Added Json Schemas

BaseCellSimulation/Organell.cs

@@ -1,4 +1,6 @@
 using System;
+using System.Text.Json;
+using System.Text.Json.Serialization;
 
 namespace BaseCellSimulation
 {
@@ -9,6 +11,43 @@ namespace BaseCellSimulation
     {
         public Resources Res;
         public EnviromentState Env = new();
+        [JsonPropertyName("energy")]
+        public EnergyPool energyPool;
+        public Dictionary<string, double> Resources => new Dictionary<string, double>();
+
+        public static CellRessources LoadRessources(string jsonPath)
+        {
+            string json = File.ReadAllText(jsonPath);
+            using var doc = JsonDocument.Parse(json);
+            var root = doc.RootElement;
+            var result = new CellRessources();
+            
+            // deserialice energy
+            if (root.TryGetProperty("energy", out JsonElement energyElement))
+            {
+                result.energyPool = JsonSerializer.Deserialize<EnergyPool>(energyElement.GetRawText());
+            }
+
+            foreach(var property in root.EnumerateObject())
+            {
+                if (property.NameEquals("energy"))
+                    continue; // already handled
+
+                if (property.Value.ValueKind == JsonValueKind.Number)
+                {
+                    result.Resources[property.Name] = property.Value.GetDouble();
+                }
+            }
+
+            return result;
+        }
+
+        public static void SaveRessources(CellRessources ressources, string jsonPath)
+        {
+            var options = new JsonSerializerOptions { WriteIndented = true };
+            string json = JsonSerializer.Serialize(ressources, options);
+            File.WriteAllText(jsonPath, json);
+        }
 
         // pH in mM-basiertem Hilfsformat (vereinfachte Umrechnung):
         public double pH_in => 3.0 - Math.Log10(Res.Ions.Protons + 1e-12);
@@ -117,6 +156,22 @@ namespace BaseCellSimulation
             }
         }
 
+        public void TransferGTP(double amount, bool toGDP)
+        {
+            if (toGDP)
+            {
+                if (Res.Energy.GTP < amount) amount = Res.Energy.GTP;
+                Res.Energy.GTP -= amount;
+                Res.Energy.GDP += amount;
+            }
+            else
+            {
+                if (Res.Energy.GDP < amount) amount = Res.Energy.GDP;
+                Res.Energy.GDP -= amount;
+                Res.Energy.GTP += amount;
+            }
+        }
+
         // --- Initialisierung mit plausiblen Startwerten ---
         /// <summary>
         /// Erzeugt eine CellRessources-Instanz mit vernünftigen Startwerten (grobe physiologische Annahmen).
@@ -143,8 +198,8 @@ namespace BaseCellSimulation
             cr.Res.Carbon.Glucose = 1.0;   // mM intrazellulär (abhängig von Aufnahme)
             cr.Res.Carbon.G6P = 0.05;
             cr.Res.Carbon.F6P = 0.02;
-            cr.Res.Carbon.FBP = 0.005;
-            cr.Res.Carbon.GAP = 0.01;
+            cr.Res.Carbon.F1_6BP = 0.005;
+            cr.Res.Carbon.GA3P = 0.01;
             cr.Res.Carbon.PBG13 = 0.005;
             cr.Res.Carbon.PG3 = 0.02;
             cr.Res.Carbon.PG2 = 0.01;
@@ -229,34 +284,114 @@ namespace BaseCellSimulation
     /// <summary>Energiemengen: ATP/ADP/AMP + NAD/NADH + GTP/GDP</summary>
     public struct EnergyPool
     {
+        /// <summary>
+        /// Adenosine-triphosphate
+        /// </summary>
         public double ATP;
+        /// <summary>
+        /// Adenosine diphosphate
+        /// </summary>
         public double ADP;
+        /// <summary>
+        /// Adenosine monophosphat
+        /// </summary>
         public double AMP;
+
+        /// <summary>
+        /// Nicotinamide adenine dinucleotide
+        /// </summary>
         public double NAD;
+
+        /// <summary>
+        /// Nicotinamide adenine dinucleotide
+        /// </summary>
         public double NADH;
+
+        /// <summary>
+        /// Nicotinamide adenine dinucleotide phosphate
+        /// </summary>
+        public double NADPH;
+
+        /// <summary>
+        /// Guanosintriphosphat
+        /// </summary>
         public double GTP;
-        public double GDP { get; internal set; }
+
+        /// <summary>
+        /// Guanosindiphosphat
+        /// </summary>
+        public double GDP;
+
+        /// <summary>
+        /// inorganic phosphate
+        /// </summary>
+        public double Pi;
+
+        /// <summary>
+        /// Pyrophosphat
+        /// </summary>
+        public double PPi;
     }
 
