public void loadPDB(string id)
{
UnitySocket.Send(CommandID.GETPDB);
UnitySocket.Send(0);
UnitySocket.Send(id);
int num0 = UnitySocket.ReceiveInt();
int num1 = UnitySocket.ReceiveInt();
//print(num);
Debug.Log(num0 + "|" + num1);
for (int k = 0; k < num0 + num1; k++)
{
UnitySocket.Send(CommandID.GETPDB);
UnitySocket.Send(k + 1);
if (k < num0)
{
string sonAtoms = UnitySocket.ReceiveString(60000);
Atoms += sonAtoms.Trim();
// Debug.Log("sonAtoms is: "+sonAtoms);
}
else
{
string sonClubs = UnitySocket.ReceiveString(68000);
Clubs += sonClubs.Trim();
}
}
string [] sArray = Atoms.Split('$');
Debug.Log("length:" + sArray.Length);
for (int i = 0; i < sArray.Length - 1; i++)
{
if (sArray[i] == "")
{
continue;
}
string [] ssArray = sArray[i].Split('#');
// Debug.Log(i+"|"+sArray[i]+"////");
float[] vect = new float[3];
float.TryParse(ssArray[0], out vect[0]);
float.TryParse(ssArray[1], out vect[1]);
float.TryParse(ssArray[2], out vect[2]);
// for(int kk=0;kk<vect.Length;kk++)
// {
// Debug.Log(i+"|"+vect[kk]+"////");
// }
typelist.Add(AtomModel.GetModel(ssArray[3]));
alist.Add(vect);
}
Debug.Log(Clubs);
Vector3 minPoint = Vector3.zero;
Vector3 maxPoint = Vector3.zero;
MoleculeModel.atomsLocationlist = alist;
MoleculeModel.atomsTypelist = typelist;
//MoleculeModel.bondList=ControlMolecule.CreateBondsList(alist,typelist);
//Debug.Log("======================= Bond List" + MoleculeModel.bondList.ToString());
MoleculeModel.bondEPList = ControlMolecule.CreateBondsEPList(alist, typelist);
MoleculeModel.bondEPSugarList = ControlMolecule.CreateBondsEPList(MoleculeModel.atomsSugarLocationlist, MoleculeModel.atomsSugarTypelist);
// float [] a0=alist[0] as float[];
// MoleculeModel.cameraLocation.x=MoleculeModel.target.x=a0[0];
// MoleculeModel.cameraLocation.y=MoleculeModel.target.y=a0[1];
// MoleculeModel.target.z=a0[2];
// MoleculeModel.cameraLocation.z=a0[2]-150;
//
for (int i = 0; i < alist.Count; i++)
{
float[] position = alist[i] as float[];
minPoint = Vector3.Min(minPoint, new Vector3(position[0], position[1], position[2]));
maxPoint = Vector3.Max(maxPoint, new Vector3(position[0], position[1], position[2]));
}
Vector3 centerPoint = minPoint + ((maxPoint - minPoint) / 2);
//MoleculeModel.target = centerPoint;
MoleculeModel.Offset = -centerPoint;
for (int i = 0; i < alist.Count; i++)
{
float[] position = alist[i] as float[];
float[] vect = new float[3];
vect[0] = position[0] + MoleculeModel.Offset.x;
vect[1] = position[1] + MoleculeModel.Offset.y;
vect[2] = position[2] + MoleculeModel.Offset.z;
alist[i] = vect;
}
// Debug.Log("MoleculeModel.target "+MoleculeModel.target);
MoleculeModel.cameraLocation.x = MoleculeModel.target.x;
MoleculeModel.cameraLocation.y = MoleculeModel.target.y;
// MoleculeModel.cameraLocation.z=MoleculeModel.target.z-((maxPoint - minPoint) ).z;
MoleculeModel.cameraLocation.z = MoleculeModel.target.z - ((maxPoint - minPoint)).z;
//MoleculeModel.bondList=ControlMolecule.CreateBondsList(alist,typelist);
MoleculeModel.bondEPList = ControlMolecule.CreateBondsEPList(alist, typelist);
MoleculeModel.bondEPSugarList = ControlMolecule.CreateBondsEPList(MoleculeModel.atomsSugarLocationlist, MoleculeModel.atomsSugarTypelist);
MoleculeModel.atomsnumber = alist.Count;
MoleculeModel.bondsnumber = MoleculeModel.bondEPList.Count;
string [] sClubArray = Clubs.Split('$');
for (int i = 0; i < sClubArray.Length - 1; i++)
{
string [] ssClubArray = sClubArray[i].Split('#');
float[] vect = new float[3];
vect[0] = float.Parse(ssClubArray[0]);
vect[1] = float.Parse(ssClubArray[1]);
vect[2] = float.Parse(ssClubArray[2]);
clubLocationalist.Add(vect);
float[] vectRotation = new float[3];
vectRotation[0] = float.Parse(ssClubArray[3]);
vectRotation[1] = float.Parse(ssClubArray[4]);
vectRotation[2] = 0f;
clubRotationList.Add(vectRotation);
}
