Added Json Schemas

2025-11-16 19:52:52 +01:00
16 changed files with 931 additions and 35 deletions
@@ -6,4 +6,15 @@
    <Nullable>enable</Nullable>
  </PropertyGroup>

+  <ItemGroup>
+    <None Update="EnzymData\enzymes.schema.json">
+      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+    </None>
+    <None Update="EnzymData\Enzyms.json">
+      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+    </None>
+  </ItemGroup>
+
+  <ProjectExtensions><VisualStudio><UserProperties enzymdata_4enzymes_1schema_1json__JsonSchema="https://json-schema.org/draft-07/schema" /></VisualStudio></ProjectExtensions>
+
 </Project>
@@ -0,0 +1,63 @@
+{
+  "$schema": "cellRessources.schema.json",
+  "BasicCell": {
+    "energy": {
+      "ATP": 2.5,
+      "ADP": 0.8,
+      "AMP": 0.1,
+      "NAD+": 1.0,
+      "NADH": 0.3,
+      "GTP": 0.5,
+      "GDP": 0.2
+    },
+    "Pi": 5.0,
+    "PPi": 0.1,
+
+    "glucose": 5.0,
+    "G6P": 0.5,
+    "F6P": 0.3,
+    "F1,6BP": 0.2,
+    "GA3P": 0.2,
+    "1,3BPG": 0.1,
+    "3PG": 0.4,
+    "2PG": 0.3,
+    "PEP": 0.2,
+    "Pyruvate": 1.0,
+    "Lactate": 1.5,
+
+    "CO2": 10.0,
+    "AcCoA": 0.2,
+
+    "AminoAcids": 5.0,
+    "NucleicAcids": 1.0,
+    "Nucleotides": 2.0,
+    "NTP": 0.5,
+    "dNTP": 0.1,
+
+    "mRNA": 0.5,
+    "DNA_damage": 0.0,
+
+    "SAM": 0.05,
+    "MET": 0.5,
+    "SAH": 0.02,
+    "Homocysteine": 0.01,
+    "Adenosin": 0.1,
+
+    "tRNA": 1.0,
+    "Aminocylated_tRNA": 0.3,
+
+    "H+": 0.00004,
+    "Na+": 10.0,
+    "K+": 140.0,
+
+    "H2O2": 0.001,
+
+    "B12": 0.01,
+    "THF": 0.1,
+    "MethylTHF": 0.1,
+
+    "CytoSolCA": 0.0001,
+    "rERCa": 0.3,
+    "sERCa": 0.6
+  }
+}
@@ -0,0 +1,241 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "type": "object",
+  "properties": {
+    "energy": {
+      "type": "object",
+      "properties": {
+        "ATP": {
+          "type": "number",
+          "minimum": 0,
+          "description": "Adenosine-triphosphate"
+        },
+        "ADP": {
+          "type": "number",
+          "minimum": 0,
+          "description": "Adenosine-diphosphate"
+        },
+        "AMP": {
+          "type": "number",
+          "minimum": 0,
+          "description": "Adenosine-monophosphate"
+        },
+        "NAD+": {
+          "type": "number",
+          "minimum": 0,
+          "description": "Nicotinamide adenine dinucleotide (oxidized form)"
+        },
+        "NADH": {
+          "type": "number",
+          "minimum": 0,
+          "description": "Nicotinamide adenine dinucleotide (reduced form)"
+        },
+        "GTP": {
+          "type": "number",
+          "minimum": 0,
+          "description": "Guanosine-triphosphate"
+        },
+        "GDP": {
+          "type": "number",
+          "minimum": 0,
+          "description": "Guanosine-diphosphate"
+        },
+        "Pi": {
+          "type": "number",
+          "minimum": 0,
+          "description": "Inorganic phosphate"
+        },
+        "PPi": {
+          "type": "number",
+          "minimum": 0,
+          "description": "Inorganic pyrophosphate"
+        }
+      }
+    },
+    "glucose": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Glucose concentration"
+    },
+    "G6P": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Glucose-6-phosphate concentration"
+    },
+    "F6P": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Fructose-6-phosphate concentration"
+    },
+    "F1,6BP": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Fructose-1,6-bisphosphate concentration"
+    },
+    "GA3P": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Glyceraldehyde-3-phosphate concentration"
+    },
+    "1,3BPG": {
+      "type": "number",
+      "minimum": 0,
+      "description": "1,3-Bisphosphoglycerate concentration"
+    },
+    "3PG": {
+      "type": "number",
+      "minimum": 0,
+      "description": "3-Phosphoglycerate concentration"
+    },
+    "2PG": {
+      "type": "number",
+      "minimum": 0,
+      "description": "2-Phosphoglycerate concentration"
+    },
+    "PEP": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Phosphoenolpyruvate concentration"
+    },
+    "Pyruvate": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Pyruvate concentration"
+    },
+    "Lactate": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Lactate concentration"
+    },
+    "CO2": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Carbon dioxide concentration"
+    },
+    "AcCoA": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Acetyl-Coenzyme A concentration"
+    },
+    "AminoAcids": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Total amino acids concentration"
+    },
+    "NucleicAcids": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Total nucleic acids concentration"
+    },
+    "Nucleotides": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Total nucleotides concentration"
+    },
+    "NTP": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Total nucleoside triphosphates concentration"
+    },
+    "dNTP": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Total deoxynucleoside triphosphates concentration"
+    },
+    "mRNA": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Total messenger RNA concentration"
+    },
+    "DNA_damage": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Amount of DNA damage"
+    },
+    "SAM": {
+      "type": "number",
+      "minimum": 0,
+      "description": "S-Adenosyl methionine concentration"
+    },
+    "MET": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Methionine concentration"
+    },
+    "SAH": {
+      "type": "number",
+      "minimum": 0,
+      "description": "S-Adenosyl homocysteine concentration"
+    },
+    "Homocysteine": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Homocysteine concentration"
+    },
+    "Adenosin": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Adenosine concentration"
+    },
+    "tRNA": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Total transfer RNA concentration"
+    },
+    "Aminocylated_tRNA": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Total aminoacylated tRNA concentration"
+    },
+    "H+": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Proton concentration"
