd15500_e0 1.1368683772161603e-13\n", + "EX_cpd00122_e0 -0.0\n", + "EX_cpd00129_e0 -0.0\n", + "EX_hspg_degr_5_e0 -0.0\n", + "EX_cpd00073_e0 -0.0\n", + "EX_acgalglcur_e0 -0.0\n", + "EX_cspg_a_e0 -0.0\n", + "EX_cpd00107_e0 3.6262590152880136e-12\n", + "EX_cpd00064_e0 -0.0\n", + "EX_arabttr_e0 -0.0\n", + "EX_sT_antigen_e0 -0.0\n", + "EX_dt5hsu_e0 -0.0\n", + "EX_lacdfucttr_e0 -0.0\n", + "EX_cpd00412_e0 -0.0\n", + "EX_hspg_degr_2_e0 -0.0\n", + "EX_cpd00020_e0 -0.0\n", + "EX_cpd01861_e0 -0.0\n", + "EX_amylose300_e0 -0.0\n", + "EX_cpd00322_e0 -0.0\n", + "EX_cpd00137_e0 -0.0\n", + "EX_cpd00132_e0 -0.0\n", + "EX_cpd00099_e0 -0.0\n", + "EX_cpd11606_e0 -0.0\n", + "EX_mn_e0 -0.0\n", + "EX_cpd00011_e0 1000.0\n", + "EX_cpd00143_e0 -0.0\n", + "EX_strch2_e0 -0.0\n", + "EX_cpd00540_e0 -0.0\n", + "EX_cpd00208_e0 -0.0\n", + "EX_cpd00149_e0 -0.0004668000000265238\n", + "EX_cpd05228_e0 -0.0\n", + "EX_hspg_degr_1_e0 -0.0\n", + "EX_hspg_degr_15_e0 -0.0\n", + "EX_s2l2n2m2mn_e0 -0.0\n", + "EX_amannan140_e0 -0.0\n", + "EX_cspg_c_rest_e0 -0.0\n", + "EX_hspg_rest_e0 -0.0\n", + "EX_cpd00396_e0 -0.0\n", + "EX_cpd00382_e0 -0.0\n", + "EX_lmn2_e0 -0.0\n", + "EX_hspg_degr_13_e0 -0.0\n", + "EX_leugly_e0 -0.0\n", + "EX_s2l2n2m2m_e0 -0.0\n", + "EX_metala_e0 -0.0\n", + "EX_cpd00007_e0 -1000.0\n", + "EX_cspg_ab_rest_e0 -0.0\n", + "EX_alaasp_e0 -0.0\n", + "EX_cpd11658_e0 -0.0\n", + "EX_cpd01017_e0 -463.40539898282435\n", + "EX_cpd11640_e0 -0.0\n", + "EX_cpd00041_e0 -0.0\n", + "EX_cpd00280_e0 -0.0\n", + "EX_cpd11584_e0 -0.0\n", + "EX_cpd00034_e0 -0.0004668000000265238\n", + "EX_cps_bt_e0 -0.0\n", + "EX_l2n2m2mn_e0 -0.0\n", + "EX_neulacnttr_e0 -0.0\n", + "EX_cpd00105_e0 -0.0\n", + "EX_ha_pre1_e0 -0.0\n", + "EX_argarg_e0 -0.0\n", + "EX_cpd00051_e0 -3.674850860534614e-14\n", + "EX_hspg_degr_14_e0 -0.0\n", + "EX_strch1_e0 -0.0\n", + "EX_gchola_e0 -0.0\n", + "EX_levanb_e0 -0.0\n", + "EX_cpd00489_e0 -0.0\n", + "EX_cpd00141_e0 -0.0\n", + "EX_mantr_e0 -0.0\n", + "EX_2fuclac_e0 -0.0\n", + "EX_manb_e0 -0.0\n", + "EX_cpd03279_e0 -0.0\n", + "EX_cpd10515_e0 -0.0009336000000000001\n", + "EX_acgalidour_e0 -0.0\n", + "EX_cpd00311_e0 -0.0\n", + "EX_lps_bt_e0 -0.0\n", + "EX_cpd00033_e0 96.68783651658009\n", + "EX_cpd03725_e0 -0.0\n", + "EX_cpd00030_e0 -0.0004668000000265238\n", + "EX_dsT_antigen_e0 -0.0\n", + "EX_cpd00106_e0 -0.0\n", + "EX_cpd00076_e0 -0.0\n", + "EX_cpd00067_e0 113.84222091044023\n", + "EX_oligofru4_e0 -0.0\n", + "EX_cpd00875_e0 -0.0\n", + "EX_Ser_Thr_e0 -6.252776074688882e-13\n", + "EX_acerA_e0 -0.0\n", + "EX_cpd00065_e0 -0.0\n", + "EX_s2l2n2m2masn_e0 -0.0\n", + "EX_cpd00794_e0 -0.0\n", + "EX_cpd01012_e0 -0.0\n", + "EX_cspg_b_e0 -0.0\n", + "EX_core8_e0 -0.0\n", + "EX_cpd00156_e0 -9.357098429418897e-14\n", + "EX_cpd03198_e0 -0.0\n", + "EX_cspg_c_degr_e0 -0.0\n", + "EX_cspg_c_e0 -0.0\n", + "EX_homogal_e0 -0.0\n", + "EX_cpd00066_e0 -0.0\n", + "EX_acgalidour2s_e0 -0.0\n", + "EX_cpd03105_e0 -0.0\n", + "EX_glyasp_e0 -0.0\n", + "EX_lacnttr_e0 -0.0\n", + "EX_cpd00184_e0 -0.0\n", + "EX_mqn9_e0 -0.0\n", + "EX_chtbs_e0 -0.0\n", + "EX_hspg_degr_3_e0 -0.0\n", + "EX_cpd00001_e0 -5.684341886080802e-14\n", + "EX_cpd01329_e0 -0.0\n", + "EX_hspg_degr_8_e0 -0.0\n", + "EX_cpd00069_e0 -0.0\n", + "EX_cpd11587_e0 -0.0\n", + "EX_cpd00092_e0 -0.0\n", + "EX_cpd00971_e0 -0.0004668000001402106\n", + "EX_cpd00035_e0 -2.6716406864579767e-12\n", + "EX_cpd00832_e0 -0.0\n", + "EX_alathr_e0 -0.0\n", + "EX_starch1200_e0 -0.0\n", + "EX_core7_e0 -0.0\n", + "EX_cpd00138_e0 -0.0\n", + "EX_cpd00249_e0 -0.0\n", + "EX_arabinan101_e0 -0.0\n", + "EX_pullulan1200_e0 -0.0\n", + "EX_cpd08305_e0 -0.0\n", + "EX_cpd00224_e0 -0.0\n", + "EX_phearg_e0 -0.0\n", + "EX_gncore2_e0 -0.0\n", + "EX_cpd00028_e0 -0.0004668000000265238\n", + "EX_cpd00263_e0 -0.0\n", + "EX_levanttr_e0 -0.0\n", + "EX_cpd00104_e0 -0.0\n", + "EX_cpd00246_e0 -0.0\n", + "EX_kestottr_e0 -0.0\n", + "EX_cpd00154_e0 -0.0\n", + "EX_cpd00277_e0 -0.0\n", + "EX_lacndfuchx_e0 -0.0\n", + "EX_3fuclac_e0 -0.0\n", + "EX_cpd00531_e0 -0.0\n", + "EX_cpd00428_e0 -0.0\n", + "EX_cpd00075_e0 141.05261354539797\n", + "EX_core5_e0 -0.0\n", + "EX_cpd00179_e0 -0.0\n", + "EX_cpd00220_e0 -0.0\n", + "EX_hspg_degr_12_e0 -0.0\n", + "EX_cpd01262_e0 -0.0\n", + "EX_cpd00218_e0 -0.0\n", + "EX_rhamnogalurI_e0 -0.0\n", + "EX_apio_D_e0 -0.0\n", + "EX_cpd00635_e0 -0.0\n", + "EX_cpd03047_e0 -9.102377529998796e-13\n", + "EX_kestopt_e0 -0.0\n", + "EX_lmn30_e0 -0.0\n", + "EX_manpt_e0 -0.0\n", + "EX_cpd00136_e0 -0.0\n", + "EX_hspg_degr_11_e0 -0.0\n", + "EX_glycogen1500_e0 -0.0\n", + "EX_cpd00063_e0 -0.0004668000000265238\n", + "EX_cpd15606_e0 -0.0\n", + "EX_core2_e0 -0.0\n", + "EX_glyglu_e0 -0.0\n", + "EX_sTn_antigen_e0 6.252776074688882e-13\n", + "EX_cpd00166_e0 -0.0004668000000265238\n", + "EX_sphmyln_bt_e0 -0.00046680000000000007\n", + "EX_cpd00119_e0 -0.0\n", + "EX_cpd00029_e0 388.50652646011093\n", + "EX_ha_e0 -0.0\n", + "EX_cpd00205_e0 -0.0004668000000265238\n", + "EX_cpd00054_e0 -0.0\n", + "EX_cspg_b_degr_e0 -0.0\n", + "EX_cpd15605_e0 -0.0\n", + "EX_s2l2fn2m2masn_e0 -0.0\n", + "EX_cpd00305_e0 -0.0\n", + "EX_cpd00309_e0 68.09334315214431\n", + "EX_hspg_degr_9_e0 -0.0\n", + "EX_cpd00264_e0 -0.0\n", + "EX_cpd00731_e0 -0.0\n", + "EX_cpd00453_e0 -0.0\n", + "EX_cpd00098_e0 8.96141342555945e-14\n", + "EX_cpd00355_e0 -0.0\n", + "EX_cpd00058_e0 -0.0\n", + "EX_cpd00036_e0 -0.0\n", + "EX_isoval_e0 -0.0\n", + "EX_kesto_e0 -0.0\n", + "EX_cpd00048_e0 -0.0\n", + "EX_cpd00023_e0 -0.0\n", + "EX_cpd00161_e0 -0.0\n", + "EX_cpd00117_e0 -0.0\n", + "EX_cspg_a_degr_e0 -0.0\n", + "EX_cpd15494_e0 -0.0\n", + "EX_cpd15551_e0 -0.0\n", + "EX_levan1000_e0 -0.0\n", + "EX_cpd11583_e0 2.8421709430404007e-13\n", + "EX_cpd00182_e0 -0.0\n", + "EX_cpd01399_e0 -0.0\n", + "EX_cpd00751_e0 -0.0\n", + "EX_cpd00221_e0 -0.0\n", + "EX_cpd00159_e0 -0.0\n", + "EX_cpd00363_e0 -0.0\n", + "EX_cpd00703_e0 -0.0\n", + "EX_ha_deg1_e0 -0.0\n", + "EX_cpd00644_e0 -0.0\n", + "EX_7ocholate_e0 9.102377529998796e-13\n", + "SK_cpd11416_c0 0.1\n", + "SK_cpd02701_c0 0.00046680000000000007\n" + ] + } + ], + "source": [ + "print(len(FBAHelper.solution_to_variables_dict(sol, model)))\n", + "\n", + "for k,v in sol.fluxes.items():\n", + " print(k,v)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "4e8f4642", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " 0 <= 12ETHDt_c0 <= 1000\n" + ] + } + ], + "source": [ + "for rxn in sol_dict:\n", + " print(type(rxn), rxn)\n", + " break" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "77174b2d", + "metadata": {}, + "outputs": [], + "source": [ + "from pprint import pprint\n", + "print(solutions)\n", + "pprint([(rxn, flux) for rxn, flux in sol_dict.items() if flux < 0])" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "4d8a1fe5", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "# from modelseedpy.core.fbahelper import FBAHelper\n", + "# from pprint import pprint\n", + "# # for rxn in model1.reactions:\n", + "# for rxn in FBAHelper.bio_reactions(model1):\n", + "# pprint(dir(rxn))\n", + "# # print(type(rxn.flux_expression))\n", + "# print(type(rxn.forward_variable))\n", + "# break" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "a7c6beb7", + "metadata": {}, + "outputs": [ + { + "ename": "OptimizationError", + "evalue": "Solver status is 'undefined'.", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mOptimizationError\u001b[0m Traceback (most recent call last)", + "Input \u001b[1;32mIn [4]\u001b[0m, in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[0;32m 1\u001b[0m get_ipython()\u001b[38;5;241m.\u001b[39mrun_line_magic(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrun\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m../../ModelSEEDpy/modelseedpy/fbapkg/reactionusepkg.py\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m 2\u001b[0m \u001b[38;5;66;03m# min_media.pkgmgr.removepkgobj(min_media)\u001b[39;00m\n\u001b[1;32m----> 3\u001b[0m min_media \u001b[38;5;241m=\u001b[39m \u001b[43mMinimalMedia\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodel1\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[1;32m~\\Documents\\Argonne\\ModelSEEDpy\\modelseedpy\\fbapkg\\reactionusepkg.py:101\u001b[0m, in \u001b[0;36mMinimalMedia.__init__\u001b[1;34m(self, model, min_growth)\u001b[0m\n\u001b[0;32m 98\u001b[0m \u001b[38;5;66;03m## omit the solution from the next search\u001b[39;00m\n\u001b[0;32m 99\u001b[0m BaseFBAPkg\u001b[38;5;241m.\u001b[39mbuild_constraint(\u001b[38;5;28mself\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmet\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28mlen\u001b[39m(sol_dict)\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, \u001b[38;5;28mlen\u001b[39m(sol_dict)\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, \n\u001b[0;32m 100\u001b[0m coef\u001b[38;5;241m=\u001b[39msol_dict, cobra_obj\u001b[38;5;241m=\u001b[39m\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msol\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mlen\u001b[39m(solutions)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m--> 101\u001b[0m sol \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmodel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43moptimize\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 102\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m solutions:\n\u001b[0;32m 103\u001b[0m logger\u001b[38;5;241m.\u001b[39merror(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNo simulations were feasible.