/// <summary>
/// Method which assigns van der Waals radii to the biopolymer
/// default org/openscience/cdk/config/data/pdb_atomtypes.xml
/// stored in the variable string vanDerWaalsFile.
/// </summary>
public void AssignVdWRadiiToProtein()
{
AtomTypeFactory atf = null;
var atoms = Protein.Atoms.ToArray();
try
{
atf = AtomTypeFactory.GetInstance(VanDerWaalsFile);
}
catch (Exception ex1)
{
Console.Out.WriteLine($"Problem with AtomTypeFactory due to:{ex1.ToString()}");
}
for (int i = 0; i < atoms.Length; i++)
{
try
{
atf.Configure(atoms[i]);
}
catch (Exception ex2)
{
Trace.TraceError($"Problem with atf.configure due to:{ex2.ToString()}");
}
}
}
public void TestRebond_IAtomContainer()
{
var rebonder = new RebondTool(2.0, 0.5, 0.5);
var methane = builder.NewAtomContainer();
methane.Atoms.Add(builder.NewAtom("C", new Vector3(0.0, 0.0, 0.0)));
methane.Atoms.Add(builder.NewAtom("H", new Vector3(0.6, 0.6, 0.6)));
methane.Atoms.Add(builder.NewAtom("H", new Vector3(-0.6, -0.6, 0.6)));
methane.Atoms.Add(builder.NewAtom("H", new Vector3(0.6, -0.6, -0.6)));
methane.Atoms.Add(builder.NewAtom("H", new Vector3(-0.6, 0.6, -0.6)));
// configure atoms
var factory = AtomTypeFactory.GetInstance("NCDK.Config.Data.jmol_atomtypes.txt");
//IAtom[] atoms = methane.GetAtoms();
for (int i = 0; i < methane.Atoms.Count; i++)
{
factory.Configure(methane.Atoms[i]);
}
// rebond
rebonder.Rebond(methane);
Assert.AreEqual(5, methane.Atoms.Count);
Assert.AreEqual(4, methane.Bonds.Count);
}
private SybylAtomTypeMatcher()
{
var stream = ResourceLoader.GetAsStream(SYBYL_ATOM_TYPE_LIST);
factory = AtomTypeFactory.GetInstance(stream, "owl");
cdkMatcher = CDK.AtomTypeMatcher;
var mapStream = ResourceLoader.GetAsStream(CDK_TO_SYBYL_MAP);
mapper = AtomTypeMapper.GetInstance(CDK_TO_SYBYL_MAP, mapStream);
}
public void TestToString()
{
var factory = AtomTypeFactory.GetInstance("NCDK.Dict.Data.cdk-atom-types.owl");
var type = factory.GetAtomType("C.sp3");
Assert.IsTrue(type is ImmutableAtomType);
var output = type.ToString();
Assert.IsTrue(output.Contains("ImmutableAtomType("));
Assert.IsTrue(output.Contains("MBO:"));
}
public static void Script12_1()
{
var factory = AtomTypeFactory.GetInstance("NCDK.Dict.Data.cdk-atom-types.owl");
var atomType = factory.GetAtomType("C.sp3");
Console.WriteLine($"element: {atomType.Symbol}");
Console.WriteLine($"formal charge: {atomType.FormalCharge}");
Console.WriteLine($"hybridization: {atomType.Hybridization}");
Console.WriteLine($"neighbors: {atomType.FormalNeighbourCount}");
Console.WriteLine($"lone pairs: {atomType.GetProperty<int>(NCDK.CDKPropertyName.LonePairCount)}");
Console.WriteLine($"pi bonds: {atomType.GetProperty<int>(NCDK.CDKPropertyName.PiBondCount)}");
}
public void TestCloseEnoughToBond_IAtom_IAtom_Double()
{
var filename = "NCDK.Data.XYZ.viagra.xyz";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new XYZReader(ins);
var atf = AtomTypeFactory.GetInstance("NCDK.Config.Data.jmol_atomtypes.txt");
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
foreach (var atom in mol.Atoms)
{
atf.Configure(atom);
}
Assert.IsTrue(BondTools.CloseEnoughToBond(mol.Atoms[0], mol.Atoms[1], 1));
Assert.IsFalse(BondTools.CloseEnoughToBond(mol.Atoms[0], mol.Atoms[8], 1));
}
public SmilesValencyChecker(string atomTypeList)
{
structgenATF = AtomTypeFactory.GetInstance(atomTypeList);
Trace.TraceInformation($"Using configuration file: {atomTypeList}");
}