+    },
+    "Na+": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Sodium ion concentration"
+    },
+    "K+": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Potassium ion concentration"
+    },
+    "H2O2": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Hydrogen peroxide concentration"
+    },
+    "B12": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Vitamin B12 concentration"
+    },
+    "THF": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Tetrahydrofolate concentration"
+    },
+    "MethylTHF": {
+      "type": "number",
+      "minimum": 0,
+      "description": "5-Methyltetrahydrofolate concentration"
+    },
+    "CytoSolCA": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Cytosolic calcium concentration"
+    },
+    "rERCa": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Rough endoplasmic reticulum calcium concentration"
+    },
+    "sERCa": {
+      "type": "number",
+      "minimum": 0,
+      "description": "Smooth endoplasmic reticulum calcium concentration"
+    }
+  }
+}
@@ -0,0 +1,78 @@
+{
+  "$schema": "enzymes.schema.json",
+  "Cytosolic": [
+    {
+      "Name": "HexokinaseI",
+      "Km": {
+        "Value": 0.05,
+        "Min": 0.02,
+        "Max": 0.1
+      },
+      "Vmax": {
+        "Value": 2.5,
+        "Min": 0.5,
+        "Max": 2.5
+      },
+      "Type": "MichelisMenten",
+      "Description": "Phosphorylates glucose to form glucose-6-phosphate."
+    },
+    {
+      "Name": "HexokinaseII",
+      "Km": {
+        "Value": 0.1,
+        "Min": 0.05,
+        "Max": 0.15
+      },
+      "Vmax": {
+        "Value": 5,
+        "Min": 1,
+        "Max": 10
+      },
+      "Type": "MichelisMenten",
+      "Description": "Phosphorylates glucose to form glucose-6-phosphate."
+    },
+    {
+      "Name": "HexokinaseIII",
+      "Km": {
+        "Value": 0.05,
+        "Min": 0.01,
+        "Max": 0.1
+      },
+      "Vmax": {
+        "Value": 1,
+        "Min": 0.1,
+        "Max": 2
+      },
+      "Type": "MichelisMenten",
+      "Description": "Phosphorylates glucose to form glucose-6-phosphate."
+    },
+    {
+      "Name": "HexokinaseIV_Gluko",
+      "Km": {
+        "Value": 8.5,
+        "Min": 7,
+        "Max": 10
+      },
+      "Vmax": {
+        "Value": 5,
+        "Min": 1,
+        "Max": 10
+      },
+      "Hill": {
+        "Value": 1.7,
+        "Min": 1.6,
+        "Max": 1.9
+      },
+      "Type": "Hill",
+      "Description": "Phosphorylates glucose to form glucose-6-phosphate."
+    },
+    {
+      "Name": "Phosphofructokinase",
+      "K0_5": 0.1,
+      "Hill": 2.0,
+      "Vmax": 80.0,
+      "Type": "Hill",
+      "Description": "Catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate."
+    }
+  ]
+}
@@ -0,0 +1,136 @@
+{
+  "$schema": "https://json-schema.org/draft-07/schema",
+  "title": "Enzyme Parameter Schema",
+  "type": "object",
+  "additionalProperties": {
+    "type": "array",
+    "items": {
+      "type": "object",
+      "properties": {
+        "Name": {
+          "type": "string"
+        },     
+        "Vmax": {
+          "type": "object",
+          "properties": {
+            "Value": {
+              "type": "number",
+              "minimum": 0
+            },
+            "Min": {
+              "type": "number",
+              "minimum": 0
+            },
+            "Max": {
+              "type": "number",
+              "minimum": 0
+            }
+          }
+        },
+        "Type": {
+          "type": "string",
+          "enum": [ "Hill", "MichelisMenten", "Linear" ]
+        },
+        "Substrates": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "Name": { "type": "string" },
+              "Amount": {
+                "type": "number",
+                "minimum": 0
+              },
+              "Km": {
+                "type": "object",
+                "properties": {
+                  "Value": {
+                    "type": "number",
+                    "minimum": 0
+                  },
+                  "Min": {
+                    "type": "number",
+                    "minimum": 0
+                  },
+                  "Max": {
+                    "type": "number",
+                    "minimum": 0
+                  }
+                }
+              },
+              "Hill": {
+                "type": "object",
+                "properties": {
+                  "Value": {
+                    "type": "number",
+                    "minimum": 0
+                  },
+                  "Min": {
+                    "type": "number",
+                    "minimum": 0
+                  },
+                  "Max": {
+                    "type": "number",
+                    "minimum": 0
+                  }
+                }
+              }
+            },
+            "oneOf": [
+              { "required": [ "Km" ] },
+              { "required": [ "Hill" ] }
+            ]
+          }
+        },
+        "Products": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "Name": { "type": "string" },
+              "Amount": {
+                "type": "number",
+                "minimum": 0
+              }
+            }
+          }
+        },
+        "ConsumATPtoADP": {
+          "type": "number",
+          "minimum": 0
+        },
+        "ProduceATPfromADP": {
+          "type": "number",
+          "minimum": 0
+        },
+        "ConsumATPtoAMP": {
+          "type": "number",
+          "minimum": 0
+        },
+        "ProduceATPfromAMP": {
+          "type": "number",
+          "minimum": 0
+        },
+        "ConsumeNADtoNADH": {
+          "type": "number",
+          "minimum": 0
+        },
+        "ProduceNADfromNADH": {
+          "type": "number",
+          "minimum": 0
+        },
+        "ConsumeGDPtoGTP": {
+          "type": "number",
+          "minimum": 0
+        },
+        "ProduceGDPfromGTP": {
+          "type": "number",
+          "minimum": 0
+        },
+        "Description": { "type": "string" }
+      },
+      "required": [ "Vmax", "Type", "Name", "Substrates", "Products" ],
+      "additionalProperties": false
+    }
+  }
+}
@@ -19,14 +19,14 @@ namespace BaseCellSimulation.Enzyms.Cytosol