Debug.Log(clubRotationList.Count);
}
/*
* private string GetClosest(Vector3 pos) {
* float minDist = float.MaxValue;
* float dist;
* string type = "";
* for(int i=0; i<locations.Count; i++) {
* dist = Vector3.SqrMagnitude(pos - locations[i]);
* if (dist < minDist) {
* minDist = dist;
* type = types[i];
* }
* }
* return type;
* }
*
* private void ColorVerticesWithLists(Mesh mesh) {
* int nbVertices = mesh.vertices.Length;
* Vector3[] vertices = mesh.vertices;
* Color32[] meshColors = new Color32[nbVertices];
* string type;
*
* for(int i=0; i<nbVertices; i++) {
* type = GetClosest(vertices[i]);
* meshColors[i] = AtomModel.GetAtomColor(type);
* }
* mesh.colors32 = meshColors;
* }
*/
private void ColorVertices(Mesh mesh)
{
int nbVertices = mesh.vertices.Length;
float valtype;
List <float> BFactorList = MoleculeModel.BFactorList;
Vector3[] vertices = mesh.vertices;
Color32[] meshColors = new Color32[nbVertices];
if (slowColoring)
{
List <float[]> atomLocs = MoleculeModel.atomsLocationlist;
atomLocations = new List <Vector3>();
for (int i = 0; i < atomLocs.Count; i++)
{
atomLocations.Add(new Vector3(atomLocs[i][0], atomLocs[i][1], atomLocs[i][2]));
}
atomColors = MoleculeModel.atomsColorList;
}
string type;
for (int i = 0; i < nbVertices; i++)
{
//if(UI.UIData.atomtype == UI.UIData.AtomType.particleball){
type = atomTree.GetClosestAtomType(vertices[i]);
if (UI.UIData.surfColChain)
{
Ribbons.InitCol();
meshColors[i] = Ribbons.GetColorChain(type);
}
else if (UI.UIData.surfColHydroKD)
{
HydrophobicScales.InitKyteDoo();
meshColors[i] = HydrophobicScales.GetColorHydro(type);
}
else if (UI.UIData.surfColHydroEng)
{
HydrophobicScales.InitEngleman();
meshColors[i] = HydrophobicScales.GetColorHydro(type);
}
else if (UI.UIData.surfColHydroEis)
{
HydrophobicScales.InitEisenberg();
meshColors[i] = HydrophobicScales.GetColorHydro(type);
}
else if (UI.UIData.surfColPChim)
{
HydrophobicScales.InitPhysChim();
meshColors[i] = HydrophobicScales.GetColorHydro(type);
}
else if (UI.UIData.surfColHydroWO)
{
HydrophobicScales.InitWhiteOct();
meshColors[i] = HydrophobicScales.GetColorHydro(type);
}
else if (UI.UIData.surfColBF)
{
valtype = float.Parse(type);
if (valmax == 0)
{
valmin = BFactorRep.GetMin(BFactorList);
valmax = BFactorRep.GetMax(BFactorList);
}
valtype = (valtype - valmin) / (valmax - valmin);
bftype = BFactorRep.GetBFStyle(valtype);
meshColors[i] = AtomModel.GetModel(bftype).baseColor;
}
else
{
meshColors[i] = MoleculeModel.GetAtomColor(type);
}
//This part of the code wasn't working
//Anyway i dunno why we want to use another way to color surfaces when not in particles mode
//}
/*else
* if(slowColoring){
* meshColors[i] = GetClosestAtomColor(vertices[i]);
* }else{
* type = atomTree.GetClosestAtomType(vertices[i]);
* meshColors[i] = MoleculeModel.GetAtomColor(type);
* //meshColors[i] = atomTree.GetClosestAtomColor(vertices[i]);
* }*/
}
mesh.colors32 = meshColors;
}
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();
}
//TODO: avoid reading the file 3 times
public void ReadXGMML(String xml_content)
{
List <float[]> alist = new List <float[]>();
List <float[]> CSRadiusList = new List <float[]>();
List <AtomModel> typelist = new List <AtomModel>();
// List<string> chainlist = new List<string>();
List <int[]> edgelist = new List <int[]>();
List <string> resnamelist = new List <string>();
List <string[]> CSSGDList = new List <string[]>();
List <string[]> CSColorList = new List <string[]>();
List <string[]> CSLabelList = new List <string[]>();
List <int[]> CSidList = new List <int[]>();
XmlReader reader = new XmlTextReader(new StringReader(xml_content));
while (reader.Read())
{
if (reader.ReadToFollowing("node"))
{
float[] vect = new float[3];
// Vector3 v=new Vector3();
float [] intarrayw = new float[1];
while (reader.MoveToNextAttribute()) // Read the attributes.
