Expanded cell specialization effects

src/auto-evo/mutations/CommonMutationFunctions.cs

@@ -90,7 +90,9 @@ public static MicrobeSpecies GenerateRandomSpecies(MicrobeSpecies mutated, Patch
             MutationLogicFunctions.ColourNewMicrobeSpecies(random, mutated);
         }
 
-        mutated.ModifiableTolerances.CopyFrom(forPatch.GenerateTolerancesForMicrobe(mutated.Organelles));
+        mutated.ModifiableTolerances.CopyFrom(forPatch.GenerateTolerancesForMicrobe(mutated.Organelles,
+            MicrobeInternalCalculations.CalculateSpecializationBonus(mutated.Organelles,
+                new Dictionary<OrganelleDefinition, int>())));
 
         // Override the default species starting name to have more variability in the names
         var nameGenerator = SimulationParameters.Instance.NameGenerator;

src/auto-evo/simulation/SimulationCache.cs

@@ -140,12 +140,11 @@ public EnergyBalanceInfoSimple GetEnergyBalanceForSpecies(MicrobeSpecies species
         // TODO: check if caching instances of these objects would be better than always recreating
         var cached = new EnergyBalanceInfoSimple();
 
-        // Assume here that the species specialization factor may not be up to date, so recalculate here
-        var specialization = MicrobeInternalCalculations.CalculateSpecializationBonus(species.Organelles, workMemory1);
+        var totalSpecializationBonus = species.CellTypeSpecializationBonus;
 
         // Auto-evo uses the average values of compound during the course of a simulated day
         ProcessSystem.ComputeEnergyBalanceSimple(species.Organelles, biomeConditions,
-            GetEnvironmentalTolerances(species, biomeConditions), specialization, species.MembraneType,
+            GetEnvironmentalTolerances(species, biomeConditions), totalSpecializationBonus, species.MembraneType,
             maximumMovementDirection, true, species.PlayerSpecies, worldSettings, CompoundAmountType.Average, this,
             cached);
 
@@ -169,8 +168,13 @@ public float GetSpeedForSpecies(MicrobeSpecies species)
             return speed;
         }
 
-        var cached = MicrobeInternalCalculations.CalculateSpeed(species.Organelles.Organelles, species.MembraneType,
-            species.MembraneRigidity, species.IsBacteria, true);
+        var organelles = species.Organelles;
+
+        // For MicrobeSpecies, Cell Type Specialization = Total Specialization Bonus
+        var totalSpecializationBonus = species.CellTypeSpecializationBonus;
+
+        var cached = MicrobeInternalCalculations.CalculateSpeed(organelles.Organelles, species.MembraneType,
+            species.MembraneRigidity, species.IsBacteria, totalSpecializationBonus, true);
 
         cachedBaseSpeeds.Add(key, cached);
         return cached;
@@ -202,7 +206,12 @@ public float GetRotationSpeedForSpecies(MicrobeSpecies species)
         // prey species by multiple predators might benefit ever so slightly, but it seems kind of unlikely).
         // A more useful thing would be to cache this directly in the species when calculating other movement cached
         // properties.
-        return MicrobeInternalCalculations.CalculateRotationSpeed(species.Organelles.Organelles);
+        var organelles = species.Organelles;
+
+        // For MicrobeSpecies, Cell Type Specialization = Total Specialization Bonus
+        var totalSpecializationBonus = species.CellTypeSpecializationBonus;
+
+        return MicrobeInternalCalculations.CalculateRotationSpeed(organelles.Organelles, totalSpecializationBonus);
     }
 
     public float GetCompoundConversionScoreForSpecies(CompoundDefinition fromCompound, CompoundDefinition toCompound,
@@ -390,9 +399,13 @@ public float GetPredationScore(Species predatorSpecies, Species preySpecies, Bio
             }
         }
 
+        // This will be used at several points to mimic the effect the specialization bonus has on organelles
+        var specializationBonus = predator.CellTypeSpecializationBonus;
+        var preySpecializationBonus = prey.CellTypeSpecializationBonus;
+
         var predatorHexSize = GetBaseHexSizeForSpecies(predator);
         var preyHexSize = GetBaseHexSizeForSpecies(prey);
-        var enzymesScore = GetEnzymesScore(predator, prey.MembraneType.DissolverEnzyme);
+        var enzymesScore = GetEnzymesScore(predator, prey.MembraneType.DissolverEnzyme, specializationBonus);
         var canDigestPrey = predatorHexSize / preyHexSize > Constants.ENGULF_SIZE_RATIO_REQ && canEngulf &&
             enzymesScore > 0.0f;
 
