protected void InitMeasure(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
base.InitMeasure(dcd, alignFile, flag, refJuryProfile);
DCDReader readDCD = new DCDReader(dcd);
pdbs = new PDBFiles();
readDCD.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
int counter = 0;
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter wStream = new StreamWriter(mStream);
cont=readDCD.ReadAndSavePDB(wStream);
string name = "Model" + counter++;
mStream.Position = 0;
pdbs.AddPDB(mStream, allAtoms, name);
}
while(cont);
readDCD.FinishDCDReading();
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
structNames = CheckAvailableStructures();
atomDic=pdbs.MakeAllAtomsDic();
}
protected void InitMeasure(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
base.InitMeasure(dcd, alignFile, flag, refJuryProfile);
DCDReader readDCD = new DCDReader(dcd);
pdbs = new PDBFiles();
readDCD.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
int counter = 0;
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter wStream = new StreamWriter(mStream);
cont = readDCD.ReadAndSavePDB(wStream);
string name = "Model" + counter++;
mStream.Position = 0;
pdbs.AddPDB(mStream, allAtoms, name);
}while(cont);
readDCD.FinishDCDReading();
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
structNames = CheckAvailableStructures();
atomDic = pdbs.MakeAllAtomsDic();
}
//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);
}
public Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
: base(dcd, alignFile, flag, refJuryProfile)
{
DCDReader readDCD = new DCDReader(dcd);
dirSettings.Load();
pdbs = new PDBFiles();
readDCD.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
int counter = 0;
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter wStream = new StreamWriter(mStream);
cont = readDCD.ReadAndSavePDB(wStream);
string name = "Model" + counter++;
mStream.Position = 0;
pdbs.AddPDB(mStream, allAtoms, name);
}while(cont);
readDCD.FinishDCDReading();
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
if (pdbs is ErrorBase)
{
AddErrors(pdbs.errors);
}
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
//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 Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
: base(dcd, alignFile, flag, refJuryProfile)
{
DCDReader readDCD = new DCDReader(dcd);
dirSettings.Load();
pdbs = new PDBFiles();
readDCD.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
int counter = 0;
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter wStream = new StreamWriter(mStream);
cont=readDCD.ReadAndSavePDB(wStream);
string name = "Model" + counter++;
mStream.Position = 0;
pdbs.AddPDB(mStream, allAtoms, name);
}
while(cont);
readDCD.FinishDCDReading();
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
if(pdbs is ErrorBase)
AddErrors(pdbs.errors);
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
public Rmsd(string dirName,string alignFile,bool flag,PDBMODE allAtoms,string refJuryProfile=null)
{
this.dirName = dirName;
this.alignFile = alignFile;
this.flag = flag;
this.allAtoms = allAtoms;
this.refJuryProfile = refJuryProfile;
}
public Rmsd(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
this.fileNames = fileNames;
this.alignFile = alignFile;
this.flag = flag;
this.allAtoms = allAtoms;
this.refJuryProfile = refJuryProfile;
}
public Rmsd(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms,string refJuryProfile=null)
{
this.fileNames = fileNames;
this.alignFile = alignFile;
this.flag = flag;
this.allAtoms = allAtoms;
this.refJuryProfile = refJuryProfile;
}
public Rmsd(string dirName, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
this.dirName = dirName;
this.alignFile = alignFile;
this.flag = flag;
this.allAtoms = allAtoms;
this.refJuryProfile = refJuryProfile;
}
public void AddPDB(List <string> structures, PDBMODE flag, ref int currentProgress)
{
molDic = new Dictionary <string, MolData>(structures.Count);
foreach (var item in structures)
{
AddPDB(item, flag);
currentProgress++;
}
}
public Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
order = true;
dirSettings.Load();
