//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();
}
internal Residue(Molecule molecule, Atom atom,PDBMODE flag)
{
// this.molecule = molecule;
//this.residueName = atom.ResidueName;
this.residueName = (char)atom.tabParam[0];
//this.chainIdentifier = atom.ChainIdentifier;
this.tabParam[0] = atom.tabParam[1];
//this.residueSequenceNumber = atom.ResidueSequenceNumber;
//this.residueSequenceNumber = atom.tabParam[2];
this.tabParam[1] = atom.tabParam[2];
atoms = new List<Atom>();
this.atoms.Add(atom);
//AddAtom(atom);
//this.residueIdentifier = Residue.GetResidueIdentifier(this.residueName);
}
public bool ReadMolData(MemoryStream stream, PDBMODE flag,string modelName)
{
StreamReader rr = new StreamReader(stream);
mol = new Molecule(flag);
bool res = mol.ReadMolecule(rr);
if (!res)
{
return false;
}
if (mol.Chains.Count == 0)
{
ErrorBase.AddErrors("Error in reading file: " + modelName + "\nCannot find residues, file will not be considered!");
return false;
}
molLength = mol.Chains[0].chainSequence.Length;
return true;
//CenterMol();
}
public void CleanMolData()
{
mol = null;
}
public void CleanMolData()
{
mol = null;
}