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 TestRemoveAromaticityFlagsFromHoseCode_String()
{
string hosecode1 = "***HO*SE*CODE***";
string cleanHoseCode = ForceFieldConfigurator.RemoveAromaticityFlagsFromHoseCode(hosecode1);
Assert.AreEqual("HOSECODE", cleanHoseCode);
string hosecode2 = "HOSECODE";
cleanHoseCode = ForceFieldConfigurator.RemoveAromaticityFlagsFromHoseCode(hosecode2);
Assert.AreEqual("HOSECODE", cleanHoseCode);
}
public void TestConfigureMMFF94BasedAtom_IAtom_String_boolean_propanamide()
{
string pasmi = "NC(=O)CC";
var parser = CDK.SmilesParser;
var pa = parser.ParseSmiles(pasmi);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mmff94");
IAtom amideN = pa.Atoms[0];
ffc.ConfigureMMFF94BasedAtom(amideN, new HOSECodeGenerator().GetHOSECode(pa, amideN, 3), false);
Assert.AreEqual("NC=O", amideN.AtomTypeName);
}
public void TestConfigureMMFF94BasedAtom_IAtom_String_boolean_urea()
{
string usmi = "NC(N)=O";
var parser = CDK.SmilesParser;
var urea = parser.ParseSmiles(usmi);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mmff94");
IAtom amideN = urea.Atoms[0];
ffc.ConfigureMMFF94BasedAtom(amideN, new HOSECodeGenerator().GetHOSECode(urea, amideN, 3), false);
// Console.Error.WriteLine(amideN.AtomTypeName);
Assert.AreEqual("NC=O", amideN.AtomTypeName);
}
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);
}
[TestMethod(), Ignore()] // Old atom typing method - see new Mmff class
public void TestConfigureMMFF94BasedAtom_IAtom_String_boolean_hydroxyurea()
{
string husmi = "NC(=O)NO";
var parser = CDK.SmilesParser;
var hu = parser.ParseSmiles(husmi);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mmff94");
IAtom N1 = hu.Atoms[0];
IAtom N2 = hu.Atoms[3];
ffc.ConfigureAtom(N1, new HOSECodeGenerator().GetHOSECode(hu, N1, 3), false);
ffc.ConfigureAtom(N2, new HOSECodeGenerator().GetHOSECode(hu, N2, 3), false);
Assert.AreEqual("NC=O", N1.AtomTypeName);
Assert.AreEqual("N2OX", N2.AtomTypeName);
}
public void TestMapTemplates_IAtomContainer_Double()
{
var ac = TestMoleculeFactory.MakeBicycloRings();
var th3d = TemplateHandler3D.Instance;
var ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mm2");
var ringSetMolecule = ffc.AssignAtomTyps(ac);
var ringSystems = RingPartitioner.PartitionRings(ringSetMolecule);
var largestRingSet = RingSetManipulator.GetLargestRingSet(ringSystems);
var largestRingSetContainer = RingSetManipulator.GetAllInOneContainer(largestRingSet);
th3d.MapTemplates(largestRingSetContainer, largestRingSetContainer.Atoms.Count);
for (int i = 0; i < ac.Atoms.Count; i++)
{
Assert.IsNotNull(ac.Atoms[i].Point3D);
}
ModelBuilder3DTest.CheckAverageBondLength(ac);
}
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);
}
}
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);
}