        public override void ApplyChanges(CellRessources res, double dt)
        {
-            double used = Math.Min(rate * dt, res.Res.Carbon.FBP);
-            res.Res.Carbon.FBP -= used;
-            res.Res.Carbon.GAP += 2 * used;
+            double used = Math.Min(rate * dt, res.Res.Carbon.F1_6BP);
+            res.Res.Carbon.F1_6BP -= used;
+            res.Res.Carbon.GA3P += 2 * used;
        }

        public override void ComputeRate(Resources res)
        {
-            Michaelis_Menten(res.Carbon.FBP);
+            Michaelis_Menten(res.Carbon.F1_6BP);
        }
    }
 }
@@ -25,8 +25,8 @@ namespace BaseCellSimulation.Enzyms.Cytosol

        public override void ApplyChanges(CellRessources res, double dt)
        {
-            double used = Math.Min(rate * dt, Math.Min(res.Res.Carbon.GAP, res.Res.Energy.NAD));
-            res.Res.Carbon.GAP     -= used;
+            double used = Math.Min(rate * dt, Math.Min(res.Res.Carbon.GA3P, res.Res.Energy.NAD));
+            res.Res.Carbon.GA3P     -= used;
            res.Res.Carbon.PBG13   += used;
            res.TransferNADH(used, false);
            res.Res.Ions.Protons += 1.0 * used;
@@ -34,7 +34,7 @@ namespace BaseCellSimulation.Enzyms.Cytosol

