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 (UIData.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 (UIData.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();
}
/// <summary>
/// Trace interpolation points from C-alpha positions.
/// Recreate interpolation points for carbon alpha splines.
/// </summary>
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;
}