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "File \u001b[1;32m~\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\core\\model.py:1090\u001b[0m, in \u001b[0;36mModel.optimize\u001b[1;34m(self, objective_sense, raise_error)\u001b[0m\n\u001b[0;32m 1086\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mobjective\u001b[38;5;241m.\u001b[39mdirection \u001b[38;5;241m=\u001b[39m {\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmaximize\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmax\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mminimize\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmin\u001b[39m\u001b[38;5;124m\"\u001b[39m}\u001b[38;5;241m.\u001b[39mget(\n\u001b[0;32m 1087\u001b[0m objective_sense, original_direction\n\u001b[0;32m 1088\u001b[0m )\n\u001b[0;32m 1089\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mslim_optimize()\n\u001b[1;32m-> 1090\u001b[0m solution \u001b[38;5;241m=\u001b[39m \u001b[43mget_solution\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mraise_error\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mraise_error\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 1091\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mobjective\u001b[38;5;241m.\u001b[39mdirection \u001b[38;5;241m=\u001b[39m original_direction\n\u001b[0;32m 1092\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m solution\n", + "File \u001b[1;32m~\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\core\\solution.py:236\u001b[0m, in \u001b[0;36mget_solution\u001b[1;34m(model, reactions, metabolites, raise_error)\u001b[0m\n\u001b[0;32m 210\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mget_solution\u001b[39m(model, reactions\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, metabolites\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, raise_error\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m 211\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[0;32m 212\u001b[0m \u001b[38;5;124;03m Generate a solution representation of the current solver state.\u001b[39;00m\n\u001b[0;32m 213\u001b[0m \n\u001b[1;32m (...)\u001b[0m\n\u001b[0;32m 234\u001b[0m \u001b[38;5;124;03m legacy solvers.\u001b[39;00m\n\u001b[0;32m 235\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[1;32m--> 236\u001b[0m \u001b[43mcheck_solver_status\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msolver\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mstatus\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mraise_error\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mraise_error\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m 237\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m reactions \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m 238\u001b[0m reactions \u001b[38;5;241m=\u001b[39m model\u001b[38;5;241m.\u001b[39mreactions\n", + "File \u001b[1;32m~\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\util\\solver.py:560\u001b[0m, in \u001b[0;36mcheck_solver_status\u001b[1;34m(status, raise_error)\u001b[0m\n\u001b[0;32m 556\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m OptimizationError(\n\u001b[0;32m 557\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mModel is not optimized yet or solver context has been switched.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m 558\u001b[0m )\n\u001b[0;32m 559\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m--> 560\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m OptimizationError(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mSolver status is \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mstatus\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "\u001b[1;31mOptimizationError\u001b[0m: Solver status is 'undefined'." + ] + } + ], + "source": [ + "%run ../../ModelSEEDpy/modelseedpy/fbapkg/reactionusepkg.py\n", + "# min_media.pkgmgr.removepkgobj(min_media)\n", + "min_media = MinimalMedia(model1)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a19bd0b4", + "metadata": {}, + "outputs": [], + "source": [ + "# # from modelseedpy.core.fbahelper import FBAHelper\n", + "# from pprint import pprint\n", + "# print(dir(model1.variables))\n", + "# # pprint(model1.variables)\n", + "# for var, value in model1.variables.items():\n", + "# # pprint(dir(var))\n", + "# print(type(var), var, type(value), value)\n", + "# # print(type(rxn.flux_expression))\n", + "# # print(type(rxn.forward_variable))\n", + "# break" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6ea04582-cae6-4ffe-a6b3-d620069d762c", + "metadata": {}, + "outputs": [], + "source": [ + "1.76583881e+05\n", + "1.77176550e+05" + ] + }, + { + "cell_type": "markdown", + "id": "4daa4b27", + "metadata": {}, + "source": [ + "# Test Jenga method" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "f20b513e", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\io\\dict.py:71: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.