public static void Run()
{
Console.WriteLine("Parsing PDB File");
PrimaryStructure primaryStructure = PDBStructureParser.GetPrimaryStructure(inputFilePath + inputFileName);
// dump structure to PDB file. Can check this file against the original input file for equivalence
string tmpFileName = tmpFilePath + @"tempStructure.pdb";
PDBStructureCreator pdbCreator = new PDBStructureCreator(primaryStructure, null);
pdbCreator.CreatePDBFile(tmpFileName, true, true);
// FileUtil.DeleteFile(tmpFileName);
}
public static SecondaryStructure CreateFromPrimaryStructure(PrimaryStructure primaryStructure, string strideExePath, string tmpFilePath)
{
string tmpFileName = tmpFilePath + @"tempStructure.pdb";
PDBStructureCreator pdbCreator = new PDBStructureCreator(primaryStructure, null);
//pdbCreator.CreatePDBFile(tmpFileName, true, true, true);
pdbCreator.CreatePDBFile(tmpFileName);
SecondaryStructure secondaryStructure = null;
try {
StrideAnalysis stride = new StrideAnalysis(strideExePath);
secondaryStructure = stride.GetSecondaryStructure(tmpFileName);
}
finally {
FileUtil.DeleteFile(tmpFileName);
}
return(secondaryStructure);
}
private SecondaryStructure CalculateSecondaryStructure(int frameNumber)
{
string tmpFileName = tmpFilePath + @"tempStructure_" + frameNumber + ".pdb";
PDBStructureCreator pdbCreator = new PDBStructureCreator(primaryStructure, primaryTrajectory.GetFrame(frameNumber));
pdbCreator.CreatePDBFile(tmpFileName, true, true, true);
SecondaryStructure frame = null;
try {
StrideAnalysis stride = new StrideAnalysis(strideExePath);
frame = stride.GetSecondaryStructure(tmpFileName);
}
catch (StrideException ex) {
throw new StrideException(ex.Message);
}
finally {
FileUtil.DeleteFile(tmpFileName);
}
return(frame);
}
