public void LoadPDBResource(string resource_name)
{
TextAsset text_data = Resources.Load(resource_name) as TextAsset;
StringReader sr = new StringReader(text_data.text);
//ReadPDB(sr);
ControlMolecule.CreateMolecule(sr);
}
public void LoadPDBRequest(string file_base_name, bool withData = true)
{
StreamReader sr;
// FileInfo file=new FileInfo(file_base_name+".pdb");
sr = new StreamReader(file_base_name + ".pdb");
//ReadPDB(sr);
ControlMolecule.CreateMolecule(sr);
if (withData)
{
FileInfo fieldlinefile = new FileInfo(file_base_name + ".json");
FileInfo apffile = new FileInfo(file_base_name + ".apf");
if (fieldlinefile.Exists)
{
LoadJsonRequest("file://" + file_base_name + ".json", MoleculeModel.Offset);
MoleculeModel.fieldLineFileExists = true;
}
else if (apffile.Exists)
{
LoadJsonRequest("file://" + file_base_name + ".apf", MoleculeModel.Offset);
MoleculeModel.fieldLineFileExists = true;
}
else
{
MoleculeModel.fieldLineFileExists = false;
MoleculeModel.FieldLineList = null;
}
FileInfo Surfacefile = new FileInfo(file_base_name + ".obj");
FileInfo Surfacefile0 = new FileInfo(file_base_name + "0.obj");
if (Surfacefile.Exists || Surfacefile0.Exists)
{
LoadOBJRequest(file_base_name);
MoleculeModel.surfaceFileExists = true;
GUIMoleculeController.modif = true;
}
else
{
MoleculeModel.surfaceFileExists = false;
}
FileInfo dxfile = new FileInfo(file_base_name + ".dx");
MoleculeModel.dxFileExists = false; // otherwise a molecule might load dx data from a previous molecule
if (dxfile.Exists)
{
MoleculeModel.dxFileExists = true;
LoadDxRequest(file_base_name + ".dx", MoleculeModel.Offset);
}
}
}
public IEnumerator LoadPDBWWW(string file_name)
{
WWW www = new WWW(file_name);
progress = 0;
isDone = false;
while (!www.isDone)
{
// Debug.Log("*** PDB: "+www.progress);
progress = www.progress;
yield return(new WaitForEndOfFrame());
}
Debug.Log("read");
//ReadPDB(new StringReader(www.text));
ControlMolecule.CreateMolecule(new StringReader(www.text));
isDone = true;
}
public void FetchPDB(string url, string id, string proxyserver = "", int proxyport = 0)
{
StreamReader sr;
Stream dataStream = null;
HttpWebResponse response = null;
HttpWebRequest request = (HttpWebRequest)WebRequest.Create(url + id + ".pdb");
// If required by the server, set the credentials.
request.Credentials = CredentialCache.DefaultCredentials;
//Set proxy information if needed
Debug.Log("LoadPDB: " + proxyserver + " " + proxyport);
if (proxyserver != "")
{
request.Proxy = new WebProxy(proxyserver, proxyport);
}
// Get the response.
response = (HttpWebResponse)request.GetResponse();
// Display the status.
Debug.Log("LoadPDB Status :: " + response.StatusDescription);
// Get the stream containing content returned by the server.
dataStream = response.GetResponseStream();
// Open the stream using a StreamReader for easy access.
