BFactorRep.cs

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using UnityEngine;
using System.Collections;
using System.Collections.Generic;
using Molecule.Model;
using UI;
using Molecule.Control;

public class BFactorRep {
    public static List<float[]> backupCaList = MoleculeModel.backupCatomsLocationlist ;
    public static List<string> backupCaChainList = MoleculeModel.backupCaSplineChainList ;
    public static List<float> backupBfactCAList;
    public static float minValue;
    public static float maxValue;
    public static string minval = "";
    public static string maxval = "";

    public static void CreateBFRep() {
        List<float[]>   alist           =   MoleculeModel.atomsLocationlist;
        List<float[]>   calist          =   new List<float[]>(MoleculeModel.backupCatomsLocationlist);
        List<string>    caChainlist     =   new List<string>(MoleculeModel.backupCaSplineChainList);
        List<string>    atomsNameList   =   MoleculeModel.atomsNamelist;
        List<AtomModel> typelist        =   MoleculeModel.atomsTypelist;
            //C.R
        List<float>     Bfactorlist     =   MoleculeModel.BFactorList;
        List<int>       residlist       =   MoleculeModel.residueIds;
        List<float>     BfactCAlist     =   new List<float> ();
        //List<string>  resnamelist     =   MoleculeModel.atomsResnamelist;

            
        // Trace interpolation from C-alpha positions
        // Only if there are more than 2 C-alpha

        if(calist.Count > 2) {

            // Compute bfactor mean by residue
            int comp = 0; //counter number of residues
            float b = 0;
            float bfac = residlist[0];
            int j = 0; //counter CA

            for(int i=1;i<residlist.Count;i++){

                if(i+1 == residlist.Count){
                    bfac = b/comp;
                    BfactCAlist.Add (bfac);
                }

                if((atomsNameList[i-1] == atomsNameList[i]) && (residlist[i-1] == residlist[i])){
                    if (atomsNameList[i] == "CA"){
                        calist.RemoveAt(j);
                        caChainlist.RemoveAt(j);
                        //Debug.Log ("Remove");
                    }
                }

                if(residlist[i-1] == residlist[i]){
                    b += Bfactorlist[i];
                    comp++;
                }

                else{
                    bfac = b/comp;
                    BfactCAlist.Add (bfac);
                    j++;
                    b = Bfactorlist[i];
                    comp = 1;
                }
            }

            // Compute bfactor min
            if(SecondaryStructureOldGUI.isRescale)
                minValue = float.Parse (minval);
            else{
                minValue = GetMin(BfactCAlist);
            }

            for(int i=0; i<BfactCAlist.Count;i++)
                BfactCAlist[i] = BfactCAlist[i] - minValue;

            // End of bfactor min

            // Compute Bfactor max
            if(SecondaryStructureOldGUI.isRescale)
                maxValue = (float.Parse (maxval) - float.Parse (minval));
            else{
                maxValue = GetMax(BfactCAlist);
            }

            //bfactor value between 0 and 1
            for(int i=0; i<BfactCAlist.Count;i++){
                BfactCAlist[i] = BfactCAlist[i]/maxValue;
            }

            GenInterpolationArray_BF geninterpolationarray = new GenInterpolationArray_BF();
            geninterpolationarray.InputKeyNodes=calist;
            geninterpolationarray.InputTypeArray=caChainlist;
            geninterpolationarray.InputBfactArray=BfactCAlist;

            geninterpolationarray.CalculateSplineArray();

            calist=null;
            caChainlist=null;
            Bfactorlist=null;

            calist=geninterpolationarray.OutputKeyNodes;
            caChainlist=geninterpolationarray.OutputTypeArray;
            Bfactorlist=geninterpolationarray.OutputBfactArray;
        }

        MoleculeModel.CaSplineList=calist;
        MoleculeModel.CaSplineTypeList = new List<AtomModel>();

        string typebf;

        for (int k=0; k<calist.Count; k++) {
            typebf = GetBFStyle(Bfactorlist[k]);
            MoleculeModel.CaSplineTypeList.Add (AtomModel.GetModel (typebf));
            }

        MoleculeModel.CaSplineChainList=caChainlist;
            
        if(UIData.ffType == UIData.FFType.HiRERNA)
            MoleculeModel.bondEPList=ControlMolecule.CreateBondsList_HiRERNA(atomsNameList);
        else {
            //MoleculeModel.bondList=ControlMolecule.CreateBondsList(alist,typelist);
            MoleculeModel.bondEPList=ControlMolecule.CreateBondsEPList(alist,typelist);
            MoleculeModel.bondCAList=ControlMolecule.CreateBondsCAList(caChainlist);    
        }
        MoleculeModel.atomsnumber = alist.Count;
        MoleculeModel.bondsnumber = MoleculeModel.bondEPList.Count;
        MoleculeModel.CaSplineChainList=caChainlist;
        minval = minValue.ToString ();
        maxval = (maxValue+minValue).ToString ();
    }  

    public static string GetBFStyle(float BFValue){
        string typebf;
        if (BFValue < 0.1)
            typebf = "BF1";
        else if (BFValue <0.2)
            typebf = "BF2";
        else if (BFValue <0.3)
            typebf = "BF3";
        else if (BFValue <0.4)
            typebf = "BF4";
        else if (BFValue <0.5)
            typebf = "BF5";
        else if (BFValue <0.6)
            typebf = "BF6";
        else if (BFValue <0.7)
            typebf = "BF7";
        else if (BFValue <0.8)
            typebf = "BF8";
        else if (BFValue <0.9)
            typebf = "BF9";
        else
            typebf = "BF10";
        return typebf;
    }

    public static float GetMin (List<float> ListValues){
        float mymin = ListValues[0];
        foreach (float g in ListValues)
            if (g<mymin)
                mymin =g;
        return mymin;
    }

    public static float GetMax (List<float> ListValues){
        float mymax = ListValues [0];
        foreach (float f in ListValues)
            if (f>mymax)
                mymax =f;
        return mymax;
    }

}