{
if (reader.Name == "label")
{
string [] intarray = new string[1];
intarray[0] = reader.Value;
CSLabelList.Add(intarray);
}
else if (reader.Name == "id")
{
int [] intarray = new int[1];
intarray[0] = int.Parse(reader.Value);
CSidList.Add(intarray);
}
// Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
}
// if(reader.NodeType==XmlNodeType.Element)
// {
// Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
// string [] intarray= new string[1];
// intarray[0]=reader.Value;
// if(reader.LocalName=="SGD symbol")CSSGDList.Add(intarray);
//
// }
reader.ReadToFollowing("graphics");
while (reader.MoveToNextAttribute()) // Read the attributes.
{
if (reader.Name == "type")
{
}
else if (reader.Name == "h")
{
}
else if (reader.Name == "w")
{
// Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
intarrayw[0] = float.Parse(reader.Value) / 60;
CSRadiusList.Add(intarrayw);
}
else if (reader.Name == "x")
{
// Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
//Take the opposite of y beceause Unity is left-handed
vect[0] = float.Parse(reader.Value) / 60;
}
else if (reader.Name == "y")
{
// Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
//Take the opposite of y beceause screen is directed in -y
vect[1] = -float.Parse(reader.Value) / 60;
}
else if (reader.Name == "fill")
{
string [] intarray = new string[1];
intarray[0] = reader.Value;
CSColorList.Add(intarray);
}
else if (reader.Name == "width")
{
}
else if (reader.Name == "outline")
{
}
// Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
}
//Take the opposite for z to make the node pop out toward the user
vect[2] = -GUIMoleculeController.depthfactor * intarrayw[0];
alist.Add(vect);
typelist.Add(AtomModel.GetModel("S"));
// modellist.Add(model);
}
}
reader.Close();
XmlReader reader2 = new XmlTextReader(new StringReader(xml_content));
while (reader2.Read())
{
if (reader2.ReadToFollowing("edge"))
{
int[] vectint = new int[2];
while (reader2.MoveToNextAttribute()) // Read the attributes.
{
if (reader2.Name == "label")
{
}
else if (reader2.Name == "source")
{
// Debug.Log(" " + reader2.Name + "='" + reader2.Value + "'");
vectint[0] = int.Parse(reader2.Value);
}
else if (reader2.Name == "target")
{
// Debug.Log(" " + reader2.Name + "='" + reader2.Value + "'");
vectint[1] = int.Parse(reader2.Value);
}
// Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
}
// Debug.Log(" vectint[0]:" + vectint[0]+", vectint[1]:" + vectint[1]);
edgelist.Add(vectint);
}
}
reader2.Close();
XmlReader reader3 = new XmlTextReader(new StringReader(xml_content));
while (reader3.Read())
{
if (reader3.NodeType == XmlNodeType.Element)
{
while (reader3.MoveToNextAttribute()) // Read the attributes.
