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);
}