public static ModelBuilder3D GetInstance(TemplateHandler3D templateHandler, string ffname)
{
if (ffname == null || ffname.Length == 0)
{
throw new CDKException("The given ffname is null or empty!");
}
if (templateHandler == null)
{
throw new CDKException("The given template handler is null!");
}
var builderCode = $"{templateHandler.GetType().FullName}#{ffname}";
return(memyselfandi.GetOrAdd(builderCode, n => new ModelBuilder3D(templateHandler, ffname)));
}
public void TestMapTemplatesCyclicMol2()
{
TemplateHandler3D tmphandler3d = TemplateHandler3D.Instance;
string cyclicMolSmi = "CC(C)(C)NC(=O)C1CN(CCN1CC(CC(Cc1ccccc1)C(=O)NC1c2ccccc2CC1O)O)Cc1cccnc1";
IChemObjectBuilder builder = ChemObjectBuilder.Instance;
SmilesParser smiparser = new SmilesParser(builder);
var molecule = smiparser.ParseSmiles(cyclicMolSmi);
ForceFieldConfigurator forcefconf = new ForceFieldConfigurator();
forcefconf.SetForceFieldConfigurator("mmff94");
IRingSet rings = forcefconf.AssignAtomTyps(molecule);
var ringSystems = RingPartitioner.PartitionRings(rings);
IRingSet largestRingSet = RingSetManipulator.GetLargestRingSet(ringSystems);
IAtomContainer allAtomsInOneContainer = RingSetManipulator.GetAllInOneContainer(largestRingSet);
tmphandler3d.MapTemplates(allAtomsInOneContainer, allAtomsInOneContainer.Atoms.Count);
for (int j = 0; j < allAtomsInOneContainer.Atoms.Count; j++)
{
Assert.IsNotNull(allAtomsInOneContainer.Atoms[j].Point3D);
}
}
private static BitArray ParseBitSet(string str)
{
return(TemplateHandler3D.GetBitSetFromFile(Strings.Tokenize(str, '\t', ' ', ';', '{', ',', '}')));
}
/// <summary>
/// Constructor for the ModelBuilder3D object.
/// </summary>
/// <param name="templateHandler">templateHandler Object</param>
/// <param name="ffname">name of force field</param>
private ModelBuilder3D(TemplateHandler3D templateHandler, string ffname)
{
SetTemplateHandler(templateHandler);
SetForceField(ffname);
}
/// <summary>
/// Sets the templateHandler attribute of the ModelBuilder3D object.
/// </summary>
/// <param name="templateHandler">The new templateHandler value</param>
private void SetTemplateHandler(TemplateHandler3D templateHandler)
{
this.templateHandler = templateHandler ?? throw new ArgumentNullException(nameof(templateHandler), "The given template handler is null!");
}