        public override void ComputeRate(Resources res)
        {
-            rate = Vmax * (res.Carbon.GAP / (Km + res.Carbon.GAP)) * (res.Energy.NAD / (Km_NAD + res.Energy.NAD));
+            rate = Vmax * (res.Carbon.GA3P / (Km + res.Carbon.GA3P)) * (res.Energy.NAD / (Km_NAD + res.Energy.NAD));
        }
    }
 }
@@ -0,0 +1,16 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol.Hexokinasen
+{
+    public class HK1 : Hexokinasis
+    {
+        public HK1() : base()
+        {
+
+        }
+    }
+}
@@ -0,0 +1,12 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol.Hexokinasen
+{
+    internal class HK2
+    {
+    }
+}
@@ -0,0 +1,12 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol.Hexokinasen
+{
+    internal class HK3
+    {
+    }
+}
@@ -0,0 +1,12 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol.Hexokinasen
+{
+    internal class HK4_GK
+    {
+    }
+}
@@ -4,14 +4,16 @@ using System.Linq;
 using System.Text;
 using System.Threading.Tasks;

-namespace BaseCellSimulation.Enzyms.Cytosol
+namespace BaseCellSimulation.Enzyms.Cytosol.Hexokinasen
 {
-    public class Hexokinasis : InternalEnzym
+    public abstract class Hexokinasis : InternalEnzym
    {
        public Hexokinasis() {
            Km = 0.05;
            Vmax = 5;

+            Type = EnzymType.MichelisMenten;
+
            KmRange = new(0.01, 0.1);
            VmaxRange = new(0.5, 20);
        }
@@ -27,7 +27,7 @@ namespace BaseCellSimulation.Enzyms.Cytosol
        {
            double used = Math.Min(rate * dt, Math.Min(res.Res.Energy.ATP, res.Res.Carbon.F6P));
            res.Res.Carbon.F6P     -= used;
-            res.Res.Carbon.FBP     += used;
+            res.Res.Carbon.F1_6BP     += used;
            res.ConsumeATP(used);
            res.Res.Ions.Protons += used;
        }
@@ -3,37 +3,173 @@ using System.Collections.Generic;
 using System.Linq;
 using System.Text;
 using System.Threading.Tasks;
+using System.Text.Json.Serialization;

 namespace BaseCellSimulation.Enzyms
 {
-    public abstract class Enzym
+    public enum EnzymType
    {
-        /// <summary>
-        /// mM/S
-        /// </summary>
-        public double Vmax { get; set; }
+        Hill,
+        MichelisMenten,
+        Linear
+    }
+
+    public struct Substrate
+    {
+        public string Name { get; set; }
+        public double Amount { get; set; }
+
        /// <summary>
        /// mM
        /// </summary>
-        public double Km { get; set; }
+        [JsonPropertyName("Km")]
+        public ValueRange Km { get; set; }

-        public ValueRange VmaxRange { get; protected set; }
+        [JsonPropertyName("Hill")]
+        public ValueRange n_Hill { get; set; }
+    }

-        public ValueRange KmRange { get; protected set; }
+    public struct Product
+    {
+        public string Name { get; set; }
+        public double Amount { get; set; }
+    }
+
+    public class Enzym
+    {
+        [JsonPropertyName("Name")]
+        public string Name { get; set; }
+
+        /// <summary>
+        /// mM/S
+        /// </summary>
+        [JsonPropertyName("Vmax")]
+        public ValueRange Vmax { get; set; }
+
+        [JsonPropertyName("Type")]
+        public EnzymType Type { get; set; }
+
+        [JsonPropertyName("ConsumATPtoADP")]
+        public double ConsumATPtoADP { get; set; }
+        [JsonPropertyName("ProduceATPfromADP")]
+        public double ProduceATPfromADP { get; set; }
+        [JsonPropertyName("ConsumATPtoAMP")]
+        public double ConsumATPtoAMP { get; set; }
+        [JsonPropertyName("ProduceATPfromAMP")]
+        public double ProduceATPfromAMP { get; set; }
+        [JsonPropertyName("ConsumeNADtoNADH")]
+        public double ConsumeNADtoNADH { get; set; }
+        [JsonPropertyName("ProduceNADfromNADH")]
+        public double ProduceNADfromNADH { get; set; }
+        [JsonPropertyName("ConsumeGDPtoGTP")]
+        public double ConsumeGDPtoGTP { get; set; }
+        [JsonPropertyName("ProduceGDPfromGTP")]
+        public double ProduceGDPfromGTP { get; set; }
+
+        [JsonPropertyName("Substrates")]
+        public List<Substrate> Substrates { get; set; } = new List<Substrate>();
+
+        [JsonPropertyName("Products")]
+        public List<Product> Products { get; set; } = new List<Product>();

        protected double rate; 

