public void TestGiveAngleFromMiddle_IAtom_IAtom_IAtom()
{
var filename = "NCDK.Data.MDL.testdoublebondconfig.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
Assert.AreEqual(2.0943946986086157, BondTools.GiveAngleFromMiddle(mol.Atoms[0], mol.Atoms[2], mol.Atoms[3]), 0.2);
}
public void TestIsLeft_IAtom_IAtom_IAtom()
{
var filename = "NCDK.Data.MDL.testdoublebondconfig.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
Assert.IsFalse(BondTools.IsLeft(mol.Atoms[1], mol.Atoms[0], mol.Atoms[2]));
}
public void TestBug2831420()
{
var filename = "NCDK.Data.MDL.bug2831420.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
Assert.IsTrue(BondTools.IsStereo(mol, mol.Atoms[5]));
}
public void TestIsSquarePlanar_IAtomContainer_IAtom()
{
var filename = "NCDK.Data.MDL.squareplanar.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
Assert.IsTrue(BondTools.IsSquarePlanar(mol, mol.Atoms[0]));
Assert.IsFalse(BondTools.IsSquarePlanar(mol, mol.Atoms[1]));
}
public void TestMakeUpDownBonds_IAtomContainer()
{
var filename = "NCDK.Data.MDL.tetrahedral_2_lazy.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
BondTools.MakeUpDownBonds(mol);
Assert.AreEqual(BondStereo.Down, mol.Bonds[3].Stereo);
}
public void TestIsTrigonalBipyramidalOrOctahedral_IAtomContainer_IAtom()
{
var filename = "NCDK.Data.MDL.trigonal_bipyramidal.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
Assert.AreEqual(BondTools.IsTrigonalBipyramidalOrOctahedral(mol, mol.Atoms[0]), 1);
Assert.AreEqual(BondTools.IsTrigonalBipyramidalOrOctahedral(mol, mol.Atoms[1]), 0);
}
public void TestGiveAngleBothMethods_Point2d_Point2d_Point2d_bool()
{
var filename = "NCDK.Data.MDL.testdoublebondconfig.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
Assert.AreEqual(2.0943946986086157, BondTools.GiveAngleBothMethods(mol.Atoms[0].Point2D.Value, mol
.Atoms[2].Point2D.Value, mol.Atoms[3].Point2D.Value, true), 0.2);
Assert.AreEqual(2.0943946986086157, BondTools.GiveAngleBothMethods(mol.Atoms[0].Point2D.Value, mol
.Atoms[2].Point2D.Value, mol.Atoms[3].Point2D.Value, false), 0.2);
}
public void TestIsStereo_IAtomContainer_IAtom_forinvalid()
{
var filename = "NCDK.Data.MDL.trigonal_bipyramidal.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
for (int i = 1; i < 6; i++)
{
mol.Atoms[i].Symbol = "C";
}
Assert.IsFalse(BondTools.IsStereo(mol, mol.Atoms[0]));
Assert.IsFalse(BondTools.IsStereo(mol, mol.Atoms[1]));
}
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 void TestStereosAreOpposite_IAtomContainer_IAtom()
{
var filename = "NCDK.Data.MDL.squareplanar.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
Assert.IsFalse(BondTools.StereosAreOpposite(mol, mol.Atoms[0]));
filename = "NCDK.Data.MDL.tetrahedral_with_four_wedges.mol";
ins = ResourceLoader.GetAsStream(filename);
reader = new MDLV2000Reader(ins);
chemFile = reader.Read(builder.NewChemFile());
mol = chemFile[0][0].MoleculeSet[0];
Assert.IsTrue(BondTools.StereosAreOpposite(mol, mol.Atoms[0]));
}
public void TestIsValidDoubleBondConfiguration_IAtomContainer_IBond()
{
var filename = "NCDK.Data.MDL.testdoublebondconfig.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
Assert.IsTrue(BondTools.IsValidDoubleBondConfiguration(mol, mol.Bonds[0]));
Assert.IsFalse(BondTools.IsValidDoubleBondConfiguration(mol, mol.Bonds[1]));
Assert.IsFalse(BondTools.IsValidDoubleBondConfiguration(mol, mol.Bonds[2]));
Assert.IsFalse(BondTools.IsValidDoubleBondConfiguration(mol, mol.Bonds[3]));
Assert.IsFalse(BondTools.IsValidDoubleBondConfiguration(mol, mol.Bonds[4]));
Assert.IsFalse(BondTools.IsValidDoubleBondConfiguration(mol, mol.Bonds[5]));
Assert.IsFalse(BondTools.IsValidDoubleBondConfiguration(mol, mol.Bonds[6]));
Assert.IsFalse(BondTools.IsValidDoubleBondConfiguration(mol, mol.Bonds[7]));
}
public void TestIsTetrahedral_IAtomContainer_IAtom_bool()
{
var filename = "NCDK.Data.MDL.tetrahedral_1.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
Assert.AreEqual(BondTools.IsTetrahedral(mol, mol.Atoms[0], true), 1);
Assert.AreEqual(BondTools.IsTetrahedral(mol, mol.Atoms[1], true), 0);
filename = "NCDK.Data.MDL.tetrahedral_1_lazy.mol";
ins = ResourceLoader.GetAsStream(filename);
reader = new MDLV2000Reader(ins);
chemFile = reader.Read(builder.NewChemFile());
mol = chemFile[0][0].MoleculeSet[0];
Assert.AreEqual(BondTools.IsTetrahedral(mol, mol.Atoms[0], true), 0);
Assert.AreEqual(BondTools.IsTetrahedral(mol, mol.Atoms[0], false), 3);
}
