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 static int getBondCount(IChemSequence sequence)
{
int count = 0;
for (int i = 0; i < sequence.ChemModelCount; i++)
{
count += ChemModelManipulator.getBondCount(sequence.getChemModel(i));
}
return count;
}
/// <summary> Puts all the Molecules of this container together in one
/// AtomCcntainer.
///
/// </summary>
/// <returns> The AtomContainer with all the Molecules of this container
///
/// </returns>
/// <deprecated> This method has a serious performace impact. Try to use
/// other methods.
/// </deprecated>
public static IAtomContainer getAllInOneContainer(IChemSequence sequence)
{
IAtomContainer container = sequence.Builder.newAtomContainer();
for (int i = 0; i < sequence.ChemModelCount; i++)
{
IChemModel model = sequence.getChemModel(i);
container.add(ChemModelManipulator.getAllInOneContainer(model));
}
return container;
}
public static int getBondCount(IChemSequence sequence)
{
int count = 0;
for (int i = 0; i < sequence.ChemModelCount; i++)
{
count += ChemModelManipulator.getBondCount(sequence.getChemModel(i));
}
return(count);
}
public static System.Collections.IList getAllChemObjects(IChemSequence sequence)
{
System.Collections.ArrayList list = new System.Collections.ArrayList();
list.Add(sequence);
for (int i = 0; i < sequence.ChemModelCount; i++)
{
list.AddRange(ChemModelManipulator.getAllChemObjects(sequence.getChemModel(i)));
}
return(list);
}
// Private procedures
//UPGRADE_NOTE: Access modifiers of method 'write' were changed to 'public'. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1204'"
public void write(IChemSequence cs)
{
int count = cs.ChemModelCount;
for (int i = 0; i < count; i++)
{
write("frame: " + (i + 1) + "\n");
write(cs.getChemModel(i).Crystal);
}
}
/// <summary> Puts all the Molecules of this container together in one
/// AtomCcntainer.
///
/// </summary>
/// <returns> The AtomContainer with all the Molecules of this container
///
/// </returns>
/// <deprecated> This method has a serious performace impact. Try to use
/// other methods.
/// </deprecated>
public static IAtomContainer getAllInOneContainer(IChemSequence sequence)
{
IAtomContainer container = sequence.Builder.newAtomContainer();
for (int i = 0; i < sequence.ChemModelCount; i++)
{
IChemModel model = sequence.getChemModel(i);
container.add(ChemModelManipulator.getAllInOneContainer(model));
}
return(container);
}
public static System.Collections.IList getAllChemObjects(IChemSequence sequence)
{
System.Collections.ArrayList list = new System.Collections.ArrayList();
list.Add(sequence);
for (int i = 0; i < sequence.ChemModelCount; i++)
{
list.AddRange(ChemModelManipulator.getAllChemObjects(sequence.getChemModel(i)));
}
return list;
}