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); }