public void TestArsenic()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom atom1 = builder.NewAtom("As");
atom1.ImplicitHydrogenCount = 0;
mol.Atoms.Add(atom1);
for (int i = 0; i < 3; i++)
{
IAtom atom = builder.NewAtom("Cl");
mol.Atoms.Add(atom);
IBond bond = builder.NewBond(atom, atom1,
BondOrder.Single);
mol.Bonds.Add(bond);
}
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "As3", matched);
for (int i = 1; i < mol.Atoms.Count; i++)
{
IAtom atom = mol.Atoms[i];
matched = matcher.FindMatchingAtomType(mol, atom);
AssertAtomType(testedAtomTypes, "atom " + i + " failed to match", "Cl1", matched);
}
}
public void TestN3acid()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom n = builder.NewAtom("N");
IAtom o = builder.NewAtom("O");
IAtom h = builder.NewAtom("H");
IBond b1 = builder.NewBond(n, o, BondOrder.Double);
IBond b2 = builder.NewBond(n, h, BondOrder.Single);
mol.Atoms.Add(n);
mol.Atoms.Add(o);
mol.Atoms.Add(h);
mol.Bonds.Add(b1);
mol.Bonds.Add(b2);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "N3", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "O2", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[2]);
AssertAtomType(testedAtomTypes, "H1", matched);
}
public void TestS4()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom s = builder.NewAtom("S");
mol.Atoms.Add(s);
for (int i = 0; i < 6; i++)
{
IAtom f = builder.NewAtom("F");
mol.Atoms.Add(f);
IBond bond = builder.NewBond(s, f, BondOrder.Single);
mol.Bonds.Add(bond);
}
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "S4", matched);
for (int i = 1; i < mol.Atoms.Count; i++)
{
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[i]);
AssertAtomType(testedAtomTypes, "atom " + i + " failed to match", "F1", matched);
}
}
public void TestB3()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom b = builder.NewAtom("B");
IAtom f1 = builder.NewAtom("F");
IAtom f2 = builder.NewAtom("F");
IAtom f3 = builder.NewAtom("F");
IBond b1 = builder.NewBond(b, f1, BondOrder.Single);
IBond b2 = builder.NewBond(b, f2, BondOrder.Single);
IBond b3 = builder.NewBond(b, f3, BondOrder.Single);
mol.Atoms.Add(b);
mol.Atoms.Add(f1);
mol.Atoms.Add(f2);
mol.Atoms.Add(f3);
mol.Bonds.Add(b1);
mol.Bonds.Add(b2);
mol.Bonds.Add(b3);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "B3", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "F1", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[2]);
AssertAtomType(testedAtomTypes, "F1", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[3]);
AssertAtomType(testedAtomTypes, "F1", matched);
}
public void TestN3cyanide()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom n = builder.NewAtom("N");
IAtom c1 = builder.NewAtom("C");
IAtom c2 = builder.NewAtom("C");
c1.ImplicitHydrogenCount = 0;
c2.ImplicitHydrogenCount = 3;
IBond b1 = builder.NewBond(n, c1, BondOrder.Triple);
IBond b2 = builder.NewBond(c1, c2, BondOrder.Single);
mol.Atoms.Add(n);
mol.Atoms.Add(c1);
mol.Atoms.Add(c2);
mol.Bonds.Add(b1);
mol.Bonds.Add(b2);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "N3", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "C4", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[2]);
AssertAtomType(testedAtomTypes, "C4", matched);
}
public void TestOxygen1()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom carbon = builder.NewAtom("C");
IAtom o1 = builder.NewAtom("O");
IAtom o2 = builder.NewAtom("O");
carbon.ImplicitHydrogenCount = 1;
o1.ImplicitHydrogenCount = 1;
o2.ImplicitHydrogenCount = 0;
IBond bond1 = builder.NewBond(carbon, o1, BondOrder.Single);
IBond bond2 = builder.NewBond(carbon, o2, BondOrder.Double);
mol.Atoms.Add(carbon);
mol.Atoms.Add(o1);
mol.Atoms.Add(o2);
mol.Bonds.Add(bond1);
mol.Bonds.Add(bond2);
StructGenMatcher matcher = new StructGenMatcher();
// look at the sp2 O first
IAtomType matched = matcher.FindMatchingAtomType(mol, mol.Atoms[2]);
AssertAtomType(testedAtomTypes, "O2", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "C4", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "O2", matched);
}
public void TestS3()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom s = builder.NewAtom("S");
IAtom o1 = builder.NewAtom("O");
IAtom o2 = builder.NewAtom("O");
IBond b1 = builder.NewBond(s, o1, BondOrder.Double);
