private static void ProcessChemFile(IChemFile chemFile, ISettings settings, FileUsage usage, MoleculeLoadingResults results, LoadingProgress progress) { MoleculeProcessingProgress molProcessing = new MoleculeProcessingProgress(progress); progress.MoveToNextProcess(molProcessing); // calc size int numModels = 0; for (int seq = 0; seq < chemFile.ChemSequenceCount; seq++) { IChemSequence chemSeq = chemFile.getChemSequence(seq); numModels += chemSeq.ChemModelCount; } float modelSz = 1.0f / (float)numModels; results.NumSequences = chemFile.ChemSequenceCount; for (int seq = 0; seq < chemFile.ChemSequenceCount; seq++) { IChemSequence chemSeq = chemFile.getChemSequence(seq); results.NumModels += chemSeq.ChemModelCount; for (int model = 0; model < chemSeq.ChemModelCount; model++) { ProcessChemModel(chemSeq.getChemModel(model), settings, usage, results, molProcessing, modelSz); } molProcessing.Log("Processed Sequence", LogItem.ItemLevel.Success); } molProcessing.Log("Processed File", LogItem.ItemLevel.Success); }
private static void ProcessChemModel(IChemModel chemModel, ISettings settings, FileUsage usage, MoleculeLoadingResults results, MoleculeProcessingProgress progress, float sectionSz) { //if (ChemModelManipulator.getAllInOneContainer(chemModel).getBondCount() == 0) //{ // return; //} // check for coordinates if ((GeometryTools.has2DCoordinatesNew(ChemModelManipulator.getAllInOneContainer(chemModel)) != 0))// { results.Num2DCoords++; } // usage == FileUsage.TwoD) //{ // throw new UserLevelException("File has no 2D coords", UserLevelException.ExceptionType.FileLoading, // typeof(MoleculeLoader), null); //} if ((GeometryTools.has2DCoordinatesNew(ChemModelManipulator.getAllInOneContainer(chemModel)) != 0))// && { results.Num3DCoords++; } // usage == FileUsage.ThreeD) //{ // throw new UserLevelException("File has no 3D coords", UserLevelException.ExceptionType.FileLoading, // typeof(MoleculeLoader), null); //} ElementPTFactory elements = ElementPTFactory.Instance; // calc item sz int numItems = 0; if (chemModel.SetOfMolecules != null) { results.NumMolecules += chemModel.SetOfMolecules.MoleculeCount; for (int mol = 0; mol < chemModel.SetOfMolecules.MoleculeCount; mol++) { numItems += chemModel.SetOfMolecules.Molecules[mol].Atoms.Length; //numItems += chemModel.SetOfMolecules.Molecules[mol].Bonds.Length; } } float itemSz = sectionSz / (float)numItems; if (chemModel.SetOfMolecules != null) { results.NumMolecules += chemModel.SetOfMolecules.MoleculeCount; for (int mol = 0; mol < chemModel.SetOfMolecules.MoleculeCount; mol++) { IMolecule molecule = chemModel.SetOfMolecules.Molecules[mol]; results.NumAtoms += molecule.Atoms.Length; results.NumBonds += molecule.Bonds.Length; foreach (IAtom atom in molecule.Atoms) { PeriodicTableElement pe = elements.getElement(atom.Symbol); if (pe != null) { atom.AtomicNumber = pe.AtomicNumber; atom.Properties["PeriodicTableElement"] = pe; atom.Properties["Period"] = int.Parse(pe.Period); } else { progress.Log(string.Format("Failed to find periodic element: {0}", atom.Symbol), LogItem.ItemLevel.Failure); } progress.UpdateProgress(itemSz); } progress.Log(string.Format("Processed {0} atoms", molecule.Atoms.Length), LogItem.ItemLevel.Info); } } progress.Log("Processed Model", LogItem.ItemLevel.Success); }