sr = new StreamReader(dataStream);
ControlMolecule.CreateMolecule(sr);
//ReadPDB(sr);
if (dataStream != null && response != null)
{
dataStream.Close();
response.Close();
}
}
public static void LoadSymmetry(float Xorigin, float Yorigin, float Zorigin, float Xdirection, float Ydirection, float Zdirection)
{
Debug.Log(MoleculeModel.atomsLocationlist[0][0] + " " + MoleculeModel.atomsLocationlist[0][1] + " " + MoleculeModel.atomsLocationlist[0][2]);
Debug.Log("REORIENTATION");
//Vector3 origin = new Vector3 (Xorigin, Yorigin, Zorigin);
Vector3 direction = new Vector3(Xdirection, Ydirection, Zdirection);
direction.Normalize();
//float[] position= MoleculeModel.atomsLocationlist[0] as float[];
// Re-orientation of pdb coordinates to be oriented according to the symmetry axis
//Vector3 orientation = direction;
//axis = self.symmetry_axes[0].direction
float angle = Vector3.Angle(direction, -Vector3.up);
Vector3 rot_axis = Vector3.Cross(direction, -Vector3.up);
Debug.Log("Axis: " + rot_axis);
Debug.Log("Angle: " + angle);
Quaternion rotate = Quaternion.AngleAxis(angle, rot_axis);
// Vector3 test = new Vector3 (2.0f, 2.0f, 2.0f);
// Vector3 result = rotate * test;
// Debug.Log ("Result: "+result);
for (int i = 0; i < MoleculeModel.atomsLocationlist.Count; i++)
{
float[] position = MoleculeModel.atomsLocationlist[i] as float[];
Vector3 vec_pos = new Vector3(position[0], position[1], position[2]);
Vector3 new_vec = rotate * vec_pos;
position[0] = new_vec.x;
position[1] = new_vec.y;
position[2] = new_vec.z;
MoleculeModel.atomsLocationlist[i] = position;
}
Debug.Log(MoleculeModel.MinValue);
ControlMolecule.BuildMoleculeComponents();
Debug.Log(MoleculeModel.MinValue);
// Switch on the guided navigation mode
UIData.guided = true;
UIData.resetDisplay = true;
UIData.resetBondDisplay = true;
UIData.isCubeToSphere = true;
UIData.isSphereToCube = false;
UIData.atomtype = UIData.AtomType.sphere;
BallUpdate.resetColors = true;
// BallUpdate.resetRadii = true;
MoleculeModel.newtooltip = GUI.tooltip;
Debug.Log("resname length: " + MoleculeModel.atomsResnamelist.Count);
Debug.Log("atomtype length: " + MoleculeModel.atomsTypelist.Count);
Debug.Log("resname length: " + MoleculeModel.atomsChainList.Count);
Debug.Log("resname length: " + MoleculeModel.atoms.Count);
float x_tot = 0.0f;
float y_tot = 0.0f;
float z_tot = 0.0f;
int count = 0;
for (int i = 0; i < MoleculeModel.atomsLocationlist.Count; i++)
{
if (MoleculeModel.atomsChainList[i] == "B" && MoleculeModel.residueIds[i] == 194)
{
float[] position = MoleculeModel.atomsLocationlist[i] as float[];
x_tot += position[0];
y_tot += position[1];
z_tot += position[2];
count++;
}
}
float[] target = new float[3];
target[0] = x_tot / count;
target[1] = y_tot / count;
target[2] = z_tot / count;
Debug.Log("Target coordinates: " + x_tot / count + " " + y_tot / count + " " + z_tot / count);
// float[] target= MoleculeModel.atomsLocationlist[0] as float[];
//OptimalView.OptimalView.GetOptimalPosition(target, (float) 15.0);
//Refilling CA list for CA trace and BF representation
List <float[]> calist = new List <float[]>();
for (int i = 0; i < MoleculeModel.atomsNamelist.Count; i++)
{
if (MoleculeModel.atomsNamelist[i] == "CA")
{
float[] vect = new float[3];
vect[0] = MoleculeModel.atomsLocationlist[i][0];
vect[1] = MoleculeModel.atomsLocationlist[i][1];
vect[2] = MoleculeModel.atomsLocationlist[i][2];
calist.Add(vect);
}
}
MoleculeModel.CatomsLocationlist = calist;
MoleculeModel.backupCatomsLocationlist = calist;
// Refilling residuedictionaries for Ribbons
List <Dictionary <string, Vector3> > residueDictList = new List <Dictionary <string, Vector3> >();
Dictionary <string, Vector3> residueDict = new Dictionary <string, Vector3>();
List <int> residueIds = MoleculeModel.residueIds;
Vector3 testVector = Vector3.zero;
int currResId = int.MinValue + 1;
int prevResId = int.MinValue + 1;
for (int i = 0; i < MoleculeModel.atomsNamelist.Count; i++)
{
currResId = residueIds[i];
Vector3 currAtom = new Vector3(MoleculeModel.atomsLocationlist[i][0], MoleculeModel.atomsLocationlist[i][1], MoleculeModel.atomsLocationlist[i][2]);
if (currResId != prevResId)
{
if (residueDict != null && residueDict.Count > 0)
{
residueDictList.Add(residueDict);
}
residueDict = new Dictionary <string, Vector3>();
}
prevResId = currResId;
if (!residueDict.TryGetValue(MoleculeModel.atomsNamelist[i], out testVector))
{
residueDict.Add(MoleculeModel.atomsNamelist[i], currAtom);
}
}
MoleculeModel.residueDictionaries = residueDictList;
CreateAxeAndOrigin();
} // End of LoadSymmetry
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);
}
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;
}
/// <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;
}