{
if (reader3.Name == "name" && reader3.Value == "SGD symbol")
{
if (reader3.MoveToNextAttribute())
{
// Debug.Log(" " + reader3.Name + "=" + reader3.Value + " ");
string [] intarray = new string[1];
intarray[0] = reader3.Value;
CSSGDList.Add(intarray);
// Debug.Log(" " + reader3.Name + "='" + reader3.Value + "'");
}
}
}
}
}
reader3.Close();
MoleculeModel.atomsLocationlist = alist;
MoleculeModel.atomsTypelist = typelist;
MoleculeModel.atomsResnamelist = resnamelist;
MoleculeModel.CSidList = CSidList;
MoleculeModel.CSLabelList = CSLabelList;
MoleculeModel.CSRadiusList = CSRadiusList;
MoleculeModel.CSColorList = CSColorList;
MoleculeModel.CSSGDList = CSSGDList;
//float [] a0=alist[0] as float[];
Vector3 minPoint = new Vector3(float.MaxValue, float.MaxValue, float.MaxValue);
Vector3 maxPoint = new Vector3(float.MinValue, float.MinValue, float.MinValue);
for (int i = 0; i < alist.Count; i++)
{
float[] position = alist[i] as float[];
// Debug.Log(position[0]+","+position[1]+","+position[2]);
minPoint = Vector3.Min(minPoint, new Vector3(position[0], position[1], position[2]));
maxPoint = Vector3.Max(maxPoint, new Vector3(position[0], position[1], position[2]));
}
Vector3 centerPoint = minPoint + ((maxPoint - minPoint) / 2);
//MoleculeModel.target = centerPoint;
Camera.main.transform.position = new Vector3(0, 0, 0);
MoleculeModel.Offset = -centerPoint;
MoleculeModel.MinValue = minPoint;
MoleculeModel.MaxValue = maxPoint;
Debug.Log("centerPoint=" + centerPoint);
for (int i = 0; i < alist.Count; i++)
{
float[] position = alist[i] as float[];
float[] vectarray = new float[3];
vectarray[0] = position[0] + MoleculeModel.Offset.x;
vectarray[1] = position[1] + MoleculeModel.Offset.y;
vectarray[2] = position[2] + MoleculeModel.Offset.z;
alist[i] = vectarray;
}
// Debug.Log("MoleculeModel.target "+MoleculeModel.target);
MoleculeModel.cameraLocation.x = MoleculeModel.target.x;
MoleculeModel.cameraLocation.y = MoleculeModel.target.y;
// MoleculeModel.cameraLocation.z=MoleculeModel.target.z-((maxPoint - minPoint) ).z;
MoleculeModel.cameraLocation.z = -80;
// MoleculeModel.cameraLocation.z=MoleculeModel.target.z;
// MoleculeModel.bondList=ControlMolecule.CreateBondsList(alist,typelist);
// MoleculeModel.bondEPList=ControlMolecule.CreateBondsEPList(alist,typelist);
MoleculeModel.bondEPList = ControlMolecule.CreateBondsCSList(edgelist);
MoleculeModel.atomsnumber = alist.Count;
MoleculeModel.bondsnumber = MoleculeModel.bondEPList.Count;
MoleculeModel.networkLoaded = true; // there should be a network loaded, if all went well
// return alist;
}
// Regex RE = new Regex("\n", RegexOptions.Multiline);
// MatchCollection theMatches = RE.Matches(text);
// int matchescount=theMatches.Count;
public static void ReadPDB(TextReader sr, List <float[]> alist,
List <float[]> calist,
List <float> BFactorList,
List <string> resnamelist,
List <string> atomsNameList,
List <string> caChainlist,
List <AtomModel> typelist,
List <string> chainList,
List <Color> colorList,
List <float[]> sshelixlist,
List <float[]> sssheetlist)
{
string[] dnaBackboneAtoms = new string[] { "C5'" };