this.dcd = dcd;
this.alignFile = alignFile;
this.flag = flag;
this.allAtoms = allAtoms;
this.refJuryProfile = refJuryProfile;
}
public string ParseAtomLine(Molecule molecule, string pdbLine, PDBMODE flag)
{
try
{
string atomName = pdbLine.Substring(12, 4).Trim();
if (!CheckAtomName(atomName))
{
return("Wrong Atom name: " + atomName + " atom will be removed");
}
string residueName = pdbLine.Substring(17, 3).Trim();
if (!CheckResidue(residueName))
{
return("Incorrect residue name: " + residueName);
}
this.AtomName = atomName;
//ResidueName = ResidueIdentifier(residueName);
tabParam[0] = (short)ResidueIdentifier(residueName);
//ResidueSequenceNumber = Convert.ToInt16(pdbLine.Substring(22, 4));
tabParam[2] = Convert.ToInt16(pdbLine.Substring(22, 4));
//ChainIdentifier = (pdbLine.Substring(21, 1))[0];
tabParam[1] = (short)(pdbLine.Substring(21, 1))[0];
//if (ResidueName == 'O') ChainIdentifier = ' ';
//if (tabParam[0] == 'O') ChainIdentifier = ' ';
if (tabParam[0] == 'O')
{
tabParam[1] = (short)' ';
}
else //if (ChainIdentifier == ' ') ChainIdentifier = '1';
if (tabParam[1] == ' ')
{
tabParam[1] = (short)'1';
}
float x = float.Parse(pdbLine.Substring(30, 7), CultureInfo.InvariantCulture);
float y = float.Parse(pdbLine.Substring(38, 7), CultureInfo.InvariantCulture);
float z = float.Parse(pdbLine.Substring(46, 7), CultureInfo.InvariantCulture);
if (flag != PDBMODE.ONLY_SEQ)
{
Position = new Point3D(x, y, z);
}
}
catch (Exception ex)
{
return("Error in reading ATOM line: " + ex.Message);
}
return(null);
}
public Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
order = true;
dirSettings.Load();
this.dcd = dcd;
this.alignFile=alignFile;
this.flag=flag;
this.allAtoms=allAtoms;
this.refJuryProfile = refJuryProfile;
}
public Rmsd(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
: base(fileNames, alignFile, flag, refJuryProfile)
{
dirSettings.Load();
pdbs = new PDBFiles();
pdbs.AddPDB(fileNames, allAtoms);
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(null);
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
public void AddPDB(string [] structures, PDBMODE flag, ref int currentProgress)
{
if (mode == INPUTMODE.RNA)
{
flag = PDBMODE.ONLY_P;
}
foreach (var item in structures)
{
AddPDB(item, flag);
currentProgress++;
}
}
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);
}
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 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 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 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();
}
protected void InitMeasure(string dirName, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
base.InitMeasure(dirName, alignFile, flag, refJuryProfile);
pdbs = new PDBFiles();
string[] files;
if (dirSettings.extension == null)
{
files = Directory.GetFiles(dirName);
}
else
{
files = Directory.GetFiles(dirName, dirSettings.extension);
}
if (files.Length == 0)
{
throw new Exception("In selected directory " + dirName + " there are no files with extesion " + dirSettings.extension);
}
maxV = files.Length;
string refSeqFile = dirName + ".ref";
pdbs.ReadRefSeq(refSeqFile);
currentV = 0;
pdbs.AddPDB(files, allAtoms, ref currentV);
if (pdbs.molDic.Keys.Count == 0)
{
throw new Exception("Non pdb files correctly read");
}
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
structNames = CheckAvailableStructures();
order = true;
atomDic = pdbs.MakeAllAtomsDic();
}
public Rmsd(string dirName, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null) : base(dirName, alignFile, flag, refJuryProfile)
{
dirSettings.Load();
pdbs = new PDBFiles();
string[] files;
if (dirSettings.extension == null)
{
files = Directory.GetFiles(dirName);
}
else
{
files = Directory.GetFiles(dirName, dirSettings.extension);
}
if (files.Length == 0)
{
throw new Exception("In selected directory " + dirName + " there are no files with extesion " + dirSettings.extension);
}
string refSeqFile = dirName + ".ref";
pdbs.ReadRefSeq(refSeqFile);
pdbs.AddPDB(files, allAtoms);
if (pdbs.molDic.Keys.Count == 0)
{
throw new Exception("Non pdb files correctly read");
}
