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);
}
[TestMethod(), Ignore()] // Old atom typing method - see new Mmff class
public void TestAssignAtomTyps_test4_hydroxyurea()
{
var smiles = "C(=O)(NO)N";
string[] originalAtomTypes = { "C.sp2", "O.sp2", "N.amide", "O.sp3", "N.amide" };
string[] expectedAtomTypes = { "C=", "O=", "NC=O", "O", "N2OX" };
IAtomContainer molecule = null;
string[] ffAtomTypes = null;
var smilesParser = CDK.SmilesParser;
molecule = smilesParser.ParseSmiles(smiles);
ffAtomTypes = new string[molecule.Atoms.Count];
for (int i = 0; i < molecule.Atoms.Count; i++)
{
Assert.AreEqual(originalAtomTypes[i], molecule.Atoms[i].AtomTypeName);
}
forceFieldConfigurator.SetForceFieldConfigurator("mmff94");
IRingSet moleculeRingSet = forceFieldConfigurator.AssignAtomTyps(molecule);
//no rings
Assert.AreEqual(0, moleculeRingSet.Count);
for (int i = 0; i < molecule.Atoms.Count; i++)
{
IAtom mmff94atom = molecule.Atoms[i];
Assert.IsTrue(mmff94atom.IsAliphatic);
ffAtomTypes[i] = mmff94atom.AtomTypeName;
}
Assert.AreEqual(expectedAtomTypes, ffAtomTypes);
}
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);
}
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);
}
/// <summary>
/// Generate 3D coordinates with force field information.
/// </summary>
public IAtomContainer Generate3DCoordinates(IAtomContainer molecule, bool clone)
{
var originalAtomTypeNames = molecule.Atoms.Select(n => n.AtomTypeName).ToArray();
Debug.WriteLine("******** GENERATE COORDINATES ********");
foreach (var atom in molecule.Atoms)
{
atom.IsPlaced = false;
atom.IsVisited = false;
}
//CHECK FOR CONNECTIVITY!
Debug.WriteLine($"#atoms>{molecule.Atoms.Count}");
if (!ConnectivityChecker.IsConnected(molecule))
{
throw new CDKException("Molecule is NOT connected, could not layout.");
}
// setup helper classes
AtomPlacer atomPlacer = new AtomPlacer();
AtomPlacer3D ap3d = new AtomPlacer3D(parameterSet);
AtomTetrahedralLigandPlacer3D atlp3d = new AtomTetrahedralLigandPlacer3D(parameterSet);
if (clone)
{
molecule = (IAtomContainer)molecule.Clone();
}
atomPlacer.Molecule = molecule;
if (ap3d.NumberOfUnplacedHeavyAtoms(molecule) == 1)
{
Debug.WriteLine("Only one Heavy Atom");
ap3d.GetUnplacedHeavyAtom(molecule).Point3D = new Vector3(0.0, 0.0, 0.0);
try
{
atlp3d.Add3DCoordinatesForSinglyBondedLigands(molecule);
}
catch (CDKException ex3)
{
Trace.TraceError($"PlaceSubstitutensERROR: Cannot place substitutents due to:{ex3.Message}");
Debug.WriteLine(ex3);
throw new CDKException("PlaceSubstitutensERROR: Cannot place substitutents due to:" + ex3.Message,
ex3);
}
return(molecule);
}
//Assing Atoms to Rings,Aliphatic and Atomtype
IRingSet ringSetMolecule = ffc.AssignAtomTyps(molecule);
IRingSet largestRingSet = null;
int numberOfRingAtoms = 0;
IReadOnlyList <IRingSet> ringSystems = null;
if (ringSetMolecule.Count > 0)
{
if (templateHandler == null)
{
throw new CDKException("You are trying to generate coordinates for a molecule with rings, but you have no template handler set. Please do SetTemplateHandler() before generation!");
}
ringSystems = RingPartitioner.PartitionRings(ringSetMolecule);
largestRingSet = RingSetManipulator.GetLargestRingSet(ringSystems);
IAtomContainer largestRingSetContainer = RingSetManipulator.GetAllInOneContainer(largestRingSet);
numberOfRingAtoms = largestRingSetContainer.Atoms.Count;
templateHandler.MapTemplates(largestRingSetContainer, numberOfRingAtoms);
if (!CheckAllRingAtomsHasCoordinates(largestRingSetContainer))
{
throw new CDKException("RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be layout.");
}
SetAtomsToPlace(largestRingSetContainer);
SearchAndPlaceBranches(molecule, largestRingSetContainer, ap3d, atlp3d, atomPlacer);
largestRingSet = null;
}
else
{
//Debug.WriteLine("****** Start of handling aliphatic molecule ******");
IAtomContainer ac = AtomPlacer.GetInitialLongestChain(molecule);
SetAtomsToUnVisited(molecule);
SetAtomsToUnplaced(molecule);
ap3d.PlaceAliphaticHeavyChain(molecule, ac);
//ZMatrixApproach
ap3d.ZMatrixChainToCartesian(molecule, false);
SearchAndPlaceBranches(molecule, ac, ap3d, atlp3d, atomPlacer);
}
LayoutMolecule(ringSystems, molecule, ap3d, atlp3d, atomPlacer);
//Debug.WriteLine("******* PLACE SUBSTITUENTS ******");
try
{
atlp3d.Add3DCoordinatesForSinglyBondedLigands(molecule);
}
catch (CDKException ex3)
{
Trace.TraceError($"PlaceSubstitutensERROR: Cannot place substitutents due to:{ex3.Message}");
Debug.WriteLine(ex3);
throw new CDKException("PlaceSubstitutensERROR: Cannot place substitutents due to:" + ex3.Message, ex3);
}
// restore the original atom type names
for (int i = 0; i < originalAtomTypeNames.Length; i++)
{
molecule.Atoms[i].AtomTypeName = originalAtomTypeNames[i];
}
return(molecule);
}
