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);
}
public void LoadFile(string file)
{
MoleculeLoadingResults results = null;
try
{
renderSource = new ChemRenderingSource3D(MoleculeLoader.LoadFromFile(file, settings, MoleculeLoader.FileUsage.ThreeD, null, out results));
if (renderContext != null)
{
renderContext.ChemRenderSource = renderSource;
renderContext.OnResize(Width, Height);
renderContext.Render(null);
}
}
catch (UserLevelException ule)
{
// post to user
MessageBox.Show(ule.Message, "Loading File", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
UleDlg dlg = new UleDlg(results, null);
dlg.ShowDialog();
dlg.Dispose();
}
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);
}
internal static IChemFile LoadFromFile(string filename, ISettings settings, FileUsage usage,
LoadingProgress progress, out MoleculeLoadingResults results)
{
IChemObjectReader reader;
results = new MoleculeLoadingResults();
results.Filename = filename;
MoleculeLoadingProgress molLoading = new MoleculeLoadingProgress(Path.GetFileName(filename), progress);
progress.MoveToNextProcess(molLoading);
try
{
molLoading.Log("Reading file", LogItem.ItemLevel.StageInfo);
StreamReader file = new StreamReader(filename, System.Text.Encoding.Default);
ReaderFactory readerFactory = new ReaderFactory();
molLoading.Log("Creating Reader", LogItem.ItemLevel.DebugInfo);
reader = readerFactory.createReader(filename, file);
file.Close();
if (reader != null)
{
reader.setReader(new StreamReader(filename, System.Text.Encoding.Default));
}
else
{
throw new UserLevelException("Format not recognised", UserLevelException.ExceptionType.FileLoading,
typeof(MoleculeLoader), null);
}
results.FileFormat = (IChemFormat)reader.Format;
molLoading.Log("Found File Format: " + reader.Format.FormatName, LogItem.ItemLevel.UserInfo);
}
catch (FileNotFoundException fnfe)
{
throw new UserLevelException("Target file no found", UserLevelException.ExceptionType.FileLoading,
typeof(MoleculeLoader), fnfe);
}
molLoading.Log("Loaded Molecule File", LogItem.ItemLevel.Success);
//catch (IOException ioe)
//{
// throw new UserLevelException("Problem reading from file", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), ioe);
//}
//catch (UserLevelException ule)
//{
// results.Result = MoleculeLoadingResults.Results.Problems;
// throw ule;
//}
//catch (Exception e)
//{
// results.Result = MoleculeLoadingResults.Results.Errors;
// throw new UserLevelException("Problem loading file", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), e);
//}
IChemFile chemFile;
ChemModel chemModel;
if (reader.accepts(typeof(IChemFile)))
{
// try to read a ChemFile
//try
//{
chemFile = (IChemFile)reader.read((IChemObject) new ChemFile());
molLoading.UpdateProgress(1);
if (chemFile != null)
{
ProcessChemFile(chemFile, settings, usage, results, progress);
}
return(chemFile);
//}
//catch (UserLevelException ule)
//{
// throw ule;
//}
//catch (Exception e)
//{
// results.Result = MoleculeLoadingResults.Results.Errors;
// throw new UserLevelException("Problem reading/processing file", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), e);
//}
}
if (reader.accepts(typeof(ChemModel)))
{
// try to read a ChemModel
//try
//{
chemModel = (ChemModel)reader.read((IChemObject) new ChemModel());
molLoading.UpdateProgress(1);
if (chemModel != null)
{
MoleculeProcessingProgress molProcessing = new MoleculeProcessingProgress(progress);
progress.MoveToNextProcess(molProcessing);
ProcessChemModel(chemModel, settings, usage, results, molProcessing, 1);
}
//}
//catch (UserLevelException ule)
//{
// throw ule;
//}
//catch (Exception e)
//{
// throw new UserLevelException("Problem reading/processing file", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), e);
//}
}
else
{
throw new UserLevelException("Unable to process reading", UserLevelException.ExceptionType.FileLoading,
typeof(MoleculeLoader), null);
}
return(null);
}