IBond b2 = builder.NewBond(s, o2, BondOrder.Double);
mol.Atoms.Add(s);
mol.Atoms.Add(o1);
mol.Atoms.Add(o2);
mol.Bonds.Add(b1);
mol.Bonds.Add(b2);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "S3", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "O2", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[2]);
AssertAtomType(testedAtomTypes, "O2", matched);
}
public void TestFlourine()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom atom1 = builder.NewAtom("C");
atom1.ImplicitHydrogenCount = 0;
mol.Atoms.Add(atom1);
for (int i = 0; i < 4; i++)
{
IAtom floruineAtom = builder.NewAtom("F");
mol.Atoms.Add(floruineAtom);
IBond bond = builder.NewBond(floruineAtom, atom1);
mol.Bonds.Add(bond);
}
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "C4", matched);
for (int i = 1; i < mol.Atoms.Count; i++)
{
IAtom atom = mol.Atoms[i];
matched = matcher.FindMatchingAtomType(mol, atom);
AssertAtomType(testedAtomTypes, "atom " + i + " failed to match", "F1", matched);
}
}
public void TestN3()
{
var mol = builder.NewAtomContainer();
var atom = builder.NewAtom("N");
atom.ImplicitHydrogenCount = 3;
mol.Atoms.Add(atom);
StructGenMatcher atm = new StructGenMatcher();
IAtomType matched = atm.FindMatchingAtomType(mol, atom);
Assert.IsNotNull(matched);
Assert.AreEqual("N", matched.Symbol);
}
public void TestP3()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom p = builder.NewAtom("P");
IAtom o1 = builder.NewAtom("O");
IAtom o2 = builder.NewAtom("O");
IAtom o3 = builder.NewAtom("O");
IAtom c1 = builder.NewAtom("C");
IAtom c2 = builder.NewAtom("C");
IAtom c3 = builder.NewAtom("C");
c1.ImplicitHydrogenCount = 3;
c2.ImplicitHydrogenCount = 3;
c3.ImplicitHydrogenCount = 3;
IBond bond1 = builder.NewBond(p, o1, BondOrder.Single);
IBond bond2 = builder.NewBond(p, o2, BondOrder.Single);
IBond bond3 = builder.NewBond(p, o3, BondOrder.Single);
IBond bond4 = builder.NewBond(c1, o1, BondOrder.Single);
IBond bond5 = builder.NewBond(c2, o2, BondOrder.Single);
IBond bond6 = builder.NewBond(c3, o3, BondOrder.Single);
mol.Atoms.Add(p);
mol.Atoms.Add(o1);
mol.Atoms.Add(o2);
mol.Atoms.Add(o3);
mol.Atoms.Add(c1);
mol.Atoms.Add(c2);
mol.Atoms.Add(c3);
mol.Bonds.Add(bond1);
mol.Bonds.Add(bond2);
mol.Bonds.Add(bond3);
mol.Bonds.Add(bond4);
mol.Bonds.Add(bond5);
mol.Bonds.Add(bond6);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
string[] atomTypes = { "P3", "O2", "O2", "O2", "C4", "C4", "C4" };
for (int i = 0; i < mol.Atoms.Count; i++)
{
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[i]);
AssertAtomType(testedAtomTypes, atomTypes[i], matched);
}
}
public void TestLithium()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom atom1 = builder.NewAtom("Li");
IAtom atom2 = builder.NewAtom("F");
IBond bond = builder.NewBond(atom1, atom2);
mol.Atoms.Add(atom1);
mol.Atoms.Add(atom2);
mol.Bonds.Add(bond);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "Li1", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "F1", matched);
}
public void TestSi4()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom si = builder.NewAtom("Si");
IAtom c1 = builder.NewAtom("C");
IAtom cl1 = builder.NewAtom("Cl");
IAtom cl2 = builder.NewAtom("Cl");
IAtom cl3 = builder.NewAtom("Cl");
c1.ImplicitHydrogenCount = 3;
IBond bond1 = builder.NewBond(si, c1, BondOrder.Single);
IBond bond2 = builder.NewBond(si, cl1, BondOrder.Single);
IBond bond3 = builder.NewBond(si, cl2, BondOrder.Single);
IBond bond4 = builder.NewBond(si, cl3, BondOrder.Single);
mol.Atoms.Add(si);
mol.Atoms.Add(c1);
mol.Atoms.Add(cl1);
mol.Atoms.Add(cl2);
mol.Atoms.Add(cl3);
mol.Bonds.Add(bond1);
mol.Bonds.Add(bond2);
mol.Bonds.Add(bond3);
mol.Bonds.Add(bond4);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "Si4", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "C4", matched);
for (int i = 3; i < mol.Atoms.Count; i++)
{
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[i]);
AssertAtomType(testedAtomTypes, "atom " + i + " failed to match", "Cl1", matched);
}
}
public void TestSe2()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom se = builder.NewAtom("Se");
IAtom o = builder.NewAtom("O");
IBond b1 = builder.NewBond(se, o, BondOrder.Double);
mol.Atoms.Add(se);
mol.Atoms.Add(o);
