User defined constraints

.gitignore

@@ -104,6 +104,7 @@ ipython_config.py
 .idea/**/dynamic.xml
 .idea/**/uiDesigner.xml
 .idea/**/dbnavigator.xml
+.idea/
 
 # Gradle
 .idea/**/gradle.xml

src/cobra/core/model.py

@@ -4,9 +4,12 @@
 import logging
 from copy import copy, deepcopy
 from functools import partial
+from typing import List
 from warnings import warn
 
 import optlang
+from optlang import Constraint, Variable
+from optlang.container import Container
 from optlang.symbolics import Basic, Zero
 
 from cobra.core.configuration import Configuration
@@ -60,6 +63,8 @@ class Model(Object):
     groups : DictList
         A DictList where the key is the group identifier and the value a
         Group
+    user_defined_const : UserDefinedConstraint
+        A Dictlist to store UserDefinedConstraints
     solution : Solution
         The last obtained solution from optimizing the model.
 
@@ -97,6 +102,8 @@ def __init__(self, id_or_model=None, name=None):
             self.reactions = DictList()  # A list of cobra.Reactions
             self.metabolites = DictList()  # A list of cobra.Metabolites
             self.groups = DictList()  # A list of cobra.Groups
+            self.user_defined_const = Container()  # A list of UserDefinedConstraints
+            self._const_ids = set()
             # genes based on their ids {Gene.id: Gene}
             self._compartments = {}
             self._contexts = []
@@ -326,6 +333,7 @@ def copy(self):
             "notes",
             "annotation",
             "groups",
+            "user_defined_const",
         }
         for attr in self.__dict__:
             if attr not in do_not_copy_by_ref:
@@ -403,6 +411,8 @@ def copy(self):
                 new_objects.append(new_object)
             new_group.add_members(new_objects)
 
+        new.user_defined_const = deepcopy(self.user_defined_const)
+
         try:
             new._solver = deepcopy(self.solver)
             # Cplex has an issue with deep copies
@@ -870,6 +880,77 @@ def get_associated_groups(self, element):
         # check whether the element is associated with the model
         return [g for g in self.groups if element in g.members]
 
+    def add_user_defined_constraints(self, constraints: List[Constraint]) -> None:
+        """Adds User defined constraints (FBC V3) to the model
+
+        Parameters
+        ----------
+        constraints: list
+            a list of UserDefinedConstraints
+        """
+
+        if isinstance(constraints, Constraint):
+            logger.warning(
+                f"The constraints passed must be inside a list: {constraints}")
+            constraints = [constraints]
+        if not isinstance(constraints, list):
+            # if single Constraint, convert to a list
+            raise TypeError(
+                f"The constraints passed must be inside a list: {constraints}"
+            )
+
+        list_of_var_cons = []
+        for constraint in constraints:
+            constraint: "Constraint"
+            if not isinstance(constraint, Constraint):
+                raise TypeError(
+                    f"The user defined constraints passed must be of "
+                    f"type 'Constraints': {constraint}"
+                )
+
+            variable_substituions = dict()
+            for variable in constraint.variables:
+                if self.variables.get(variable.name, None):
+                    variable_substituions[variable] = self.variables.get(variable.name)
+                if variable.name in self.reactions:
+                    variable_substituions[variable] = self.reactions.get_by_id(variable.name).flux_expression
+            constraint._expression = constraint.expression.xreplace(variable_substituions)
+
+            list_of_var_cons.append(constraint)
+            self.user_defined_const.has_key(constraint.name) or self.user_defined_const.append(constraint)
+        self.add_cons_vars(list_of_var_cons)
+
+    def remove_user_defined_constraints(self, constraints: List[Constraint]) -> None:
+        """Remove the constraints from the model
+
+        Parameters
+        ----------
+        constraints: list
+            a list of UserDefinedConstraints
+        """
+        if isinstance(constraints, Constraint):
+            logger.warning(
+                f"The constraints passed must be inside a list: {constraints}")
+            constraints = [constraints]
+        if not isinstance(constraints, list):
+            # if single Constraint, convert to a list
+            raise TypeError(
+                f"The constraints passed must be inside a list: {constraints}"
+            )
+
+        cons_to_remove = []
+        for constraint in constraints:
+            constraint: "Constraint"
+            if not isinstance(constraint, Constraint):
+                raise TypeError(
+                    f"The user defined constraints passed must be of "
+                    f"type 'Constraint': {constraint}"
+                )
+            self._const_ids.remove(constraint.name)
+            cons_to_remove = self.constraints[constraint.name]
+            self.user_defined_const.__delitem__(constraint.name)
+        self.remove_cons_vars(cons_to_remove)
+
     def add_cons_vars(self, what, **kwargs):
         """Add constraints and variables to the model's mathematical problem.