\n", + "Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations\n", + " value: Union[str, np.float, np.bool, Set, Dict]\n", + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\io\\dict.py:71: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.\n", + "Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations\n", + " value: Union[str, np.float, np.bool, Set, Dict]\n", + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\requests\\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.9) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version!\n", + " warnings.warn(\"urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported \"\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cobrakbase 0.2.8\n" + ] + } + ], + "source": [ + "import warnings\n", + "warnings.filterwarnings(action='once')\n", + "\n", + "# define the environment path \n", + "from pprint import pprint\n", + "from json import dump\n", + "import os\n", + "local_cobrakbase_path = os.path.join('C:', 'Users', 'Andrew Freiburger','Documents','Argonne','cobrakbase')\n", + "os.environ[\"HOME\"] = local_cobrakbase_path\n", + "\n", + "# import the models\n", + "import cobrakbase\n", + "token = 'CKYZK6AZ5V2CT5ILYP7JAXFPW3OLT6VF'\n", + "kbase_api = cobrakbase.KBaseAPI(token)\n", + "\n", + "model1 = kbase_api.get_from_ws(\"E_iAH991V2\",40576)\n", + "model2 = kbase_api.get_from_ws(\"E_iML1515.kb\",40576)\n", + "com_model = kbase_api.get_from_ws(\"CMM_iAH991V2_iML1515.kb\",40576)\n", + "models = [model1, model2]" + ] + }, + { + "cell_type": "markdown", + "id": "a1b3bb51", + "metadata": {}, + "source": [ + "### testing old logic" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "a608b906", + "metadata": { + "collapsed": true, + "jupyter": { + "outputs_hidden": true + }, + "tags": [] + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\medium\\minimal_medium.py:112: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.\n", + " medium = pd.Series()\n" + ] + }, + { + "ename": "NameError", + "evalue": "name 'FBAHelper' is not defined", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mNameError\u001b[0m Traceback (most recent call last)", + "Input \u001b[1;32mIn [2]\u001b[0m, in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[0;32m 1\u001b[0m get_ipython()\u001b[38;5;241m.\u001b[39mrun_line_magic(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrun\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m../../ModelSEED/old_jenga.py\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m----> 2\u001b[0m comm_media, jenga_removals \u001b[38;5;241m=\u001b[39m \u001b[43mminimal_community_media\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodels\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcom_model\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[1;32m~\\Documents\\Argonne\\ModelSEED\\old_jenga.py:14\u001b[0m, in \u001b[0;36mminimal_community_media\u001b[1;34m(models, com_model, syntrophy, min_growth, conserved_cpds, export, printing)\u001b[0m\n\u001b[0;32m 12\u001b[0m media[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmembers\u001b[39m\u001b[38;5;124m\"\u001b[39m][model\u001b[38;5;241m.\u001b[39mid][\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmedia\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m minimal_medium(model, min_growth, minimize_components\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\u001b[38;5;241m.\u001b[39mto_dict()\n\u001b[0;32m 13\u001b[0m model\u001b[38;5;241m.\u001b[39mmedium \u001b[38;5;241m=\u001b[39m media[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmembers\u001b[39m\u001b[38;5;124m\"\u001b[39m][model\u001b[38;5;241m.\u001b[39mid][\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmedia\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m---> 14\u001b[0m media[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmembers\u001b[39m\u001b[38;5;124m\"\u001b[39m][model\u001b[38;5;241m.\u001b[39mid][\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msolution\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[43mFBAHelper\u001b[49m\u001b[38;5;241m.\u001b[39msolution_to_dict(model\u001b[38;5;241m.\u001b[39moptimize())\n\u001b[0;32m 15\u001b[0m media[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcommunity_media\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m FBAHelper\u001b[38;5;241m.\u001b[39msum_dict(model\u001b[38;5;241m.