/// <summary>
/// RemovePseudoAtoms
/// </summary>
/// <param name="mol"></param>
/// <returns>Pseudo atom count</returns>
public static int RemovePseudoAtoms(IAtomContainer mol)
{
List <IAtom> pseudoAtoms = new List <IAtom>();
for (int ai = 0; ai < mol.getAtomCount(); ai++)
{
IAtom atom = mol.getAtom(ai);
if (atom is IPseudoAtom)
{
pseudoAtoms.Add(atom);
}
}
if (pseudoAtoms.Count == 0)
{
return(0);
}
foreach (IAtom atom in pseudoAtoms)
{
mol.removeAtomAndConnectedElectronContainers(atom);
}
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
mol = AtomContainerManipulator.suppressHydrogens(mol);
GetHydrogenAdder().addImplicitHydrogens(mol);
return(pseudoAtoms.Count);
}
/// <summary>
/// Remove the following features from a molecule
/// - Atom non-standard mass
/// - Stereo chemistry
/// - explicit hydrogens
/// </summary>
/// <param name="src"></param>
/// <returns>Modified mol</returns>
public static IAtomContainer RemoveIsotopesStereoExplicitHydrogens(
IAtomContainer src)
{
IAtom[] atoms = new IAtom[src.getAtomCount()];
IBond[] bonds = new IBond[src.getBondCount()];
IChemObjectBuilder builder = src.getBuilder();
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = src.getAtom(i);
IAtom atom2 = (IAtom)builder.newInstance(typeof(IAtom), atom.getSymbol());
SetImplicitHydrogenCount(atom2, GetImplicitHydrogenCount(atom));
atom2.setPoint2d(atom.getPoint2d());
atoms[i] = atom2;
}
for (int i = 0; i < bonds.Length; i++)
{
IBond bond = src.getBond(i);
int u = src.getAtomNumber(bond.getAtom(0));
int v = src.getAtomNumber(bond.getAtom(1));
IBond bond2 = (IBond)builder.newInstance(typeof(IBond), atoms[u], atoms[v]);
bond2.setIsAromatic(bond.isAromatic());
bond2.setIsInRing(bond.isInRing());
bond2.setOrder(bond.getOrder());
bond2.setFlag(CDKConstants.ISAROMATIC, bond.getFlag(CDKConstants.ISAROMATIC));
bond2.setFlag(CDKConstants.SINGLE_OR_DOUBLE, bond.getFlag(CDKConstants.SINGLE_OR_DOUBLE));
bonds[i] = bond2;
}
IAtomContainer dest = (IAtomContainer)builder.newInstance(typeof(IAtomContainer));
dest.setAtoms(atoms);
dest.setBonds(bonds);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(dest);
dest = AtomContainerManipulator.suppressHydrogens(dest);
GetHydrogenAdder().addImplicitHydrogens(dest);
return(dest);
}
public static void ConfigureAtomContainer(IAtomContainer mol)
{
//SystemUtil.LoadAssembly(@"C:\Mobius_OpenSource\MobiusClient\Client\bin\Debug\IKVM.OpenJDK.XML.Parse.dll");
//var s = new [email protected]();
//var t = new com.sun.org.apache.xalan.@internal.xsltc.trax.TransformerFactoryImpl();
try // Throws “Provider com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl not found”
{
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); // Perceive Configure atoms
}
catch (Exception ex) { ex = ex; }
GetHydrogenAdder().addImplicitHydrogens(mol); // Be sure implicit hydrogens have been added
ApplyAromaticity(mol);
//// If bond order 4 was present, deduce bond orders
// DeduceBondSystemTool dbst = new DeduceBondSystemTool();
// mol = dbst.fixAromaticBondOrders(mol);
return;
}
/// <summary>
/// Integrate MMP difference and common fragments
/// </summary>
/// <param name="smilesFrags"></param>
/// <returns>Molfile of integrated mol with difference fragment hilighted via special atom isotope values </returns>
public string IntegrateAndHilightMmpStructure(
string smilesFrags)
{
IAtomContainer mol;
IAtom atom;
string frag, context1, context2, molfile, chime = "", molfile2 = "";
int ai, atomCount;
//IsotopeConversionTest(""); // debug
DateTime t0 = DateTime.Now;
try
{
Lex.Split(smilesFrags, ":", out frag, out context1, out context2);
if (Lex.Eq(context2, "NULL"))
{
context2 = ""; // fixup for undefined Redshift fragment smiles fragment represented as "NULL" rather than a blank string
}
mol = SmilesToAtomContainer(frag);
atomCount = mol.getAtomCount();
for (ai = 0; ai < atomCount; ai++) // set isotope labels to mark difference frag
{
atom = mol.getAtom(ai);
int mn = GetMassNumber(atom);
if (mn == 0)
{
SetMassNumber(atom, hilightIsotopeValue); // mark with special value
}
else if (mn > 0)
{
SetMassNumber(atom, -mn); // negate original value to indicate part of difference frag
}
}
if (Lex.IsDefined(context1))
{
JoinMmpFragments(mol, context1, 1);
atomCount = mol.getAtomCount();
}
if (Lex.IsDefined(context2))
{
JoinMmpFragments(mol, context2, 2);
atomCount = mol.getAtomCount();
}
mol = AtomContainerManipulator.suppressHydrogens(mol); // fix potential valency issues
atomCount = mol.getAtomCount();
for (ai = 0; ai < atomCount; ai++) // clean up structure for good display
{
atom = mol.getAtom(ai);
if (atom.getValency() != null && atom.getValency().intValue() != 0)
{
atom.setValency(new java.lang.Integer(0));
}
if (GetImplicitHydrogenCount(atom) != 0)
{
SetImplicitHydrogenCount(atom, 0);
}
}
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
mol = AtomContainerManipulator.suppressHydrogens(mol);
GetHydrogenAdder().addImplicitHydrogens(mol);
mol = GenerateCoordinates(mol);
atomCount = mol.getAtomCount();
molfile = ConvertIsotopeValuesToHilighting(mol); // about 3.0 ms per IntegrateAndHilightMmpStructure call
double msTime = TimeOfDay.Delta(t0);
IntegrateAndHilightMmpStructureCount++;
IntegrateAndHilightMmpStructureTotalTime += msTime;
IntegrateAndHilightMmpStructureAvgTime = IntegrateAndHilightMmpStructureTotalTime / IntegrateAndHilightMmpStructureCount;
return(molfile);
}
catch (Exception ex)
{
string msg = "Error integrating Smiles Fragments: " + smilesFrags + DebugLog.FormatExceptionMessage(ex, true);
DebugLog.Message(msg);
return("");
}
}
