/// <summary> Retrieves the set of all rings and performs an aromaticity detection based
/// on Hueckels 4n + 2 rule. An AllRingsFinder with customized timeout may be
/// assigned to this method.
/// </summary>
/// <param name="removeAromatictyFlags"> When true, we leaves ChemObjects that
/// are already marked as aromatic as they are
/// </param>
/// <param name="atomContainer"> AtomContainer to be searched for
/// </param>
/// <param name="arf"> AllRingsFinder to be employed for the
/// ringsearch. Use this to customize the
/// AllRingsFinder timeout feature
/// rings
/// </param>
/// <returns> True, if molecule has aromatic features
/// </returns>
/// <exception cref="CDKException"> Thrown in case of errors or an
/// AllRingsFinder timeout
/// </exception>
public static bool detectAromaticity(IAtomContainer atomContainer, bool removeAromatictyFlags, AllRingsFinder arf)
{
//logger.debug("Entered Aromaticity Detection");
//logger.debug("Starting AllRingsFinder");
long before = (System.DateTime.Now.Ticks - 621355968000000000) / 10000;
if (arf == null)
{
arf = new AllRingsFinder();
arf.setTimeout(timeout);
}
ringSet = arf.findAllRings(atomContainer);
long after = (System.DateTime.Now.Ticks - 621355968000000000) / 10000;
//logger.debug("time for finding all rings: " + (after - before) + " milliseconds");
//logger.debug("Finished AllRingsFinder");
if (ringSet.AtomContainerCount > 0)
{
return detectAromaticity(atomContainer, ringSet, removeAromatictyFlags);
}
return false;
}
/// <summary> Generate canonical SMILES from the <code>molecule</code>. This method
/// canonicaly lables the molecule but dose not perform any checks on the
/// chemical validity of the molecule. Does not care about multiple molecules.
/// IMPORTANT: A precomputed Set of All Rings (SAR) can be passed to this
/// SmilesGenerator in order to avoid recomputing it. Use setRings() to
/// assign the SAR.
///
/// </summary>
/// <param name="molecule"> The molecule to evaluate
/// </param>
/// <param name="chiral"> true=SMILES will be chiral, false=SMILES
/// will not be chiral.
/// </param>
/// <param name="doubleBondConfiguration"> Description of Parameter
/// </param>
/// <returns> Description of the Returned Value
/// </returns>
/// <exception cref="CDKException"> At least one atom has no Point2D;
/// coordinates are needed for creating the chiral smiles. This excpetion
/// can only be thrown if chiral smiles is created, ignore it if you want a
/// non-chiral smiles (createSMILES(AtomContainer) does not throw an
/// exception).
/// </exception>
/// <seealso cref="org.openscience.cdk.graph.invariant.CanonicalLabeler.canonLabel(IAtomContainer)">
/// </seealso>
//UPGRADE_NOTE: Synchronized keyword was removed from method 'createSMILESWithoutCheckForMultipleMolecules'. Lock expression was added. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1027'"
public virtual System.String createSMILESWithoutCheckForMultipleMolecules(IMolecule molecule, bool chiral, bool[] doubleBondConfiguration)
{
lock (this)
{
if (molecule.AtomCount == 0)
{
return "";
}
canLabler.canonLabel(molecule);
brokenBonds.Clear();
ringMarker = 0;
IAtom[] all = molecule.Atoms;
IAtom start = null;
for (int i = 0; i < all.Length; i++)
{
IAtom atom = all[i];
if (chiral && atom.getPoint2d() == null)
{
throw new CDKException("Atom number " + i + " has no 2D coordinates, but 2D coordinates are needed for creating chiral smiles");
}
//System.out.println("Setting all VISITED flags to false");
atom.setFlag(CDKConstants.VISITED, false);
if ((long)((System.Int64)atom.getProperty("CanonicalLable")) == 1)
{
start = atom;
}
}
//detect aromaticity
if (rings == null)
{
if (ringFinder == null)
{
ringFinder = new AllRingsFinder();
}
rings = ringFinder.findAllRings(molecule);
}
HueckelAromaticityDetector.detectAromaticity(molecule, rings, false);
if (chiral && rings.AtomContainerCount > 0)
{
System.Collections.ArrayList v = RingPartitioner.partitionRings(rings);
//System.out.println("RingSystems: " + v.size());
for (int i = 0; i < v.Count; i++)
{
int counter = 0;
IAtomContainer allrings = RingSetManipulator.getAllInOneContainer((IRingSet)v[i]);
for (int k = 0; k < allrings.AtomCount; k++)
{
if (!BondTools.isStereo(molecule, allrings.getAtomAt(k)) && hasWedges(molecule, allrings.getAtomAt(k)) != null)
{
IBond bond = molecule.getBond(allrings.getAtomAt(k), hasWedges(molecule, allrings.getAtomAt(k)));
if (bond.Stereo == CDKConstants.STEREO_BOND_UP)
{
allrings.getAtomAt(k).setProperty(RING_CONFIG, UP);
}
else
{
allrings.getAtomAt(k).setProperty(RING_CONFIG, DOWN);
}
counter++;
}
}
if (counter == 1)
{
for (int k = 0; k < allrings.AtomCount; k++)
{
allrings.getAtomAt(k).setProperty(RING_CONFIG, UP);
}
}
}
}
System.Text.StringBuilder l = new System.Text.StringBuilder();
createSMILES(start, l, molecule, chiral, doubleBondConfiguration);
rings = null;
return l.ToString();
}
}