void Main()
{
IAtomContainer mol = null;
#region
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
IAtomContainer molecule = mb3d.Generate3DCoordinates(mol, false);
#endregion
}
public void TestAlkanes()
{
string smiles1 = "CCCCCCCCCCCCCCCCCC";
string smiles2 = "CCCCCC(CCCC)CCCC";
var parser = CDK.SmilesParser;
var nonBranchedAlkane = parser.ParseSmiles(smiles1);
var branchedAlkane = parser.ParseSmiles(smiles2);
ModelBuilder3D.GetInstance().Generate3DCoordinates(nonBranchedAlkane,
false);
ModelBuilder3D.GetInstance().Generate3DCoordinates(branchedAlkane, false);
}
public void HydrogenAsFirstAtomInEthane()
{
SmilesParser smipar = CDK.SmilesParser;
var ethane = smipar.ParseSmiles("[H]C([H])([H])C([H])([H])[H]");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(ethane);
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
mb3d.Generate3DCoordinates(ethane, false);
foreach (var atom in ethane.Atoms)
{
Assert.IsNotNull(atom.Point3D);
}
}
public void TestModelBuilder3D_bug_1241421()
{
var mb3d = ModelBuilder3D.GetInstance();
var filename = "NCDK.Data.MDL.bug1241421.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile).ToReadOnlyList();
IAtomContainer ac = new Silent.AtomContainer(containersList[0]);
ac = mb3d.Generate3DCoordinates(ac, false);
CheckAverageBondLength(ac);
}
public void TestModelBuilder3D_C1CCCCCCC1CC()
{
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
string smile = "C1CCCCCCC1CC";
var sp = CDK.SmilesParser;
var mol = sp.ParseSmiles(smile);
AddExplicitHydrogens(mol);
mol = mb3d.Generate3DCoordinates(mol, false);
for (int i = 0; i < mol.Atoms.Count; i++)
{
Assert.IsNotNull(mol.Atoms[i].Point3D);
}
CheckAverageBondLength(mol);
}
public void TestModelBuilder3D_Konstanz()
{
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
string smile = "C12(-[H])-C3(-C(-[H])(-[H])-C(-C4(-C5(-C(-Cl)(-Cl)-C(-C-3-4-[H])(-Cl)-C(-Cl)(-[H])-C-5(-Cl)-[H])-Cl)-[H])(-[H])-C-2(-O-1)-[H])-[H]";
var sp = CDK.SmilesParser;
var mol = sp.ParseSmiles(smile);
AddExplicitHydrogens(mol);
mol = mb3d.Generate3DCoordinates(mol, false);
for (int i = 0; i < mol.Atoms.Count; i++)
{
Assert.IsNotNull(mol.Atoms[i].Point3D);
}
CheckAverageBondLength(mol);
}
public void TestModelBuilder3D_232()
{
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
var filename = "NCDK.Data.MDL.allmol232.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile).ToReadOnlyList();
IAtomContainer ac = new Silent.AtomContainer(containersList[0]);
AddExplicitHydrogens(ac);
ac = mb3d.Generate3DCoordinates(ac, false);
Assert.IsNotNull(ac.Atoms[0].Point3D);
CheckAverageBondLength(ac);
}
public void TestModelBuilder3D_CF()
{
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
Vector3 c_coord = new Vector3(1.392, 0.0, 0.0);
Vector3 f_coord = new Vector3(0.0, 0.0, 0.0);
Vector3 h1_coord = new Vector3(1.7439615035767404, 1.0558845107302222, 0.0);
Vector3 h2_coord = new Vector3(1.7439615035767404, -0.5279422553651107, 0.914422809754875);
Vector3 h3_coord = new Vector3(1.7439615035767402, -0.5279422553651113, -0.9144228097548747);
var sp = CDK.SmilesParser;
var mol = sp.ParseSmiles("CF");
AddExplicitHydrogens(mol);
//mb3d.SetTemplateHandler();
mol = mb3d.Generate3DCoordinates(mol, false);
AssertAreEqual(c_coord, mol.Atoms[0].Point3D, 0.0001);
AssertAreEqual(f_coord, mol.Atoms[1].Point3D, 0.0001);
