public string AddPDB(string fileName, PDBMODE flag, CHAIN_MODE flagChain = CHAIN_MODE.SINGLE)
{
string name = Path.GetFileName(fileName);
if (molDic != null && molDic.ContainsKey(name))
{
return(name);
}
try
{
MolData molD = new MolData(fileName, flag, mode, flagChain);
if ((molD.mol == null || molD.mol.Chains == null || molD.mol.Chains.Count == 0))
{
ErrorBase.AddErrors("PDB reading: file " + fileName + " is removed from consideration it looks that it has wrong format");
return(null);
}
molDic.Add(name, molD);
return(name);
}
catch (IncorrectSideChainException ex)
{
ErrorBase.AddErrors("PDB reading: file " + fileName + " is removed from consideration because\n" + ex.Message);
}
catch (Exception ee)
{
ErrorBase.AddErrors("PDB reading: file " + fileName + " is removed from consideration because\n" + ee.Message);
}
return(null);
}
public string AddPDB(MemoryStream stream, PDBMODE flag, string modelName)
{
try
{
MolData molD = new MolData();
if (!molD.ReadMolData(stream, flag, modelName))
{
return(null);
}
molDic.Add(modelName, molD);
return(modelName);
}
catch (IncorrectSideChainException ex)
{
ErrorBase.AddErrors("PDB reading: file " + modelName + " is removed from consideration because\n" + ex.Message);
}
return(null);
}
public static float[,] GetFullStructure(MolData mol)
{
float[,] structure = new float [mol.indexMol.Length,3];
for (int i = 0; i < mol.indexMol.Length; i++)
if (mol.indexMol[i] != -1 && mol.mol.Residues[mol.indexMol[i]].ResidueName != 'X')
{
//Take only first Atom (should be CA)
Atom atom=mol.mol.Residues[mol.indexMol[i]].Atoms[0];
structure[i, 0] = atom.Position.X;
structure[i, 1] = atom.Position.Y;
structure[i, 2] = atom.Position.Z;
}
else
{
structure[i, 0] = float.MaxValue;
structure[i, 1] = float.MaxValue;
structure[i, 2] = float.MaxValue;
}
return structure;
}
public string AddPDB(MemoryStream stream, PDBMODE flag,string modelName)
{
try
{
MolData molD = new MolData();
if (!molD.ReadMolData(stream, flag,modelName))
{
return null;
}
molDic.Add(modelName, molD);
return modelName;
}
catch (IncorrectSideChainException ex)
{
ErrorBase.AddErrors("PDB reading: file " + modelName+ " is removed from consideration because\n" + ex.Message);
}
return null;
}
public string AddPDB(string fileName,PDBMODE flag,CHAIN_MODE flagChain=CHAIN_MODE.SINGLE)
{
string name = Path.GetFileName(fileName);
if(molDic!=null && molDic.ContainsKey(name))
return name;
try
{
MolData molD = new MolData(fileName, flag,mode,flagChain);
if ((molD.mol == null || molD.mol.Chains == null || molD.mol.Chains.Count == 0))
{
ErrorBase.AddErrors("PDB reading: file " + fileName + " is removed from consideration it looks that it has wrong format");
return null;
}
molDic.Add(name, molD);
return name;
}
catch (IncorrectSideChainException ex)
{
ErrorBase.AddErrors("PDB reading: file " + fileName + " is removed from consideration because\n" + ex.Message);
}
catch (Exception ee)
{
ErrorBase.AddErrors("PDB reading: file " + fileName + " is removed from consideration because\n" + ee.Message);
}
return null;
}
protected override void MakeProfiles(string strName, MolData molDic,StreamWriter wr)
{
Dictionary<int, List<int>> contacts = new Dictionary<int, List<int>>();
double[] dist2;
if(molDic!=null)
{
char []statesTab=Enumerable.Repeat<char>('N',molDic.mol.Residues.Count).ToArray();
molDic.CreateCAContactMap(8.5f, false);
//pdbs.molDic[strName].CreateContactMap(9.5f, "CB");
foreach (var contItem in molDic.contactMap.Keys)
{
if (!contacts.ContainsKey(contItem))
contacts.Add(contItem, new List<int>());
