Not operator

for_local_use.py

@@ -1,4 +1,12 @@
 from mobspy import *
 
 if __name__ == "__main__":
-    pass
+
+    A, B = BaseSpecies()
+    A.a1, A.a2, A.a3, B.b1, B.b2
+    C = A*B
+
+    ~C.a1 >> Zero [10]
+
+    S = Simulation(A | C)
+    print(S.compile())

mobspy/modules/compiler.py

@@ -1,3 +1,6 @@
+from mobspy.modules.compiler_operator_functions import (
+    create_all_not_reactions as cof_create_all_not_reactions
+)
 from mobspy.simulation_logging.log_scripts import (
     error as simlog_error,
     warning as simlog_warning,
@@ -326,6 +329,9 @@ def compile(
             parameters_used, parameters_for_sbml, parameters_in_counts
         )
 
+        # Invert the not$ operators in all reactions
+        reactions_set = cof_create_all_not_reactions(reactions_set)
+
         # BaseSpecies reactions for SBML with theirs respective parameters and rates
         # What do I have so far
         # Species_String_Dict and a set of reaction objects in Reactions_Set

mobspy/modules/compiler_operator_functions.py

@@ -0,0 +1,129 @@
+from itertools import product as ite_product
+
+from mobspy.modules.meta_class import Reactions
+from mobspy.modules.meta_class import Reacting_Species
+from mobspy.modules.meta_class import Zero
+
+"""
+    Species and meta-species supporting scripts
+"""
+def create_all_not_reactions(reactions):
+
+    new_reactions_set = reactions
+
+    def include_new_combinations(r, attribute_to_get):
+        ignore_flag = True
+        for x in getattr(r, attribute_to_get):
+
+            if 'not$' in x['characteristics']:
+                new_reactions_set.remove(r)
+                ignore_flag = False
+                combinations = get_all_non_listed_characteristics(
+                    x['object'],
+                    x['characteristics'] - {'not$'},
+                )
+
+                for comb in combinations:
+                    x['characteristics'] = comb
+                    new_r = new_reaction_with_new_characteristics(r, x['object'], comb)
+                    new_reactions_set.add(new_r)
+
+        return ignore_flag
+
+    has_not = True
+    while has_not:
+        has_not = False
+        loop_reactions = set(new_reactions_set)  # Snapshot
+        for r in loop_reactions:
+            if not include_new_combinations(r, "reactants"):
+                has_not = True
+            if not include_new_combinations(r, "products"):
+                has_not = True
+
+    return new_reactions_set
+
+
+
+def get_all_non_listed_characteristics(
+        species,
+        characteristics
+    ):
+    """
+        This function gets all characteristics related to a species except the ones listed bellow.
+        It uses inheritance to find all charactersitcs linked to a species
+    """
+    operator_characteristics = {c for c in characteristics if '$' in c}
+
+    multi_list_char_struct = []
+    for spe in species.get_references():
+        if characteristics:
+            dimension_cha = {e for e in spe.get_characteristics() if e not in characteristics}
+        else:
+            dimension_cha = {}
+
+        if dimension_cha:
+            multi_list_char_struct.append(dimension_cha)
+
+    combinations = [set(combo) | operator_characteristics for combo in ite_product(*multi_list_char_struct)]
+
+    return combinations
+
+
+def new_reaction_with_new_characteristics(
+        r,
+        spe_to_modify,
+        new_characteristics
+    ):
+    """
+    Create a copy of this reaction, replacing characteristics of a specific dict
+
+    :param dict_to_modify: The specific reactant/product dict to modify
+    :param new_characteristics: New characteristics set for that dict
+    :return: New Reactions object
+    """
+    # Build new reactants list
+    React = Zero
+    for reactant in r.reactants:
+        if reactant['object'] == spe_to_modify:
+            # Use the new characteristics
+            rs = Reacting_Species(
+                reactant['object'],
+                new_characteristics,
+                reactant['stoichiometry'],
+                reactant['label']
+            )
+        else:
+            # Copy existing reactant
+            rs = Reacting_Species(
+                reactant['object'],
+                reactant['characteristics'],
+                reactant['stoichiometry'],
+                reactant['label']
+            )
+
+        React = React + rs
+
+    # Build new products list
+    Product = Zero
+    for product in r.products:
+        if product['object'] == spe_to_modify:
+            # Use the new characteristics
+            ps = Reacting_Species(
+                product['object'],
+                new_characteristics,
+                product['stoichiometry'],
+                product['label']
+            )
+        else:
+            # Copy existing product
+            ps = Reacting_Species(
+                product['object'],
+                product['characteristics'],
+                product['stoichiometry'],
+                product['label']
+            )
+
+        Product = Product +ps
+
+    # Create new reaction
+    return React >> Product [r.rate]