AssertAreEqual(h1_coord, mol.Atoms[2].Point3D, 0.0001);
AssertAreEqual(h2_coord, mol.Atoms[3].Point3D, 0.0001);
AssertAreEqual(h3_coord, mol.Atoms[4].Point3D, 0.0001);
CheckAverageBondLength(mol);
}
public void TestModelBuilder3D_keepChemObjectIDs()
{
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
IAtomContainer methanol = new Silent.AtomContainer();
IChemObjectBuilder builder = methanol.Builder;
IAtom carbon1 = builder.NewAtom("C");
carbon1.Id = "carbon1";
methanol.Atoms.Add(carbon1);
for (int i = 0; i < 3; i++)
{
IAtom hydrogen = builder.NewAtom("H");
methanol.Atoms.Add(hydrogen);
methanol.Bonds.Add(builder.NewBond(carbon1, hydrogen, BondOrder.Single));
}
IAtom oxygen1 = builder.NewAtom("O");
oxygen1.Id = "oxygen1";
methanol.Atoms.Add(oxygen1);
methanol.Bonds.Add(builder.NewBond(carbon1, oxygen1, BondOrder.Single));
{
IAtom hydrogen = builder.NewAtom("H");
methanol.Atoms.Add(hydrogen);
methanol.Bonds.Add(builder.NewBond(hydrogen, oxygen1, BondOrder.Single));
}
Assert.AreEqual(6, methanol.Atoms.Count);
Assert.AreEqual(5, methanol.Bonds.Count);
mb3d.Generate3DCoordinates(methanol, false);
CheckAverageBondLength(methanol);
Assert.AreEqual("carbon1", carbon1.Id);
Assert.AreEqual("oxygen1", oxygen1.Id);
}
public void TestModel3D_bug_1610997()
{
//bool notCalculatedResults = false;
var inputList = new List <IAtomContainer>();
////////////////////////////////////////////////////////////////////////////////////////////
//generate the input molecules. This are molecules without x, y, z coordinates
string[] smiles = new string[] { "CC", "OCC", "O(C)CCC", "c1ccccc1", "C(=C)=C", "OCC=CCc1ccccc1(C=C)",
"O(CC=C)CCN", "CCCCCCCCCCCCCCC", "OCC=CCO", "NCCCCN" };
var sp = CDK.SmilesParser;
IAtomContainer[] atomContainer = new IAtomContainer[smiles.Length];
for (int i = 0; i < smiles.Length; i++)
{
atomContainer[i] = sp.ParseSmiles(smiles[i]);
inputList.Add(atomContainer[i]);
}
///////////////////////////////////////////////////////////////////////////////////////////
// Generate 2D coordinates for the input molecules with the Structure Diagram Generator
StructureDiagramGenerator str;
List <IAtomContainer> resultList = new List <IAtomContainer>();
foreach (var molecule in inputList)
{
str = new StructureDiagramGenerator()
{
Molecule = molecule
};
str.GenerateCoordinates();
resultList.Add(str.Molecule);
}
inputList = resultList;
/////////////////////////////////////////////////////////////////////////////////////////////
// Delete x and y coordinates
foreach (var molecule in inputList)
{
foreach (var atom in molecule.Atoms)
{
atom.Point2D = null;
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////
// Test for the method Model3DBuildersWithMM2ForceField
var builder = CDK.Builder;
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
for (var i = 0; i < inputList.Count; i++)
{
var input = inputList[i];
{
// shallow copy
IAtomContainer mol = builder.NewAtomContainer(input);
try
{
mol = mb3d.Generate3DCoordinates(mol, false);
foreach (var a in mol.Atoms)
{
Assert.IsNotNull(a.Point3D, $"{smiles[0]} has unplaced atom");
}
CheckAverageBondLength(mol);
}
catch (Exception e)
{
if (e is CDKException || e is IOException)
{
Assert.Fail($"3D coordinated could not be generator for {smiles[i]}: {e.StackTrace}");
}
else
{
throw;
}
}
}
}
}