foreach (var itemList in molDic.contactMap[contItem])
{
contacts[contItem].Add((int)itemList);
if (!contacts.ContainsKey((int)itemList))
{
contacts.Add((int)itemList, new List<int>());
contacts[(int)itemList].Add(contItem);
}
else
if (!contacts[(int)itemList].Contains(contItem))
contacts[(int)itemList].Add(contItem);
}
}
int num;
string profile = "";
int len = molDic.mol.Chains[0].chainSequence.Length;
for (int i = 0; i < len; i++)
{
if (contacts.ContainsKey(i))
{
num = contacts[i].Count;
if (num > 9)
num = 9;
}
else
num = 0;
profile += num;
if (i < len - 1)
profile += " ";
}
dist2 = new double[molDic.mol.Residues.Count - 2];
for (int i = 0; i < molDic.mol.Residues.Count - 2; i++)
{
Atom aux1 = molDic.mol.Residues[i].Atoms[0];
Atom aux2 = molDic.mol.Residues[i + 2].Atoms[0];
double sum = (aux1.Position.X - aux2.Position.X) * (aux1.Position.X - aux2.Position.X);
sum += (aux1.Position.Y - aux2.Position.Y) * (aux1.Position.Y - aux2.Position.Y);
sum += (aux1.Position.Z - aux2.Position.Z) * (aux1.Position.Z - aux2.Position.Z);
sum = Math.Sqrt(sum);
dist2[i] = sum;
}
for (int i = 0; i < molDic.mol.Residues.Count - 4; i++)
{
Atom aux1 = molDic.mol.Residues[i].Atoms[0];
Atom aux2 = molDic.mol.Residues[i + 4].Atoms[0];
double sum = (aux1.Position.X - aux2.Position.X) * (aux1.Position.X - aux2.Position.X);
sum += (aux1.Position.Y - aux2.Position.Y) * (aux1.Position.Y - aux2.Position.Y);
sum += (aux1.Position.Z - aux2.Position.Z) * (aux1.Position.Z - aux2.Position.Z);
sum = Math.Sqrt(sum);
if(dist2[i]>4 && dist2[i]<8)
{
if(dist2[i]<6)
{
if(sum>4 && sum<14)
{
if(sum<7)
statesTab[i] = 'H';
else
if(sum<9)
statesTab[i] = 'J';
else
if(sum<11)
statesTab[i] = 'K';
else
if(sum<13)
statesTab[i] = 'L';
}
else
statesTab[i] = 'U';//unphysical
}
else
if (sum > 4 && sum < 14)
{
if (sum < 7)
statesTab[i] = 'E';
else
if (sum < 9)
statesTab[i] = 'R';
else
if (sum < 11)
statesTab[i] = 'T';
else
if (sum < 13)
statesTab[i] = 'Y';
}
}
else
statesTab[i] = 'U';//unphysical
}
string ss = new string(statesTab);
if (profile.Length > 0)
{
wr.WriteLine(">" + strName);
wr.WriteLine(contactProfile + profile);
wr.WriteLine(ssProfile + ss);
wr.WriteLine(SEQprofile + molDic.mol.Chains[0].chainSequence);
}
molDic.CleanMolData();
}
}
public static posMOL PrepareData(MolData mol1,MolData mol2,bool atomList=false)
{
int count=0;
posMOL globPosMol = new posMOL();
Dictionary<string, int> atomNameMol1 = null;
for (int i = 0; i < mol1.mol.Residues.Count; i++)
if (mol1.mol.Residues[i].Atoms.Count > count)
count = mol1.mol.Residues[i].Atoms.Count;
atomNameMol1 = new Dictionary<string, int>(count);
count = 0;
for (int i = 0; i < mol1.indexMol.Length; i++)
if (mol1.indexMol[i] != -1 && mol2.indexMol[i] != -1)// && mol1.mol.Residues[mol1.indexMol[i]].ResidueName != 'X' && mol2.mol.Residues[mol2.indexMol[i]].ResidueName != 'X')
{
atomNameMol1.Clear();
List<Atom> atoms = mol1.mol.Residues[mol1.indexMol[i]].Atoms;
for (int j = 0; j < atoms.Count;j++ )
atomNameMol1.Add(atoms[j].AtomName, j);
foreach (var item in mol2.mol.Residues[mol2.indexMol[i]].Atoms)
if (atomNameMol1.ContainsKey(item.AtomName))
count++;
}
// index1 = mol1.indexMol;
//index2 = mol2.indexMol;
if (globPosMol.posmol1==null || count != globPosMol.posmol1.GetLength(0))
{
globPosMol.posmol1 = new float[count, 3];
globPosMol.posmol2 = new float[count, 3];
}
if (atomList)
{
globPosMol.atoms = new List<string>[mol1.indexMol.Length];
for(int i=0;i<mol1.indexMol.Length;i++)
{
globPosMol.atoms[i] = new List<string>();
}
}
count = 0;
for (int i = 0; i < mol1.indexMol.Length; i++)