List <int> residueIds = new List <int>();
List <int> splits = new List <int>();
List <int> atomsNumberList = new List <int>();
int resNb = 0;
int prevRes = int.MinValue;
int currentRes = int.MinValue + 1;
int nowline = 0;
int nbAtoms = 0;
int nbTers = 0;
string s;
int prevresnb = 0;
while ((s = sr.ReadLine()) != null)
{
if (s.StartsWith("ENDMDL"))
{
break;
}
if (s.Length > 4)
{
bool isAtomLine = s.StartsWith("ATOM");
bool isHetAtm = s.StartsWith("HETATM");
bool isHelixLine = s.StartsWith("HELIX");
bool isSheetLine = s.StartsWith("SHEET");
bool isConnectLine = s.StartsWith("CONECT");
if (s.StartsWith("TER"))
{
splits.Add(resNb);
nbTers++;
}
if (isHelixLine)
{
string chainh = s.Substring(19, 2).Trim();
string initr = s.Substring(22, 4);
string termr = s.Substring(34, 4);
string classH = s.Substring(39, 2);
string len = s.Substring(72, 5);
float[] vect = new float[4];
float initres = float.Parse(initr);
float termres = float.Parse(termr);
float length = float.Parse(len);
float classhelix = 1f;
try{
classhelix = float.Parse(classH);
}catch {
classhelix = float.Parse(s.Substring(38, 2));
}
vect[0] = initres;
vect[1] = termres;
vect[2] = length;
vect[3] = classhelix;
sshelixlist.Add(vect);
MoleculeModel.helixChainList.Add(chainh);
}
if (isSheetLine)
{
string chainS = s.Substring(21, 2).Trim();
string initr = s.Substring(23, 4);
string termr = s.Substring(34, 4);
float[] vect = new float[2];
vect[0] = float.Parse(initr);
vect[1] = float.Parse(termr);
sssheetlist.Add(vect);
MoleculeModel.strandChainList.Add(chainS);
}
if (UIData.readHetAtom)
{
isAtomLine = isAtomLine || s.StartsWith("HETATM");
}
if (!UIData.readWater)
{
try{
if ((string)s.Substring(17, 3).Trim() == "HOH")
{
isAtomLine = false;
}
}catch {
isAtomLine = false;
}
}
if (isAtomLine)
{
float[] vect = new float[3];
MoleculeModel.atomHetTypeList.Add(s.Split(' ')[0]);
string sx = s.Substring(30, 8);
string sy = s.Substring(38, 8);
string sz = s.Substring(46, 8);
string sbfactor = null;
bool parseBFactor = false;
if (s.Length > 60)
{
sbfactor = s.Substring(60, 6);
parseBFactor = true;
}
string atomsNumber = s.Substring(6, 5);
string typestring = s.Substring(12, 4).Trim();
atomsNameList.Add(typestring);
int bout;
bool b = int.TryParse(typestring[0].ToString(), out bout);
string type;
if (b)
{
type = typestring[1].ToString();
}
else
{
type = typestring[0].ToString();
}
string resname = s.Substring(17, 3).Trim();
int resid = int.Parse(s.Substring(22, 4));
residueIds.Add(resid);
currentRes = resid;
atomsNumberList.Add(int.Parse(atomsNumber));
//Unity has a left-handed coordinates system while PDBs are right-handed
//So we have to reverse the X coordinates
float x = -float.Parse(sx);
float y = float.Parse(sy);
float z = float.Parse(sz);
float bfactor = 0.0f;
if (parseBFactor == true)
{
bfactor = float.Parse(sbfactor);
}
vect[0] = x;
vect[1] = y;
vect[2] = z;
//CA case
if (typestring[0].ToString() == "C" && typestring.Length > 1)
{
if (typestring[1].ToString() == "A")
{
string chaintype = s.Substring(21, 1);
calist.Add(vect);
caChainlist.Add(chaintype);
}
}
//??
