Add first draft of code for metabolism submodel generator

wc_model_gen/eukaryote/metabolism.py

@@ -0,0 +1,76 @@
+""" Generator for metabolism submodel for eukaryotes
+
+:Author: Yin Hoon Chew <yinhoon.chew@mssm.edu>
+:Date: 2020-01-21
+:Copyright: 2020, Karr Lab
+:License: MIT
+"""
+
+import wc_model_gen
+
+
+class MetabolismSubmodelGenerator(wc_model_gen.SubmodelGenerator):
+    """ Generator for metabolism submodel 
+
+        Options:
+        * recycled_metabolites (:obj:`dict`): a dictionary with metabolite species IDs
+            as keys and recycled amounts as values
+        * atp_from_submodel (:obj:`bool`): if True, ATP requirement will be calculated 
+            from other generated submodels, else the value will be expected to be in a 
+            parameter created during model initialization; default is True     
+    """
+
+    def clean_and_validate_options(self):
+        """ Apply default options and validate options """
+        options = self.options
+
+        recycled_metabolites = options.get('recycled_metabolites', {})
+        options['recycled_metabolites'] = recycled_metabolites
+
+        atp_from_submodel = options.get('atp_from_submodel', True)
+        options['atp_from_submodel'] = atp_from_submodel
+
+    def gen_reactions(self):
+        """ Generate reactions associated with submodel 
+        
+        A biomass reaction is generated by accounting for all the metabolites that 
+        are consumed and produced by the reactions in other submodels, and the 
+        metabolites that are in the free pool
+
+        """
+        cell = self.knowledge_base.cell     
+        model = self.model
+        submodel = self.submodel
+
+        biomass_rxn = model.reactions.create(
+            submodel=submodel,
+            id='biomass_reaction',
+            name='Biomass reaction',
+            reversible=False,
+            comments='Pseudo-reaction for use as dFBA objective function')
+
+        # Add metabolites in the free pool to the RHS of the biomass reaction
+        biomass_rxn.participants.add(
+            model_species.species_coefficients.get_or_create(coefficient=participant.coefficient))
+
+        # Add metabolites to be recycled to the LHS of the biomass reaction
+
+        # Add metabolite requirement of other submodels
+		# Add ATP usage
+
+        # Add biomass reaction as objective function
+        submodel.dfba_obj = wc_lang.DfbaObjective(model=model)
+        submodel.dfba_obj.id = submodel.dfba_obj.gen_id()
+        obj_expression = biomass_rxn.id
+        dfba_obj_expression, error = wc_lang.DfbaObjectiveExpression.deserialize(
+            obj_expression, {wc_lang.Reaction: {biomass_rxn.id: biomass_rxn}})
+        assert error is None, str(error)
+        submodel.dfba_obj.expression = dfba_obj_expression
+
+    def gen_rate_laws(self):
+        """ Generate rate laws for the reactions in the submodel """
+        pass
+
+    def calibrate_submodel(self):
+        """ Calibrate the submodel using data in the KB """
+        pass