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
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 void AddPDB(string []structures,PDBMODE flag,ref int currentProgress)
{
foreach (var item in structures)
{
AddPDB(item, flag);
currentProgress++;
}
}
public void AddPDB(List<string> structures, PDBMODE flag,ref int currentProgress)
{
molDic = new Dictionary<string, MolData>(structures.Count);
foreach (var item in structures)
{
AddPDB(item, flag);
currentProgress++;
}
}
protected void InitMeasure(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
base.InitMeasure(fileNames, alignFile, flag, refJuryProfile);
dirSettings.Load();
pdbs = new PDBFiles();
maxV = fileNames.Count;
currentV = 0;
pdbs.AddPDB(fileNames, allAtoms, ref currentV);
if (pdbs.molDic.Keys.Count == 0)
{
throw new Exception("Unable to read pdb data!!");
}
pdbs.FindReferenceSeq();
if (pdbs.molDic.Count == 0)
{
throw new Exception("All pdb structures have been removed. No Data!");
}
pdbs.MakeAlignment(null);
structNames = CheckAvailableStructures();
order = true;
atomDic = pdbs.MakeAllAtomsDic();
}
internal Molecule(PDBMODE flag,CHAIN_MODE flagChain=CHAIN_MODE.SINGLE)
{
this.flag = flag;
this.flagChain=flagChain;
}
public MoleculeRNA(PDBMODE flag):base(flag)
{
}
protected void InitMeasure(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms,string refJuryProfile=null)
{
base.InitMeasure(fileNames, alignFile, flag, refJuryProfile);
dirSettings.Load();
pdbs = new PDBFiles();
maxV = fileNames.Count;
currentV = 0;
pdbs.AddPDB(fileNames, allAtoms,ref currentV);
if (pdbs.molDic.Keys.Count == 0)
throw new Exception("Unable to read pdb data!!");
pdbs.FindReferenceSeq();
if(pdbs.molDic.Count==0)
{
throw new Exception("All pdb structures have been removed. No Data!");
}
pdbs.MakeAlignment(null);
structNames = CheckAvailableStructures();
order = true;
atomDic = pdbs.MakeAllAtomsDic();
}
protected void InitMeasure(string dirName,string alignFile,bool flag,PDBMODE allAtoms,string refJuryProfile=null)
{
base.InitMeasure(dirName, alignFile, flag, refJuryProfile);
pdbs = new PDBFiles();
string[] files;
if(dirSettings.extension==null)
files = Directory.GetFiles(dirName);
else
files = Directory.GetFiles(dirName, dirSettings.extension);
if (files.Length == 0)
throw new Exception("In selected directory " + dirName + " there are no files with extesion " + dirSettings.extension);
maxV = files.Length;
string refSeqFile = dirName + ".ref";
pdbs.ReadRefSeq(refSeqFile);
currentV = 0;
pdbs.AddPDB(files, allAtoms,ref currentV);
if (pdbs.molDic.Keys.Count == 0)
throw new Exception("Non pdb files correctly read");
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
structNames = CheckAvailableStructures();
order = true;
atomDic = pdbs.MakeAllAtomsDic();
}
public Rmsd(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms,string refJuryProfile=null)
: base(fileNames, alignFile, flag,refJuryProfile)
{
dirSettings.Load();
pdbs = new PDBFiles();
pdbs.AddPDB(fileNames, allAtoms);
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(null);
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
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 MoleculeRNA(PDBMODE flag) : base(flag)
{
}
public Rmsd(string dirName,string alignFile,bool flag,PDBMODE allAtoms,string refJuryProfile=null):base(dirName,alignFile,flag,refJuryProfile)
{
dirSettings.Load();
pdbs = new PDBFiles();
string[] files;
if(dirSettings.extension==null)
files = Directory.GetFiles(dirName);
else
files = Directory.GetFiles(dirName, dirSettings.extension);
if (files.Length == 0)
throw new Exception("In selected directory " + dirName + " there are no files with extesion " + dirSettings.extension);
string refSeqFile = dirName + ".ref";
pdbs.ReadRefSeq(refSeqFile);
pdbs.AddPDB(files, allAtoms);
if (pdbs.molDic.Keys.Count == 0)
throw new Exception("Non pdb files correctly read");
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
opt=new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
internal Molecule(PDBMODE flag, CHAIN_MODE flagChain = CHAIN_MODE.SINGLE)
{
this.flag = flag;
this.flagChain = flagChain;
}
