public void TestSetMM2Parameters()
{
forceFieldConfigurator.SetMM2Parameters();
Assert.IsNotNull(forceFieldConfigurator.GetParameterSet());
var atomtypeList = forceFieldConfigurator.AtomTypes;
IAtomType atomtype1 = atomtypeList[1];
Assert.AreEqual("Csp2", atomtype1.AtomTypeName);
Assert.AreEqual(6, (int)atomtype1.AtomicNumber);
Assert.AreEqual(12, (int)atomtype1.MassNumber);
}
public void TestGetBondLengthValue_String_String()
{
var parser = CDK.SmilesParser;
var smiles = "CCCCCC";
var molecule = parser.ParseSmiles(smiles);
Assert.IsNotNull(molecule);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mmff94");
AtomPlacer3D atomPlacer3d = new AtomPlacer3D(ffc.GetParameterSet());
ffc.AssignAtomTyps(molecule);
string id1 = molecule.Atoms[1].AtomTypeName;
string id2 = molecule.Atoms[2].AtomTypeName;
string mmff94id1 = "C";
string mmff94id2 = "C";
Assert.AreNotSame(mmff94id1, id1);
Assert.AreNotSame(mmff94id2, id2);
double bondlength = atomPlacer3d.GetBondLengthValue(id1, id2);
Assert.AreEqual(1.508, bondlength, 0.001);
}
public void InvalidChain()
{
string input = "CCCCCC(CCCC)CCCC";
var sp = CDK.SmilesParser;
var m = sp.ParseSmiles(input);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mmff92");
ffc.AssignAtomTyps(m);
AtomPlacer3D ap3d = new AtomPlacer3D(ffc.GetParameterSet());
ap3d.PlaceAliphaticHeavyChain(m, m);
}
/// <summary>
/// Sets the forceField attribute of the ModeSetForceFieldConfigurator(lBuilder3D object.
/// </summary>
/// <param name="ffname">forceField name</param>
private void SetForceField(string ffname)
{
if (ffname == null)
{
ffname = "mm2";
}
try
{
forceFieldName = ffname;
ffc.SetForceFieldConfigurator(ffname);
parameterSet = ffc.GetParameterSet();
}
catch (CDKException ex1)
{
Trace.TraceError($"Problem with ForceField configuration due to>{ex1.Message}");
Debug.WriteLine(ex1);
throw new CDKException("Problem with ForceField configuration due to>" + ex1.Message, ex1);
}
}
public void TestGetAngleValue_String_String_String()
{
var parser = CDK.SmilesParser;
var smiles = "CCCCCC";
var molecule = parser.ParseSmiles(smiles);
Assert.IsNotNull(molecule);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mmff94");
AtomPlacer3D atomPlacer3d = new AtomPlacer3D(ffc.GetParameterSet());
ffc.AssignAtomTyps(molecule);
string id1 = molecule.Atoms[1].AtomTypeName;
string id2 = molecule.Atoms[2].AtomTypeName;
string id3 = molecule.Atoms[3].AtomTypeName;
double anglev = atomPlacer3d.GetAngleValue(id1, id2, id3);
Assert.AreEqual(109.608, anglev, 0.001);
}