if (mol1.indexMol[i] != -1 && mol2.indexMol[i] != -1)// && mol1.mol.Residues[mol1.indexMol[i]].ResidueName != 'X' && mol2.mol.Residues[mol2.indexMol[i]].ResidueName != 'X')
{
atomNameMol1.Clear();
List<Atom> atoms = mol1.mol.Residues[mol1.indexMol[i]].Atoms;
for (int j = 0; j < atoms.Count; j++)
atomNameMol1.Add(atoms[j].AtomName, j);
foreach (var item in mol2.mol.Residues[mol2.indexMol[i]].Atoms)
if (atomNameMol1.ContainsKey(item.AtomName))
{
Atom aux = mol1.mol.Residues[mol1.indexMol[i]].Atoms[atomNameMol1[item.AtomName]];
globPosMol.posmol1[count, 0] = aux.Position.X;
globPosMol.posmol1[count, 1] = aux.Position.Y;
globPosMol.posmol1[count, 2] = aux.Position.Z;
globPosMol.posmol2[count, 0] = item.Position.X;
globPosMol.posmol2[count, 1] = item.Position.Y;
globPosMol.posmol2[count, 2] = item.Position.Z;
if(atomList)
globPosMol.atoms[i].Add(item.AtomName);
count++;
}
}
float[] center = new float[3];
CenterMol(globPosMol.posmol1, center);
CenterMol(globPosMol.posmol2, center);
return globPosMol;
}
protected virtual void MakeProfiles(string strName,MolData molDic, StreamWriter wr)
{
Dictionary<int, List<int>> contacts = new Dictionary<int, List<int>>();
if (molDic != null)
{
residuePsi = new short[molDic.mol.Residues.Count];
residuePhi = new short[molDic.mol.Residues.Count];
if (!CalcAllDihedrals(molDic))
return;
molDic.CreateSideChainContactMap(8.5f, false);
//pdbs.molDic[strName].CreateContactMap(9.5f, "CB");
foreach (var contItem in molDic.contactMap.Keys)
{
if (!contacts.ContainsKey(contItem))
contacts.Add(contItem, new List<int>());
foreach (var itemList in molDic.contactMap[contItem])
{
contacts[contItem].Add((int)itemList);
if (!contacts.ContainsKey((int)itemList))
{
contacts.Add((int)itemList, new List<int>());
contacts[(int)itemList].Add(contItem);
}
else
if (!contacts[(int)itemList].Contains(contItem))
contacts[(int)itemList].Add(contItem);
}
}
int num;
string profile = "";
int len = molDic.mol.Chains[0].chainSequence.Length;
for (int i = 0; i < len; i++)
{
if (contacts.ContainsKey(i))
{
num = contacts[i].Count;
if (num > 9)
num = 9;
}
else
num = 0;
profile += num;
if (i < len - 1)
profile += " ";
}
string psiProfile = "";
string phiProfile = "";
string ss = "";
List<string> meso = new List<string>();
List<string> mesoDF = new List<string>();
for (int i = 0; i < molDic.mol.Residues.Count; i++)
{
string key;
psiProfile += residuePsi[i];
phiProfile += residuePhi[i];
key = BuildKey(residuePhi[i], residuePsi[i]);
meso.Add(key);
if (i < molDic.mol.Residues.Count - 1)
{
ss += " ";
psiProfile += " ";
phiProfile += " ";
}
}
char[] ssStates = new char[meso.Count];
for (int i = 0; i < meso.Count; i++)
ssStates[i] = 'C';
for (int i = 0; i < meso.Count; i++)
{
if (meso[i] == null)
continue;
if (mesoStates.ContainsKey(meso[i]))
{
//mesoDF.Add(mesoStates[meso[i]]);
if (PII.ContainsKey(mesoStates[meso[i]]))
ssStates[i] = 'P';
if (i < meso.Count - 1)
{
if (meso[i + 1] != null && mesoStates.ContainsKey(meso[i + 1]))
{
string combStates = mesoStates[meso[i]] + mesoStates[meso[i + 1]];
if (turns.ContainsKey(combStates))
{
ssStates[i] = ssStates[i + 1] = 'T';
}
}
}
}
}
for (int i = 0; i < meso.Count; i++)
{
int counter = 0;
if (meso[i] == null)
continue;
if (mesoStates.ContainsKey(meso[i]))
{
if (helix.ContainsKey(mesoStates[meso[i]]) && i < meso.Count - 5)
{
for (int k = 0; k < 5; k++)
if (meso[i + k] != null && mesoStates.ContainsKey(meso[i + k]) && helix.ContainsKey(mesoStates[meso[i + k]]))
counter++;
else
break;
if (counter == 5)
for (int k = 0; k < 5; k++)
ssStates[i + k] = 'H';
}
counter = 0;
if (i < meso.Count - 3)
