/**
* @param list
* @param source
* @param target
*/
protected synchronized void identifySingleAtomsMatchedParts(
List<CDKRMap> list, IAtomContainer source, IAtomContainer target) {
// List<IAtom> array1 = new ArrayList<>();
// List<IAtom> array2 = new ArrayList<>();
/* We have serial numbers of the bonds/Atoms to delete
* Now we will collect the actual bond/Atoms rather than
* serial number for deletion. RonP flag check whether reactant is
* mapped on product or Vise Versa
*/
TreeMap<Integer, Integer> atomNumbersFromContainer = new TreeMap<>();
for (CDKRMap rmap : list) {
// System.err.print("Map " + o.getClass());
IAtom sAtom = source.getAtom(rmap.getId1());
IAtom tAtom = target.getAtom(rmap.getId2());
// array1.add(sAtom);
// array2.add(tAtom);
int indexI = source.getAtomNumber(sAtom);
int indexJ = target.getAtomNumber(tAtom);
atomNumbersFromContainer.put(indexI, indexJ);
/*Added the Mapping Numbers to the FinalMapping*
*/
getMappings().add(atomNumbersFromContainer);
}
}
/**
* Generate Compatibility Graph Nodes
*
* @return
* @throws IOException
*/
private int compatibilityGraphNodes() throws IOException {
compGraphNodes.clear();
Set<Edge> edges = new HashSet<>();
int nodeCount = 1;
Map<IAtom, List<String>> labelAtomsBySymbolA = labelAtomsBySymbol(source);
Map<IAtom, List<String>> labelAtomsBySymbolB = labelAtomsBySymbol(target);
for (Map.Entry<IAtom, List<String>> labelA : labelAtomsBySymbolA.entrySet()) {
// System.err.println("labelA.getValue() " + labelA.getValue());
for (Map.Entry<IAtom, List<String>> labelB : labelAtomsBySymbolB.entrySet()) {
IAtom atom = labelA.getKey();
if (((atom instanceof IQueryAtom) && ((IQueryAtom) atom).matches(labelB.getKey()))
|| (!(atom instanceof IQueryAtom)
&& atom.getSymbol().equals(labelB.getKey().getSymbol()))) {
// System.err.println("labelB.getValue() " + labelB.getValue());
int atomNumberI = source.getAtomNumber(labelA.getKey());
int atomNumberJ = target.getAtomNumber(labelB.getKey());
Edge e = new Edge(atomNumberI, atomNumberJ);
if (!edges.contains(e)) {
edges.add(e);
compGraphNodes.add(atomNumberI);
compGraphNodes.add(atomNumberJ);
compGraphNodes.add(nodeCount);
nodeCount += 1;
}
}
}
}
return 0;
}
/**
* Fill the {@literal coordinates} and {@literal elevation} from the given offset index. If there
* is only one connection then the second entry (from the offset) will use the coordinates of
* <i>a</i>. The permutation parity is also built and returned.
*
* @param container atom container
* @param a the central atom
* @param connected bonds connected to the central atom
* @param coordinates the coordinates array to fill
* @param elevations the elevations of the connected atoms
* @param offset current location in the offset array
* @return the permutation parity
*/
private static PermutationParity fill2DCoordinates(
IAtomContainer container,
IAtom a,
List<IBond> connected,
Point2d[] coordinates,
int[] elevations,
int offset) {
int i = 0;
coordinates[offset + 1] = a.getPoint2d();
elevations[offset + 1] = 0;
int[] indices = new int[2];
for (IBond bond : connected) {
if (!isDoubleBond(bond)) {
IAtom other = bond.getConnectedAtom(a);
coordinates[i + offset] = other.getPoint2d();
elevations[i + offset] = elevation(bond, a);
indices[i] = container.getAtomNumber(other);
i++;
}
}
if (i == 1) {
return PermutationParity.IDENTITY;
} else {
return new BasicPermutationParity(indices);
}
}
public static IAtomContainer getMcsAsNewContainer(IAtomContainer mol1, IAtomContainer mol2)
throws CDKException, CloneNotSupportedException {
Isomorphism mcs = new Isomorphism(org.openscience.cdk.smsd.interfaces.Algorithm.DEFAULT, true);
mcs.init(mol1, mol2, true, true);
mcs.setChemFilters(true, true, true);
mol1 = mcs.getReactantMolecule();
mol2 = mcs.getProductMolecule();
IAtomContainer mcsmolecule =
DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class, mol1);
List<IAtom> atomsToBeRemoved = new ArrayList<IAtom>();
for (IAtom atom : mcsmolecule.atoms()) {
int index = mcsmolecule.getAtomNumber(atom);
if (!mcs.getFirstMapping().containsKey(index)) {
atomsToBeRemoved.add(atom);
}
}
for (IAtom atom : atomsToBeRemoved) {
mcsmolecule.removeAtomAndConnectedElectronContainers(atom);
}
return mcsmolecule;
}
/**
* Convenience method for giving a string representation of this ring based on the number of the
* atom in a given molecule.
