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(IChemFile file)
{
int count = 0;
for (int i = 0; i < file.ChemSequenceCount; i++)
{
count += ChemSequenceManipulator.getBondCount(file.getChemSequence(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(IChemFile file)
{
IAtomContainer container = file.Builder.newAtomContainer();
for (int i = 0; i < file.ChemSequenceCount; i++)
{
IChemSequence sequence = file.getChemSequence(i);
container.add(ChemSequenceManipulator.getAllInOneContainer(sequence));
}
return container;
}
/// <summary> Returns a List of all IChemObject in this ChemFile.
///
/// </summary>
/// <returns> A list of all ChemObjects
/// </returns>
public static System.Collections.IList getAllChemObjects(IChemFile file)
{
System.Collections.ArrayList list = new System.Collections.ArrayList();
list.Add(file);
for (int i = 0; i < file.ChemSequenceCount; i++)
{
list.AddRange(ChemSequenceManipulator.getAllChemObjects(file.getChemSequence(i)));
}
return(list);
}
public static int getBondCount(IChemFile file)
{
int count = 0;
for (int i = 0; i < file.ChemSequenceCount; i++)
{
count += ChemSequenceManipulator.getBondCount(file.getChemSequence(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(IChemFile file)
{
IAtomContainer container = file.Builder.newAtomContainer();
for (int i = 0; i < file.ChemSequenceCount; i++)
{
IChemSequence sequence = file.getChemSequence(i);
container.add(ChemSequenceManipulator.getAllInOneContainer(sequence));
}
return(container);
}
/// <summary> Returns a List of all IChemObject in this ChemFile.
///
/// </summary>
/// <returns> A list of all ChemObjects
/// </returns>
public static System.Collections.IList getAllChemObjects(IChemFile file)
{
System.Collections.ArrayList list = new System.Collections.ArrayList();
list.Add(file);
for (int i = 0; i < file.ChemSequenceCount; i++)
{
list.AddRange(ChemSequenceManipulator.getAllChemObjects(file.getChemSequence(i)));
}
return list;
}
public virtual IChemSequence getChemSequence(int number)
{
return(currentChemFile.getChemSequence(number));
}