@@ -446,22 +459,25 @@ public float GetPredationScore(Species predatorSpecies, Species preySpecies, Bio
         var preyToolScores = GetPredationToolsRawScores(prey);
 
         var toxicity = predatorToolScores.AverageToxicity;
-        var macrolideScore = predatorToolScores.MacrolideScore;
-        var predatorSlimeJetScore = predatorToolScores.SlimeJetScore;
-        var pullingCiliaModifier = predatorToolScores.PullingCiliaModifier;
+        oxytoxyScore *= specializationBonus;
+        cytotoxinScore *= specializationBonus;
+        channelInhibitorScore *= specializationBonus;
+        var macrolideScore = predatorToolScores.MacrolideScore * specializationBonus;
+        var predatorSlimeJetScore = predatorToolScores.SlimeJetScore * specializationBonus;
+        var pullingCiliaModifier = predatorToolScores.PullingCiliaModifier * specializationBonus;
         var strongPullingCiliaModifier = pullingCiliaModifier * pullingCiliaModifier;
         var predatorToxinResistance = predator.MembraneType.ToxinResistance;
         var predatorPhysicalResistance = predator.MembraneType.PhysicalResistance;
 
-        var preySlimeJetScore = preyToolScores.SlimeJetScore;
+        var preySlimeJetScore = preyToolScores.SlimeJetScore * preySpecializationBonus;
         var preyMucocystsScore = preyToolScores.MucocystsScore;
         var preyPilusScore = preyToolScores.PilusScore;
         var preyInjectisomeScore = preyToolScores.InjectisomeScore;
         var preyToxicity = preyToolScores.AverageToxicity;
-        var preyOxytoxyScore = preyToolScores.OxytoxyScore;
-        var preyCytotoxinScore = preyToolScores.CytotoxinScore;
-        var preyMacrolideScore = preyToolScores.MacrolideScore;
-        var preyChannelInhibitorScore = preyToolScores.ChannelInhibitorScore;
+        var preyOxytoxyScore = preyToolScores.OxytoxyScore * preySpecializationBonus;
+        var preyCytotoxinScore = preyToolScores.CytotoxinScore * preySpecializationBonus;
+        var preyMacrolideScore = preyToolScores.MacrolideScore * preySpecializationBonus;
+        var preyChannelInhibitorScore = preyToolScores.ChannelInhibitorScore * preySpecializationBonus;
         var preyOxygenMetabolismInhibitorScore = preyToolScores.OxygenMetabolismInhibitorScore;
         var defensivePilusScore = preyToolScores.DefensivePilusScore;
         var defensiveInjectisomeScore = preyToolScores.DefensiveInjectisomeScore;
@@ -1222,7 +1238,7 @@ public PredationToolsRawScores GetPredationToolsRawScores(MicrobeSpecies microbe
         return predationToolsRawScores;
     }
 
-    public float GetEnzymesScore(MicrobeSpecies predator, string dissolverEnzyme)
+    public float GetEnzymesScore(MicrobeSpecies predator, string dissolverEnzyme, float specializationBonus)
     {
         // This is not cached as it is not useful at the present time (as this is only called from places that cache
         // stuff)
@@ -1263,9 +1279,9 @@ public float GetEnzymesScore(MicrobeSpecies predator, string dissolverEnzyme)
 
         // If not digestible, mark that as a 0 score
         if (!isMembraneDigestible)
-            enzymesScore = 0;
+            return 0;
 
-        return enzymesScore;
+        return enzymesScore * specializationBonus;
     }
 
     public ResolvedMicrobeTolerances GetEnvironmentalTolerances(MicrobeSpecies species,

src/general/GameWorld.cs

@@ -260,7 +260,8 @@ public static void SetSpeciesInitialTolerances(Species species, PatchMap map, Pa
 
         if (species is MicrobeSpecies microbeSpecies)
         {
-            species.ModifiableTolerances.CopyFrom(patch.GenerateTolerancesForMicrobe(microbeSpecies.Organelles));
+            species.ModifiableTolerances.CopyFrom(patch.GenerateTolerancesForMicrobe(microbeSpecies.Organelles,
+                microbeSpecies.CellTypeSpecializationBonus));
         }
         else if (species is MulticellularSpecies multicellularSpecies)
         {

src/general/base_stage/CreatureStageBase.cs

@@ -579,7 +579,8 @@ private void CheckPerformanceEnoughForSimulationSpeed()
 
     private void AdjustTolerancesToWorkInPatch(MicrobeSpecies species, Patch currentPatch)
     {
-        var optimal = currentPatch.GenerateTolerancesForMicrobe(species.Organelles);
+        var optimal = currentPatch.GenerateTolerancesForMicrobe(species.Organelles,
+            species.CellTypeSpecializationBonus);
 
         var current = MicrobeEnvironmentalToleranceCalculations.CalculateTolerances(species, currentPatch.Biome);
 

src/general/mutation_points/CellTypeEditsFacade.cs

@@ -94,7 +94,7 @@ public bool IsBacteria
     /// </summary>
     public string? SplitFromTypeName => originalCell.SplitFromTypeName;
 