\u001b[39mmedium, media[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcommunity_media\u001b[39m\u001b[38;5;124m\"\u001b[39m])\n\u001b[0;32m 17\u001b[0m \u001b[38;5;66;03m# subtract syntrophic interactions and remove satisfied fluxes\u001b[39;00m\n", + "\u001b[1;31mNameError\u001b[0m: name 'FBAHelper' is not defined" + ] + } + ], + "source": [ + "%run ../../ModelSEED/old_jenga.py\n", + "comm_media, jenga_removals = minimal_community_media(models, com_model)" + ] + }, + { + "cell_type": "markdown", + "id": "27b70f7d-2879-44ea-9c66-a7c2aa3a52db", + "metadata": {}, + "source": [ + "### testing new logic" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "08570eb8", + "metadata": { + "collapsed": true, + "jupyter": { + "outputs_hidden": true + }, + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Bacteroides_thetaiotaomicron_VPI-5482.fbamdl.23\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\medium\\minimal_medium.py:112: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.\n", + " medium = pd.Series()\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "iML1515\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\medium\\minimal_medium.py:112: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.\n", + " medium = pd.Series()\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Initial media defined with 22 exchanges\n", + "Syntrophic fluxes examined after 0.0 minutes, with 2 change(s): {'values_changed': {\"root['EX_cpd00009_e0']\": {'new_value': 0.9808146999971643, 'old_value': 0.17640199999755168}, \"root['EX_cpd10515_e0']\": {'new_value': 12.853568999968639, 'old_value': 0.0009336000000000001}}}\n", + "The 40320 permutations of the {'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd01017_e0', 'EX_cpd03702_e0', 'EX_cpd03725_e0', 'EX_cpd00028_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0'} redundant compounds, from absolute tolerance of 1e-4, will be examined.\n", + "('EX_cpd10515_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd03702_e0')\n", + "('EX_cpd10515_e0', 'EX_cpd01017_e0', 'EX_cpd00028_e0')\n", + "('EX_cpd10515_e0', 'EX_cpd03702_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd10515_e0', 'EX_cpd00028_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd10515_e0', 'EX_cpd00009_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd10515_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd00048_e0', 'EX_cpd03702_e0', 'EX_cpd10515_e0')\n", + "('EX_cpd00048_e0', 'EX_cpd03725_e0', 'EX_cpd03702_e0')\n", + "('EX_cpd00048_e0', 'EX_cpd00028_e0', 'EX_cpd10515_e0')\n", + "('EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd10515_e0')\n", + "('EX_cpd00048_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0')\n", + "('EX_cpd03702_e0', 'EX_cpd03725_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00048_e0', 'EX_cpd10515_e0')\n", + "('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd03725_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd10515_e0')\n", + "('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd03725_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd03702_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0')\n", + "('EX_cpd03702_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd03725_e0', 'EX_cpd00028_e0')\n", + "('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0')\n", + "('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0')\n", + "('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd03702_e0')\n", + "('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd00028_e0')\n", + "('EX_cpd03725_e0', 'EX_cpd00028_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd03702_e0', 'EX_cpd00104_e0')\n", + "('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0')\n", + "('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00104_e0', 'EX_cpd03702_e0')\n", + "('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd01017_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0')\n", + "('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd01017_e0', 'EX_cpd00104_e0', 'EX_cpd00009_e0')\n", + "('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0')\n", + "('EX_cpd00028_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0')\n", + "('EX_cpd00028_e0', 'EX_cpd01017_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0')\n", + "('EX_cpd00009_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00104_e0', 'EX_cpd00028_e0')\n", + "('EX_cpd00009_e0', 'EX_cpd10515_e0', 'EX_cpd01017_e0', 'EX_cpd00104_e0', 'EX_cpd00028_e0')\n", + "[('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0'), ('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd10515_e0'), ('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd03725_e0', 'EX_cpd00048_e0'), ('EX_cpd03702_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0'), ('EX_cpd03702_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd03725_e0', 