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); }