{
for (int k = 0; k < 3; k++)
{
if (meso[i + k] != null && mesoStates.ContainsKey(meso[i + k]) && strand.ContainsKey(mesoStates[meso[i + k]]))
counter++;
else
break;
}
if (counter == 3)
for (int k = 0; k < 3; k++)
if (ssStates[i + k] == 'C' || ssStates[i + k] == 'P')
ssStates[i + k] = 'E';
}
}
}
ss = new string(ssStates);
if (profile.Length > 0)
{
wr.WriteLine(">" + strName);
wr.WriteLine(contactProfile + profile);
//wr.WriteLine(PsiProfile+psiProfile);
//wr.WriteLine(PhiProfile+phiProfile);
wr.WriteLine(ssProfile + ss);
wr.WriteLine(SEQprofile + molDic.mol.Chains[0].chainSequence);
}
molDic.CleanMolData();
}
}
public bool CalcAllDihedrals(MolData molDic)
{
Dictionary<string, Point3D> pfAtoms = new Dictionary<string, Point3D>() { { "CA", null }, { "C", null }, { "N", null }, { "PrevC", null }, { "NextN", null } };
short result = 360;
residuePsi[0]= result;
if (!CheckIfAllNeededAtomsExists(molDic))
return false;
for (int i = 0; i < molDic.mol.Residues.Count; i++)
{
foreach (var item in molDic.mol.Residues[i].Atoms)
{
if (pfAtoms.ContainsKey(item.AtomName))
pfAtoms[item.AtomName] = item.Position;
}
if (i > 0)
residuePhi[i]=(short)Math.Round(CalculateDihedralAngles(pfAtoms["PrevC"], pfAtoms["N"], pfAtoms["CA"], pfAtoms["C"]));
else
residuePhi[i] = 360;
if (i < molDic.mol.Residues.Count - 1)
{
foreach (var item in molDic.mol.Residues[i + 1].Atoms)
{
if (item.AtomName == "N")
{
pfAtoms["NextN"] = item.Position;
break;
}
}
residuePsi[i] = (short)Math.Round(CalculateDihedralAngles(pfAtoms["N"], pfAtoms["CA"], pfAtoms["C"], pfAtoms["NextN"]));
}
else
residuePsi[i] = 360;
pfAtoms["PrevC"] = pfAtoms["C"];
}
return true;
}
private bool CheckIfAllNeededAtomsExists(MolData molDic)
{
List<Residue> rList = molDic.mol.Chains[0].Residues;
for (int i = 0; i < rList.Count; i++)
{
int counter = 0;
for (int j = 0; j < rList[i].Atoms.Count; j++)
{
switch (rList[i].Atoms[j].AtomName)
{
case "CA":
case "N":
case "C":
counter++;
break;
}
}
if (counter < 3)
return false;
}
return true;
}
protected void MakeProfiles(string strName,MolData molDic,StreamWriter wr,int k)
{
if (molDic != null)
{
PDBFiles pdb = new PDBFiles();
pdb.AddPDB(strName, PDBMODE.ONLY_CA);
DebugClass.WriteMessage("Make Started");
//int []contact=pdbs.molDic[strName].CreateFullContactMap(8.5f);
//molDic.CreateFullContactMap(9.5f,contact[k]);//correct
List<string> cc=new List<string>(pdb.molDic.Keys);
pdb.molDic[cc[0]].indexMol = molDic.indexMol;
GenerateContactMap(pdb.molDic[cc[0]],k);
//pdb.molDic[cc[0]].CreateFullContactMap(8.5f, contact[k]);
//molDic.CreateFullContactMap(8.5f,contact[k]);
//pdbs.molDic[strName].CreateContactMap(9.5f, "CB");
for (int i = 0; i < contact[k].Length; i++)
if (contact[k][i] == 1)
contOne[i]++;
int j = 0;
for (int i = 0; i < contact[k].Length - 1; i++)
{
if (contact[k][i] == 1)
contactToString[k][j++] = '1';
else
contactToString[k][j++] = '0';
contactToString[k][j++] = ' ';
}
if (contact[k][contact[k].Length - 1] == 1)
contactToString[k][j] = '1';
else
contactToString[k][j] = '0';
string all = new string(contactToString[k], 0, j);
wr.WriteLine(">" + cc[0]);
//for (int i = 0; i < contact[k].Length-1; i++)
// wr.Write(contact[k][i]+" ");
//wr.Write(contact[k][contact.Length-1]);
wr.WriteLine(all);
//wr.WriteLine();
//molDic.CleanMolData();
DebugClass.WriteMessage("Make finished");
}
}
protected virtual void GenerateContactMap(MolData mol,int k)
{
mol.CreateFullContactMap(8.5f, contact[k],"CA");
}
protected override void GenerateContactMap(MolData mol, int k)
{
mol.CreateFullContactMap(15.5f, contact[k],"P");
}