     /// <summary>Inorganische Phosphate</summary>
     public struct Phosphate
     {
-        public double Pi;  // anorganisches Phosphat
-        public double PPi; // Pyrophosphat
+        /// <summary>
+        /// inorganic phosphate
+        /// </summary>
+        public double Pi;
+
+        /// <summary>
+        /// Pyrophosphat
+        /// </summary>
+        public double PPi;
     }
 
     /// <summary>Kohlenstoff- / Glykolyse-Intermediaten</summary>
     public struct CarbonPool
     {
         public double Glucose;
+
+        /// <summary>
+        /// Glucose-6-phosphate
+        /// </summary>
         public double G6P;
+
+        /// <summary>
+        /// Fructose-6-phosphate
+        /// </summary>
         public double F6P;
-        public double FBP;
-        public double GAP;
+
+        /// <summary>
+        /// Fructose 1,6-bisphosphate
+        /// </summary>
+        public double F1_6BP;
+
+        /// <summary>
+        /// Glycerinaldehyd-3-phosphat
+        /// </summary>
+        public double GA3P;
+
+        /// <summary>
+        /// 1,3-Bisphosphoglycerat
+        /// </summary>
         public double PBG13;
+
+        /// <summary>
+        /// 3-Phosphoglycerat
+        /// </summary>
         public double PG3;
+
+        /// <summary>
+        ///  2-Phosphoglycerat
+        /// </summary>
         public double PG2;
+
+        /// <summary>
+        /// Phosphoenolpyruvat
+        /// </summary>
         public double PEP;
+
         public double Pyruvate;
         public double Lactate;
         public double CO2;
@@ -271,14 +406,35 @@ namespace BaseCellSimulation
         public double Waste;
         public double NucleicAcids;
         public double Nucleotides;
+
+        /// <summary>
+        /// Nukleosidtriphosphate
+        /// </summary>
         public double NTP;
+
+        /// <summary>
+        /// Desoxyribonukleotidtriphosphate
+        /// </summary>
         public double dNTP;
         public double mRNA;
         public double DNA_damage;
         public double AcetylCoA;
+
+        /// <summary>
+        /// S-Adenosylmethionin
+        /// </summary>
         public double SAM;
+
+        /// <summary>
+        /// Methionine
+        /// </summary>
         public double MET;
+
+        /// <summary>
+        /// S-Adenosylhomocystein
+        /// </summary>
         public double SAH;
+
         public double Homocystein;
         public double Adenosin;
         internal double tRNA;
@@ -289,9 +445,22 @@ namespace BaseCellSimulation
     public struct IonPool
     {
         public double Protons; // H+ (vereinfachte Einheit mM)
-        public double ROS;     // reactive oxygen species
+
+        /// <summary>
+        /// reactive oxygen species
+        /// </summary>
+        public double ROS;
+
+        /// <summary>
+        /// NAtrium-Ionen
+        /// </summary>
         public double Na;
+
+        /// <summary>
+        /// Kalium-Ionen
+        /// </summary>
         public double K;
+
         public double H2O2;
     }
 
@@ -302,6 +471,9 @@ namespace BaseCellSimulation
 
     public struct Folates
     {
+        /// <summary>
+        /// Tetrahydrofolsäure
+        /// </summary>
         public double THF { get; internal set; }
         public double MethylTHF { get; internal set; }
     }