'EX_cpd00028_e0'), ('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0'), ('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0'), ('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd03702_e0'), ('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd00028_e0'), ('EX_cpd03725_e0', 'EX_cpd00028_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd03702_e0', 'EX_cpd00104_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00104_e0', 'EX_cpd03702_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd01017_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd01017_e0', 'EX_cpd00104_e0', 'EX_cpd00009_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0'), ('EX_cpd00028_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0'), ('EX_cpd00028_e0', 'EX_cpd01017_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0'), ('EX_cpd00009_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00104_e0', 'EX_cpd00028_e0'), ('EX_cpd00009_e0', 'EX_cpd10515_e0', 'EX_cpd01017_e0', 'EX_cpd00104_e0', 'EX_cpd00028_e0')]\n", + "[]\n", + "Unique paths:\n", + "20 [('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0'), ('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd10515_e0'), ('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd03725_e0', 'EX_cpd00048_e0'), ('EX_cpd03702_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0'), ('EX_cpd03702_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd03725_e0', 'EX_cpd00028_e0'), ('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0'), ('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0'), ('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd03702_e0'), ('EX_cpd03725_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd00028_e0'), ('EX_cpd03725_e0', 'EX_cpd00028_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd03702_e0', 'EX_cpd00104_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00104_e0', 'EX_cpd03702_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd01017_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd01017_e0', 'EX_cpd00104_e0', 'EX_cpd00009_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0'), ('EX_cpd00028_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0'), ('EX_cpd00028_e0', 'EX_cpd01017_e0', 'EX_cpd00009_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0'), ('EX_cpd00009_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00104_e0', 'EX_cpd00028_e0'), ('EX_cpd00009_e0', 'EX_cpd10515_e0', 'EX_cpd01017_e0', 'EX_cpd00104_e0', 'EX_cpd00028_e0')]\n", + "{14397: [('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0')]}\n", + "{14397: [('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0'), ('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd10515_e0')]}\n", + "{14397: [('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0'), ('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd10515_e0'), ('EX_cpd03702_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0')]}\n", + "{14397: [('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0'), ('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd10515_e0'), ('EX_cpd03702_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd03702_e0', 'EX_cpd00104_e0')]}\n", + "{14397: [('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0'), ('EX_cpd03702_e0', 'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd10515_e0'), ('EX_cpd03702_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00028_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd03702_e0', 'EX_cpd00104_e0'), ('EX_cpd00028_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00104_e0', 'EX_cpd03702_e0')]}\n", + "EX_cpd03702_e0 removed\n", + "EX_cpd00028_e0 removed\n", + "EX_cpd00104_e0 removed\n", + "EX_cpd10515_e0 removed\n", + "EX_cpd00048_e0 removed\n", + "{'EX_cpd00007_e0': 1000.0,\n", + " 'EX_cpd00009_e0': 0.9808146999971643,\n", + " 'EX_cpd00030_e0': 0.0005359000000265238,\n", + " 'EX_cpd00034_e0': 0.0005009000000265238,\n", + " 'EX_cpd00058_e0': 7.09e-05,\n", + " 'EX_cpd00063_e0': 0.0009873000000197862,\n", + " 'EX_cpd00099_e0': 0.0005204999999932625,\n", + " 'EX_cpd00149_e0': 0.0004693000000265238,\n", + " 'EX_cpd00166_e0': 0.0004668000000265238,\n", + " 'EX_cpd00205_e0': 0.019986099999982798,\n", + " 'EX_cpd00244_e0': 3.23e-05,\n", + " 'EX_cpd00254_e0': 0.0013343000000531902,\n", + " 'EX_cpd00971_e0': 0.00046679999809384753,\n", + " 'EX_cpd01017_e0': 441.5101987604282,\n", + " 'EX_cpd03725_e0': 500.33513180000017,\n", + " 'EX_cpd11574_e0': 7.000000000000001e-07,\n", + " 'EX_sphmyln_bt_e0': 0.00046680000000000007}\n", + "Jenga fluxes examined after 18.6296875 minutes, with 5 change(s): {'dictionary_item_removed': [root['EX_cpd00028_e0'], root['EX_cpd10515_e0'], root['EX_cpd00104_e0'], root['EX_cpd03702_e0'], root['EX_cpd00048_e0']]}\n" + ] + } + ], + "source": [ + "%run ../../ModelSEED/ModelSEEDpy/modelseedpy/core/minimalmediapkg.py\n", + "comm_media, jenga_removals = MinimalMediaPkg.jenga_method(models, com_model)" + ] + }, + { + "cell_type": "markdown", + "id": "9cdee4bc", + "metadata": {}, + "source": [ + "### working example" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "cb10f619", + "metadata": { + "collapsed": true, + "jupyter": { + "outputs_hidden": true + }, + "tags": [] + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Andrew Freiburger\\Documents\\Argonne\\ModelSEEDpy\\modelseedpy\\community\\mscommunity.py:213: DeprecationWarning: invalid escape sequence \\d\n", + " if re.search('^(bio)(\\d+)$', rxn.id):\n", + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\medium\\minimal_medium.py:112: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.\n", + " medium = pd.Series()\n", + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\medium\\minimal_medium.py:112: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.\n", + " medium = pd.Series()\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Initial media defined with 22 exchanges\n", + "Syntrophic fluxes examined after 0.0 minutes, with 2 change(s): {'values_changed': {\"root['EX_cpd10515_e0']\": {'new_value': 6.8362962026137515, 'old_value': 0.0009336000000000001}, \"root['EX_cpd00009_e0']\": {'new_value': 2.9779716628444723, 'old_value': 0.17640200000573714}}}\n", + "The 40320 permutations of the {'EX_cpd00028_e0', 'EX_cpd00296_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd03725_e0', 'EX_cpd00007_e0'} redundant compounds, from absolute tolerance of 1e-4, will be examined.\n", + "Unique combinations:\n", + "6 [{'EX_cpd00028_e0', 'EX_cpd00296_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0'}, {'EX_cpd00028_e0', 'EX_cpd00296_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd03725_e0'}, {'EX_cpd00028_e0', 'EX_cpd00296_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00007_e0'}, {'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0'}, {'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd00048_e0', 'EX_cpd00009_e0', 'EX_cpd03725_e0'}, {'EX_cpd00028_e0', 'EX_cpd00104_e0', 'EX_cpd10515_e0', 'EX_cpd00009_e0', 'EX_cpd00007_e0'}]\n", + "10991\n", + "4201\n", + "10950\n", + "10704\n", + "3914\n", + "10663\n", + "{'EX_cpd00007_e0': 1000,\n", + " 'EX_cpd00009_e0': 2.9779716628444723,\n", + " 'EX_cpd00028_e0': 0.0004668000000265238,\n", + " 'EX_cpd00030_e0': 0.0005359000000265238,\n", + " 'EX_cpd00034_e0': 0.0005009000000265238,\n", + " 'EX_cpd00048_e0': 0.025181600000034356,\n", + " 'EX_cpd00058_e0': 7.09e-05,\n", + " 'EX_cpd00063_e0': 0.0009873000000197862,\n", + " 'EX_cpd00099_e0': 0.0005204999999932625,\n", + " 'EX_cpd00104_e0': 2e-07,\n", + " 'EX_cpd00149_e0': 0.0004693000000265238,\n", + " 'EX_cpd00166_e0': 0.0004668000000265238,\n", + " 'EX_cpd00205_e0': 0.019986099999982798,\n", + " 'EX_cpd00244_e0': 3.23e-05,\n", + " 'EX_cpd00254_e0': 0.0013343000000531902,\n", + " 'EX_cpd00296_e0': 261.78999720518283,\n", + " 'EX_cpd00971_e0': 0.0004668000001402106,\n", + " 'EX_cpd01017_e0': 824.2636444260851,\n", + " 'EX_cpd03725_e0': 657.6688983940277,\n", + " 'EX_cpd10515_e0': 6.8362962026137515,\n", + " 'EX_cpd11574_e0': 7.000000000000001e-07,\n", + " 'EX_sphmyln_bt_e0': 0.0004668000000129604}\n" + ] + } + ], + "source": [ + "%run ../../ModelSEEDpy/modelseedpy/community/mscommunity.py\n", + "comm_media, jenga_removals = MSCommunity.estimate_minimal_community_media(models, com_model)" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "id": "4037a742", + "metadata": {}, + "outputs": [], + "source": [ + "# comm_media[\"community_media\"]\n", + "import json\n", + "with open(com_model.id+\"_media.json\", 'w') as out:\n", + " json.dump(comm_media, out, indent=3)" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "9be5951e", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'dictionary_item_removed': [root['EX_cpd10515_e0'], root['EX_cpd00028_e0'], root['EX_cpd00296_e0'], root['EX_cpd00104_e0'], root['EX_cpd00048_e0']]}" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[root['EX_cpd10515_e0'], root['EX_cpd00028_e0'], root['EX_cpd00296_e0'], root['EX_cpd00104_e0'], root['EX_cpd00048_e0']]\n", + "5\n" + ] + } + ], + "source": [ + "display(jenga_removals)\n", + "print(list(jenga_removals.values())[0])\n", + "changed_quantity = len(list(jenga_removals.values())[0])\n", + "print(changed_quantity)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "de579f43", + "metadata": { + "collapsed": true, + "jupyter": { + "outputs_hidden": true + }, + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "{'community_media': {'EX_cpd00007_e0': 1000,\n", + " 'EX_sphmyln_bt_e0': 0.0004668000000129604,\n", + " 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" 'rxn08168_c0': 0.00022779999999978363,\n", + " 'GSNt2pp_c0': 0.0,\n", + " 'rxn26464_c0': 0.0,\n", + " 'rxn01396_c0': 0.0,\n", + " 'FRUtex_e0': 0.0,\n", + " 'rxn02937_c0': 2.2300000000030425e-05,\n", + " 'rxn00260_c0': -0.28180680000038594,\n", + " 'CPGNabcpp_c0': 0.0,\n", + " ...