if (dnaBackboneAtoms.Contains(typestring))
{
string chaintype = s.Substring(21, 1);
calist.Add(vect);
caChainlist.Add(chaintype);
}
if (s.Substring(21, 1) != " ")
{
string chain = s.Substring(21, 1);
chainList.Add(chain);
}
if (parseBFactor == true)
{
BFactorList.Add(bfactor);
}
alist.Add(vect);
AtomModel aModel;
if (UIData.ffType == UIData.FFType.atomic)
{
aModel = AtomModel.GetModel(type);
}
else
{
aModel = AtomModel.GetModel(typestring);
}
if (aModel == null)
{
aModel = AtomModel.GetModel("X");
}
typelist.Add(aModel);
if (MoleculeModel.sugarResname.Contains(resname))
{
MoleculeModel.atomsSugarTypelist.Add(aModel);
}
if (UIData.ffType == UIData.FFType.atomic)
{
colorList.Add(MoleculeModel.GetAtomColor(type));
}
else
{
colorList.Add(aModel.baseColor);
}
resnamelist.Add(resname);
if (MoleculeModel.residues.ContainsKey(resid) == false)
{
MoleculeModel.residues.Add(resid, new ArrayList());
//add the chain name for each residu
MoleculeModel.resChainList.Add(s.Substring(21, 1));
//If we have a sugar, we add theses informations in some special list
if (MoleculeModel.sugarResname.Contains(resname))
{
MoleculeModel.resSugarChainList.Add(s.Substring(21, 1));
}
}
int curresnb = int.Parse(s.Substring(22, 4));
if (prevresnb == 0 && curresnb != 0)
{
MoleculeModel.firstresnb = curresnb;
}
if (curresnb != prevresnb)
{
MoleculeModel.resChainList2.Add(s.Substring(21, 1));
prevresnb = curresnb;
}
MoleculeModel.residues[resid].Add(nbAtoms);
if (prevRes != currentRes)
{
resNb++;
}
prevRes = currentRes;
nbAtoms++;
//If we have a sugar, we add theses informations in some special list
if (MoleculeModel.sugarResname.Contains(resname))
{
MoleculeModel.atomsSugarLocationlist.Add(vect);
MoleculeModel.atomsSugarResnamelist.Add(resname);
MoleculeModel.atomsSugarNamelist.Add(typestring);
}
}
if (isConnectLine)
{
if (UIData.connectivity_PDB)
{
string[] splitedStringTemp = s.Split(' '); //0 is Connect, 1 is the atom, 2,3..... is the bounded atoms
List <string> splitedString = new List <string>();
for (int j = 0; j < splitedStringTemp.Length; j++)
{
if (splitedStringTemp[j] != "")
{
splitedString.Add(splitedStringTemp[j]);
}
}
for (int j = 2; j < splitedString.Count; j++)
{
MoleculeModel.BondListFromPDB.Add(new int[2] {
int.Parse(splitedString[1]) - 1, int.Parse(splitedString[j]) - 1
});
}
}
}
nowline++;
}
}
isDone = true;
Ribbons.mustSplitDictList = (nbTers > 1);
for (int i = 0; i < typelist.Count; i++)
{
MoleculeModel.atomsLocalScaleList.Add(100.0f);
}
foreach (string name in atomsNameList)
{
if (!MoleculeModel.existingName.Contains(name))
{
MoleculeModel.existingName.Add(name);
}
}
// existingRes is created in DisplayMolecule.CheckResidues after looking for protonated HIS
foreach (string chain in chainList)
{
if (!MoleculeModel.existingChain.Contains(chain))
{
MoleculeModel.existingChain.Add(chain);
}
}
MoleculeModel.existingName.Sort();
MoleculeModel.existingChain.Sort();
sr.Close();
Debug.Log("typelist:" + typelist.Count);
Debug.Log("resnameList:" + resnamelist.Count);
Debug.Log("caChainlist:" + caChainlist.Count);
Debug.Log("chainlist:" + chainList.Count);
Debug.Log("colorList:" + colorList.Count);
Debug.Log("atomsLocalScaleList:" + MoleculeModel.atomsLocalScaleList.Count);
Debug.Log("BfactorList: " + BFactorList.Count);
if (resnamelist.Count == typelist.Count)
{
UIData.hasResidues = true;
}
if (chainList.Count == typelist.Count)
{
UIData.hasChains = true;
}
MoleculeModel.atomsLocationlist = alist;
MoleculeModel.CatomsLocationlist = calist;
MoleculeModel.CaSplineChainList = caChainlist;
MoleculeModel.atomsTypelist = typelist;
MoleculeModel.atomsNamelist = atomsNameList;
MoleculeModel.atomsNumberList = atomsNumberList;
MoleculeModel.BFactorList = BFactorList;
MoleculeModel.atomsResnamelist = resnamelist;
MoleculeModel.residueIds = residueIds;
MoleculeModel.splits = splits;
MoleculeModel.atomsChainList = chainList;
MoleculeModel.atomsColorList = colorList;
MoleculeModel.ssHelixList = sshelixlist;
MoleculeModel.ssStrandList = sssheetlist;
//MoleculeModel.residueDictionaries = residueDictList;
//Here we will fill the sortedIndex residue by the Chain ID
MoleculeModel.sortedResIndexByList = sortResIndex(MoleculeModel.resChainList);
MoleculeModel.sortedResIndexByListSugar = sortResIndex(MoleculeModel.resSugarChainList);
}
/// <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;
}