-        protected void Michaelis_Menten(double ressource)
+
+        protected double Michaelis_Menten(CellRessources res)
        {
-            rate = Michaelis_Menten(ressource, Vmax, Km);
+            double retVar = Vmax.Value;
+            foreach (Substrate substrate in Substrates)
+            {
+                if (!res.Resources.TryGetValue(substrate.Name, out double ResAmount))
+                    return 0.0;
+                if (ResAmount <= 0.0)
+                    return 0.0;
+
+                retVar *= ResAmount / (substrate.Km.Value + ResAmount);
            }

-        protected double Michaelis_Menten(double consumable,double vmax, double km)
-        {
-            return (vmax * consumable) / (km + consumable);
+            return retVar;
        }

-        public abstract void ApplyChanges(CellRessources res, double dt);
+        protected double HillEquation(CellRessources res)
+        {
+            double retVar = Vmax.Value;
+            foreach (Substrate substrate in Substrates)
+            {
+                if (!res.Resources.TryGetValue(substrate.Name, out double ResAmount))
+                    return 0.0;
+                if (ResAmount <= 0.0)
+                    return 0.0;
+
+
+                retVar *= Math.Pow(ResAmount, substrate.n_Hill.Value) / (Math.Pow(substrate.Km.Value, substrate.n_Hill.Value) + Math.Pow(ResAmount, substrate.n_Hill.Value));
+            }
+
+            return retVar;
+        }
+
+        public void ApplyChanges(CellRessources res, double dt)
+        {
+            double delta = rate * dt;
+            foreach (Substrate substrate in Substrates)
+            {
+                if (res.Resources.TryGetValue(substrate.Name, out double oldVal))
+                {
+                    delta = Math.Min(delta, oldVal / substrate.Amount);
+                }
+            }
+            foreach (Substrate substrate in Substrates)
+            {
+                if (res.Resources.TryGetValue(substrate.Name, out double oldVal))
+                {
+                    res.Resources[substrate.Name] = oldVal - substrate.Amount * delta;
+                }
+            }
+            foreach (Product product in Products)
+            {
+                if (res.Resources.ContainsKey(product.Name))
+                {
+                    res.Resources[product.Name] += product.Amount * delta;
+                }
+                else
+                {
+                    res.Resources[product.Name] = product.Amount * delta;
+                }
+            }
+
+            if(ConsumATPtoADP > 0.0)
+                res.ConsumeATP(ConsumATPtoADP * delta, false);
+            if(ProduceATPfromADP > 0.0)
+                res.RegenerateATP(ProduceATPfromADP * delta, false);
+            if(ConsumATPtoAMP > 0.0)
+                res.ConsumeATP(ConsumATPtoAMP * delta, true);
+            if(ProduceATPfromAMP > 0.0)
+                res.RegenerateATP(ProduceATPfromAMP * delta, true);
+            if(ConsumeNADtoNADH > 0.0)
+                res.TransferNADH(ConsumeNADtoNADH * delta, true);
+            if(ProduceNADfromNADH > 0.0)
+                res.TransferNADH(ProduceNADfromNADH * delta, false);
+            if(ConsumeGDPtoGTP > 0.0)
+                res.TransferGTP(ConsumeGDPtoGTP * delta, true);
+            if(ProduceGDPfromGTP > 0.0)
+                res.TransferGTP(ProduceGDPfromGTP * delta, false);
+        }
+
+        public void ComputeRate(CellRessources res)
+        {
+            switch (Type)
+            {
+                case EnzymType.Hill:
+                    rate = HillEquation(res);
+                    break;
+                case EnzymType.MichelisMenten:
+                    rate = Michaelis_Menten(res);
+                    break;
+                case EnzymType.Linear:
+                    rate = Vmax.Value * res.Resources[Substrates[0].Name];
+                    break;
+            }
+        }
    }

    public abstract class InternalEnzym : Enzym
@@ -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; }
    }
@@ -3,18 +3,23 @@ using System.Collections.Generic;
 using System.Linq;
 using System.Text;
 using System.Threading.Tasks;
+using System.Text.Json.Serialization;

 namespace BaseCellSimulation
 {
    public struct ValueRange
    {
-        public double Start;
-        public double End;
+        [JsonPropertyName("Value")]
+        public double Value;
+        [JsonPropertyName("Min")]
+        public double Min;
+        [JsonPropertyName("Max")]
+        public double Max;

        public ValueRange(double start, double end)
        {
-            Start = start;
-            End = end;
+            Min = start;
+            Max = end;
        }
    }
 }