}}}}" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "{'dictionary_item_removed': [root['EX_cpd10515_e0'], root['EX_cpd00028_e0'], root['EX_cpd00296_e0'], root['EX_cpd00104_e0'], root['EX_cpd00048_e0']]}" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "display(comm_media, jenga_removals)" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "d98196d1", + "metadata": { + "collapsed": true, + "jupyter": { + "outputs_hidden": true + }, + "tags": [] + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Andrew Freiburger\\Documents\\Argonne\\ModelSEEDpy\\modelseedpy\\community\\mscommunity.py:213: DeprecationWarning: invalid escape sequence \\d\n", + " if re.search('^(bio)(\\d+)$', rxn.id):\n", + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\medium\\minimal_medium.py:112: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.\n", + " medium = pd.Series()\n", + "C:\\Users\\Andrew Freiburger\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\cobra\\medium\\minimal_medium.py:112: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.\n", + " medium = pd.Series()\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Initial media defined with 23 exchanges\n", + "Syntrophic fluxes examined after 0.0 minutes, with 2 change(s): {'values_changed': {\"root['EX_cpd00009_e0']\": {'new_value': 2.982600809488827, 'old_value': 0.17640199999437353}, \"root['EX_cpd10515_e0']\": {'new_value': 6.892064499920052, 'old_value': 0.0009336000000000001}}}\n", + "The 362880 permutations of the {'EX_cpd00028_e0', 'EX_cpd00541_e0', 'EX_cpd00294_e0', 'EX_cpd00009_e0', 'EX_cpd03725_e0', 'EX_cpd10515_e0', 'EX_cpd00048_e0', 'EX_cpd00007_e0', 'EX_cpd00104_e0'} redundant compounds, from absolute tolerance of 1e-4, will be examined.\n", + "362879/362880\r" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Andrew Freiburger\\Documents\\Argonne\\ModelSEEDpy\\modelseedpy\\community\\mscommunity.py:213: DeprecationWarning: invalid escape sequence \\d\n", + " if re.search('^(bio)(\\d+)$', rxn.id):\n" + ] + }, + { + "ename": "KeyError", + "evalue": "0", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mKeyError\u001b[0m Traceback (most recent call last)", + "Input \u001b[1;32mIn [2]\u001b[0m, in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[0;32m 1\u001b[0m get_ipython()\u001b[38;5;241m.\u001b[39mrun_line_magic(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrun\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m../../ModelSEEDpy/modelseedpy/community/mscommunity.py\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m----> 2\u001b[0m comm_media, jenga_removals \u001b[38;5;241m=\u001b[39m \u001b[43mMSCommunity\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mestimate_minimal_community_media\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodels\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcom_model\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[1;32m~\\Documents\\Argonne\\ModelSEEDpy\\modelseedpy\\community\\mscommunity.py:701\u001b[0m, in \u001b[0;36mMSCommunity.estimate_minimal_community_media\u001b[1;34m(models, com_model, syntrophy, min_growth, conserved_cpds)\u001b[0m\n\u001b[0;32m 699\u001b[0m possible_removal_tracker \u001b[38;5;241m=\u001b[39m {best:[possible_removal]}\n\u001b[0;32m 700\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m cpdID_sum \u001b[38;5;241m==\u001b[39m best:\n\u001b[1;32m--> 701\u001b[0m \u001b[43mpossible_removal_tracker\u001b[49m\u001b[43m[\u001b[49m\u001b[43mbest\u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39mappend(possible_removal) \n\u001b[0;32m 702\u001b[0m cpds_to_remove \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(possible_removal_tracker\u001b[38;5;241m.\u001b[39mvalues())[\u001b[38;5;241m0\u001b[39m][\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m 703\u001b[0m pprint(media[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcommunity_media\u001b[39m\u001b[38;5;124m\"\u001b[39m])\n", + "\u001b[1;31mKeyError\u001b[0m: 0" + ] + } + ], + "source": [ + "%run ../../ModelSEEDpy/modelseedpy/community/mscommunity.py\n", + "comm_media, jenga_removals = MSCommunity.estimate_minimal_community_media(models, com_model)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.12" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}