CellSimulation/BaseCellSimulation/Enzyms/Enzym.cs

using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.Threading.Tasks;
using System.Text.Json.Serialization;

namespace BaseCellSimulation.Enzyms
{
    public enum EnzymType
    {
        Hill,
        MichelisMenten,
        Linear
    }

    public struct Substrate
    {
        public string Name { get; set; }
        public double Amount { get; set; }

        /// <summary>
        /// mM
        /// </summary>
        [JsonPropertyName("Km")]
        public ValueRange Km { get; set; }

        [JsonPropertyName("Hill")]
        public ValueRange n_Hill { get; 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 double Michaelis_Menten(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 *= ResAmount / (substrate.Km.Value + ResAmount);
            }

            return retVar;
        }

        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
    {
        public abstract void ComputeRate(Resources res);
    }

    public abstract class MembranEnzyme : Enzym
    {
        public abstract double CalculateGradient(CellRessources res);

        public abstract void ComputeRate(double gradient, EnviromentState Env);
    }
}