-    public float SpecializationBonus =>
+    public float CellTypeSpecializationBonus =>
         throw new NotSupportedException("This class doesn't dynamically recalculate the specialization bonus");
 
     // TODO: check that this is right (there might sometimes be too many items in removedOrganelles)

src/general/mutation_points/MicrobeEditsFacade.cs

@@ -91,7 +91,7 @@ public string CellTypeName
     /// </summary>
     public string? SplitFromTypeName => microbeSpecies.SplitFromTypeName;
 
-    public float SpecializationBonus =>
+    public float CellTypeSpecializationBonus =>
         throw new NotSupportedException("This class doesn't dynamically recalculate the specialization bonus");
 
     public int Count

src/general/world_effects/AmmoniaProductionEffect.cs

@@ -55,7 +55,7 @@ public static float GetSpeciesModifiersForEffect(Species species, out ResolvedMi
             resolvedTolerances = MicrobeEnvironmentalToleranceCalculations.ResolveToleranceValues(
                 MicrobeEnvironmentalToleranceCalculations.CalculateTolerances(microbeSpecies, biome));
 
-            specialization = microbeSpecies.SpecializationBonus;
+            specialization = microbeSpecies.CellTypeSpecializationBonus;
         }
         else if (species is MulticellularSpecies multicellularSpecies)
         {

src/microbe_stage/ICellDefinition.cs

@@ -28,6 +28,13 @@ public interface ICellDefinition : IReadOnlyCellDefinition, ISimulationPhotograp
 
     public string FormattedName { get; }
 
+    /// <summary>
+    ///   A multiplier starting from 1 and going up based on how specialized this cell type is. This is eventually
+    ///   applied to <see cref="Components.BioProcesses.OverallSpeedModifier"/> and many other systems.
+    ///   Does not include any adjacency bonus effects that may be applied later.
+    /// </summary>
+    public float CellTypeSpecializationBonus { get; set; }
+
     /// <summary>
     ///   Repositions the cell to the origin and recalculates any properties dependent on its position.
     /// </summary>
@@ -49,6 +56,8 @@ public interface IReadOnlyCellDefinition
 public interface ICellTypeDefinition : ICellDefinition, IReadOnlyCellTypeDefinition
 {
     public new int MPCost { get; set; }
+
+    public new float CellTypeSpecializationBonus { get; }
 }
 
 public interface IReadOnlyCellTypeDefinition : IReadOnlyCellDefinition, IPlayerReadableName
@@ -66,7 +75,7 @@ public interface IReadOnlyCellTypeDefinition : IReadOnlyCellDefinition, IPlayerR
     ///   A multiplier starting from 1 and going up based on how specialized this cell type is. This is eventually
     ///   applied to <see cref="Components.BioProcesses.OverallSpeedModifier"/>
     /// </summary>
-    public float SpecializationBonus { get; }
+    public float CellTypeSpecializationBonus { get; }
 }
 
 /// <summary>
@@ -127,7 +136,7 @@ public static void SetupWorldEntities(this ICellDefinition definition, IWorldSim
             workMemory1, workMemory2)
         {
             // For visualization the bonus doesn't matter, but we need to set a valid value
-            SpecializationBonus = 1,
+            CellTypeSpecializationBonus = 1,
         };
 
         species.SetupWorldEntities(worldSimulation);

src/microbe_stage/IOrganelleComponent.cs

@@ -19,6 +19,7 @@ public interface IOrganelleComponent
     ///   <see cref="UpdateSync"/>
     /// </summary>
     /// <param name="organelleContainer">Organelle container instance this organelle is inside</param>
+    /// <param name="specializationFactor">Organelle effect bonus cell from specialization and adjacency</param>
     /// <param name="microbeEntity">Entity reference of the entity that contains this organelle</param>
     /// <param name="worldSimulation">
     ///   The simulation this entity is in. Care needs to be taken on what operations are safe to perform here in an
@@ -28,7 +29,8 @@ public interface IOrganelleComponent
     /// </param>
     /// <param name="energyCostMultiplier">modifies the amount of ATP to be consumed by organelles</param>
     /// <param name="delta">Time since the last update in seconds</param>
-    public void UpdateAsync(ref OrganelleContainer organelleContainer, in Entity microbeEntity,
+    public void UpdateAsync(ref OrganelleContainer organelleContainer, ref SpecializationFactor specializationFactor,
+        in Entity microbeEntity,
         IWorldSimulation worldSimulation, float energyCostMultiplier, float delta);
 
     /// <summary>