AlphaChainSmoother.cs

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

public class AlphaChainSmoother {
    public static List<float[]> backupCaList = MoleculeModel.CatomsLocationlist ;
    public static List<string> backupCaChainList = MoleculeModel.backupCaSplineChainList ;
//  private ArrayList caChainlist;
    

    void Start () {
//      backupCAlist = (ArrayList)MoleculeModel.bondCAList.Clone();
    //  calist = backupCAlist.Clone();
    //  caChainlist = MoleculeModel.bondCAList.Clone();
    }
        
    public static void ReSpline () {
        List<float[]>   alist           = MoleculeModel.atomsLocationlist ;
        List<AtomModel> typelist        = MoleculeModel.atomsTypelist ;
        List<string>    atomsNameList   = MoleculeModel.atomsNamelist ;
        List<float[]>   calist          = new List<float[]>(MoleculeModel.CatomsLocationlist);
        List<string>    caChainlist     = new List<string>(MoleculeModel.backupCaSplineChainList);
        List<int>       residlist       =   MoleculeModel.residueIds;
        //List<string>  resnamelist     =   MoleculeModel.atomsResnamelist;
            
        // Trace interpolation from C-alpha positions
        // Only if there are more than 2 C-alpha
        if(calist.Count > 2) {

            int j = 0;
            for(int i=1;i<residlist.Count;i++){
                
                if(atomsNameList[i] == "CA"){
                    if((atomsNameList[i-1] == atomsNameList[i]) && (residlist[i-1] == residlist[i])){
                        calist.RemoveAt(j);
                        caChainlist.RemoveAt(j);
                        Debug.Log ("Remove");
                    }
                    j++;
                }
            }

            GenInterpolationArray geninterpolationarray = new GenInterpolationArray();
            geninterpolationarray.InputKeyNodes = calist ;
            geninterpolationarray.InputTypeArray = caChainlist ;
            geninterpolationarray.CalculateSplineArray();
            calist=null;
            caChainlist=null;
            calist=geninterpolationarray.OutputKeyNodes;
            caChainlist=geninterpolationarray.OutputTypeArray;
        }
        MoleculeModel.CaSplineList=calist;
        MoleculeModel.CaSplineTypeList = new List<AtomModel>();
        for (int k=0; k<calist.Count; k++)
            MoleculeModel.CaSplineTypeList.Add(AtomModel.GetModel("chain" + caChainlist[k]));
        MoleculeModel.CaSplineChainList=caChainlist;
        
        if(UIData.ffType == UIData.FFType.HiRERNA)
            MoleculeModel.bondEPList=ControlMolecule.CreateBondsList_HiRERNA(atomsNameList);
        else {
            //MoleculeModel.bondList=ControlMolecule.CreateBondsEPList(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 ;
    }
}