mol.Bonds.Add(b1);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "Se2", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "O2", matched);
}
public void TestNa1()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom na = builder.NewAtom("Na");
IAtom cl = builder.NewAtom("Cl");
IBond bond = builder.NewBond(na, cl, BondOrder.Single);
mol.Atoms.Add(na);
mol.Atoms.Add(cl);
mol.Bonds.Add(bond);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "Na1", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "Cl1", matched);
}
public void TestP4()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom p = builder.NewAtom("P");
IAtom cl1 = builder.NewAtom("Cl");
IAtom cl2 = builder.NewAtom("Cl");
IAtom cl3 = builder.NewAtom("Cl");
IAtom s = builder.NewAtom("S");
IBond bond1 = builder.NewBond(p, cl1, BondOrder.Single);
IBond bond2 = builder.NewBond(p, cl2, BondOrder.Single);
IBond bond3 = builder.NewBond(p, cl3, BondOrder.Single);
IBond bond4 = builder.NewBond(p, s, BondOrder.Double);
mol.Atoms.Add(p);
mol.Atoms.Add(cl1);
mol.Atoms.Add(cl2);
mol.Atoms.Add(cl3);
mol.Atoms.Add(s);
mol.Bonds.Add(bond1);
mol.Bonds.Add(bond2);
mol.Bonds.Add(bond3);
mol.Bonds.Add(bond4);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "P4", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[4]);
AssertAtomType(testedAtomTypes, "S2", matched);
for (int i = 1; i < 4; i++)
{
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[i]);
AssertAtomType(testedAtomTypes, "atom " + i + " failed to match", "Cl1", matched);
}
}
public void TestS2()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom s = builder.NewAtom("S");
s.ImplicitHydrogenCount = 2;
mol.Atoms.Add(s);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "S2", matched);
mol = builder.NewAtomContainer();
s = builder.NewAtom("S");
IAtom h1 = builder.NewAtom("H");
IAtom h2 = builder.NewAtom("H");
IBond b1 = builder.NewBond(s, h1, BondOrder.Single);
IBond b2 = builder.NewBond(s, h2, BondOrder.Single);
mol.Atoms.Add(s);
mol.Atoms.Add(h1);
mol.Atoms.Add(h2);
mol.Bonds.Add(b1);
mol.Bonds.Add(b2);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "S2", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "H1", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[2]);
AssertAtomType(testedAtomTypes, "H1", matched);
}
public void TestN5()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom n = builder.NewAtom("N");
IAtom o1 = builder.NewAtom("O");
IAtom o2 = builder.NewAtom("O");
IAtom c = builder.NewAtom("C");
c.ImplicitHydrogenCount = 3;
IBond b1 = builder.NewBond(n, o1, BondOrder.Double);
IBond b2 = builder.NewBond(n, o2, BondOrder.Double);
IBond b3 = builder.NewBond(n, c, BondOrder.Single);
mol.Atoms.Add(n);
mol.Atoms.Add(o1);
mol.Atoms.Add(o2);
mol.Atoms.Add(c);
mol.Bonds.Add(b1);
mol.Bonds.Add(b2);
mol.Bonds.Add(b3);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "N5", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "O2", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[2]);
AssertAtomType(testedAtomTypes, "O2", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[3]);
AssertAtomType(testedAtomTypes, "C4", matched);
}
public void TestOxygen2()
{
IAtomContainer mol = builder.NewAtomContainer();
IAtom o1 = builder.NewAtom("O");
IAtom o2 = builder.NewAtom("O");
IAtom h1 = builder.NewAtom("H");
IAtom h2 = builder.NewAtom("H");
IBond bond1 = builder.NewBond(h1, o1, BondOrder.Single);
IBond bond2 = builder.NewBond(o1, o2, BondOrder.Single);
IBond bond3 = builder.NewBond(o2, h2, BondOrder.Single);
mol.Atoms.Add(o1);
mol.Atoms.Add(o2);
mol.Atoms.Add(h1);
mol.Atoms.Add(h2);
mol.Bonds.Add(bond1);
mol.Bonds.Add(bond2);
mol.Bonds.Add(bond3);
StructGenMatcher matcher = new StructGenMatcher();
IAtomType matched;
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[0]);
AssertAtomType(testedAtomTypes, "O2", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[1]);
AssertAtomType(testedAtomTypes, "O2", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[2]);
AssertAtomType(testedAtomTypes, "H1", matched);
matched = matcher.FindMatchingAtomType(mol, mol.Atoms[3]);
AssertAtomType(testedAtomTypes, "H1", matched);
}
public void TestStructGenMatcher()
{
StructGenMatcher matcher = new StructGenMatcher();
Assert.IsNotNull(matcher);
}