public void TestRemoveHydrogensAndPreserveAtomID()
{
string rawMolSmiles = "[H]POOSC(Br)C(Cl)C(F)I";
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles(rawMolSmiles);
IAtom beforeAtom = null;
IAtom afterAtom = null;
foreach (var a in atomContainer.Atoms)
{
if (string.Equals(a.Symbol, "P", StringComparison.OrdinalIgnoreCase))
{
beforeAtom = a;
a.Id = "TEST";
break;
}
}
IAtomContainer result = SMSDNormalizer.RemoveHydrogensAndPreserveAtomID(atomContainer);
foreach (var a in result.Atoms)
{
if (string.Equals(a.Symbol, "P", StringComparison.OrdinalIgnoreCase))
{
afterAtom = a;
break;
}
}
Assert.AreEqual(afterAtom.Id, beforeAtom.Id);
}
public void TestPercieveAtomTypesAndConfigureAtoms()
{
string rawMolSmiles = "[H]POOSC(Br)C(Cl)C(F)I";
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles(rawMolSmiles);
SMSDNormalizer.PercieveAtomTypesAndConfigureAtoms(atomContainer);
Assert.IsNotNull(atomContainer);
}
public void TestConvertExplicitToImplicitHydrogens()
{
string rawMolSmiles = "[H]POOSC(Br)C(Cl)C(F)I";
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles(rawMolSmiles);
int expResult = 11;
IAtomContainer result = SMSDNormalizer.ConvertExplicitToImplicitHydrogens(atomContainer);
Assert.AreEqual(expResult, result.Atoms.Count);
}
public void TestAromatizeMolecule()
{
string rawMolSmiles = "C1=CC2=C(C=C1)C=CC=C2";
var sp = CDK.SmilesParser;
var mol = sp.ParseSmiles(rawMolSmiles);
SMSDNormalizer.AromatizeMolecule(mol);
int count = 0;
foreach (var b in mol.Bonds)
{
if (b.IsAromatic && b.Order.Equals(BondOrder.Double))
{
count++;
}
}
Assert.AreEqual(5, count);
}
public void TestGetHydrogenCount()
{
string rawMolSmiles = "[H]POOSC(Br)C(Cl)C(F)I";
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles(rawMolSmiles);
IAtom atom = null;
foreach (var a in atomContainer.Atoms)
{
if (string.Equals(a.Symbol, "P", StringComparison.OrdinalIgnoreCase))
{
atom = a;
break;
}
}
int expResult = 2;
int result = SMSDNormalizer.GetHydrogenCount(atomContainer, atom);
Assert.AreEqual(expResult, result);
}
public void TestMakeDeepCopy()
{
string rawMolSmiles = "[H]POOSC(Br)C(Cl)C(F)I";
var sp = CDK.SmilesParser;
var container = sp.ParseSmiles(rawMolSmiles);
int counter = 0;
foreach (var a in container.Atoms)
{
a.Id = (counter++).ToString();
}
IAtomContainer result = SMSDNormalizer.MakeDeepCopy(container);
for (int i = 0; i < result.Atoms.Count; i++)
{
Assert.AreEqual(result.Atoms[i].Symbol, container.Atoms[i].Symbol);
Assert.AreEqual(result.Atoms[i].Id, container.Atoms[i].Id);
}
}
