//Flag true only CA will be readed
public MolData(string fileName,PDBMODE flag,INPUTMODE mode,CHAIN_MODE chainFlag=CHAIN_MODE.SINGLE)
{
using (StreamReader rr = new StreamReader(fileName)) {
switch (mode)
{
case INPUTMODE.PROTEIN:
mol = new Molecule( flag,chainFlag);
break;
case INPUTMODE.RNA:
mol = new MoleculeRNA(flag);
break;
}
bool res = mol.ReadMolecule(rr);
if (!res)
return;
if (mol.Chains.Count == 0)
{
ErrorBase.AddErrors("Error in reading file: " + fileName + "\nCannot find residues, file will not be considered!");
rr.Close();
return;
}
molLength = mol.Chains[0].chainSequence.Length;
}
//CenterMol();
}
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);
}
//Flag true only CA will be readed
public MolData(string fileName, PDBMODE flag, INPUTMODE mode, CHAIN_MODE chainFlag = CHAIN_MODE.SINGLE)
{
using (StreamReader rr = new StreamReader(fileName)) {
switch (mode)
{
case INPUTMODE.PROTEIN:
mol = new Molecule(flag, chainFlag);
break;
case INPUTMODE.RNA:
mol = new MoleculeRNA(flag);
break;
}
bool res = mol.ReadMolecule(rr);
if (!res)
{
return;
}
if (mol.Chains.Count == 0)
{
ErrorBase.AddErrors("Error in reading file: " + fileName + "\nCannot find residues, file will not be considered!");
rr.Close();
return;
}
molLength = mol.Chains[0].chainSequence.Length;
}
//CenterMol();
}
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;
}
internal Molecule(PDBMODE flag,CHAIN_MODE flagChain=CHAIN_MODE.SINGLE)
{
this.flag = flag;
this.flagChain=flagChain;
}
internal Molecule(PDBMODE flag, CHAIN_MODE flagChain = CHAIN_MODE.SINGLE)
{
this.flag = flag;
this.flagChain = flagChain;
}