*
* @param molecule A molecule to determine an atom number for each ring atom
* @return string representation of this ring
*/
private String toString(IRing ring, IAtomContainer molecule) throws Exception {
String str = "";
for (int f = 0; f < ring.getAtomCount(); f++) {
str += molecule.getAtomNumber(ring.getAtom(f)) + " - ";
}
return str;
}
@Override
public int seed(IAtomContainer molecule, IAtom atom, BitSet mask) {
double sum = 0;
for (IBond bond : molecule.getConnectedBondsList(atom)) {
if (mask.get(molecule.getAtomNumber(bond.getConnectedAtom(atom))))
sum += order(bond.getOrder());
}
return ((Double) sum).hashCode();
}
/**
* Create an encoder for axial 3D stereochemistry for the given start and end atoms.
*
* @param container the molecule
* @param start start of the cumulated system
* @param startBonds bonds connected to the start
* @param end end of the cumulated system
* @param endBonds bonds connected to the end
* @return an encoder
*/
private static StereoEncoder axial3DEncoder(
IAtomContainer container,
IAtom start,
List<IBond> startBonds,
IAtom end,
List<IBond> endBonds) {
Point3d[] coordinates = new Point3d[4];
PermutationParity perm =
new CombinedPermutationParity(
fill3DCoordinates(container, start, startBonds, coordinates, 0),
fill3DCoordinates(container, end, endBonds, coordinates, 2));
GeometricParity geom = new Tetrahedral3DParity(coordinates);
int u = container.getAtomNumber(start);
int v = container.getAtomNumber(end);
return new GeometryEncoder(new int[] {u, v}, perm, geom);
}
protected void process(
IAtomContainer target,
List<Integer> unmapped_atoms_molB,
int mappingSize,
List<Integer> i_bond_setB,
List<String> c_bond_setB,
List<Integer> mapped_atoms,
int counter) {
int unmapped_numB = unmapped_atoms_molB.size();
boolean bond_considered = false;
boolean normal_bond = true;
for (int atomIndex = 0; atomIndex < target.getBondCount(); atomIndex++) {
Integer indexI = target.getAtomNumber(target.getBond(atomIndex).getAtom(0));
Integer indexJ = target.getAtomNumber(target.getBond(atomIndex).getAtom(1));
IBond bond = target.getBond(atomIndex);
Integer order = (bond.getOrder().ordinal() + 1);
for (int b = 0; b < unmapped_numB; b++) {
if (unmapped_atoms_molB.get(b).equals(indexI)) {
normal_bond =
unMappedAtomsEqualsIndexI(
target, mappingSize, atomIndex, counter, mapped_atoms, indexI, indexJ, order);
bond_considered = true;
} else if (unmapped_atoms_molB.get(b) == indexJ) {
normal_bond =
unMappedAtomsEqualsIndexJ(
target, mappingSize, atomIndex, counter, mapped_atoms, indexI, indexJ, order);
bond_considered = true;
}
if (normal_bond && bond_considered) {
markNormalBonds(atomIndex, i_bond_setB, c_bond_setB, indexI, indexJ, order);
normal_bond = true;
break;
}
}
bond_considered = false;
}
}
/**
* Positions the aliphatic substituents of a ring system
*
* @param rs The RingSystem for which the substituents are to be laid out
* @return A list of atoms that where laid out
*/
public IAtomContainer placeRingSubstituents(IRingSet rs, double bondLength) {
logger.debug("RingPlacer.placeRingSubstituents() start");
IRing ring = null;
IAtom atom = null;
IRingSet rings = null;
IAtomContainer unplacedPartners = rs.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer sharedAtoms = rs.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer primaryAtoms = rs.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer treatedAtoms = rs.getBuilder().newInstance(IAtomContainer.class);
Point2d centerOfRingGravity = null;
for (int j = 0; j < rs.getAtomContainerCount(); j++) {
ring = (IRing) rs.getAtomContainer(j); /* Get the j-th Ring in RingSet rs */
for (int k = 0; k < ring.getAtomCount(); k++) {
unplacedPartners.removeAllElements();
sharedAtoms.removeAllElements();
primaryAtoms.removeAllElements();
atom = ring.getAtom(k);
rings = rs.getRings(atom);
centerOfRingGravity = GeometryTools.get2DCenter(rings);
atomPlacer.partitionPartners(atom, unplacedPartners, sharedAtoms);
atomPlacer.markNotPlaced(unplacedPartners);
try {
for (int f = 0; f < unplacedPartners.getAtomCount(); f++) {
logger.debug(
"placeRingSubstituents->unplacedPartners: "
+ (molecule.getAtomNumber(unplacedPartners.getAtom(f)) + 1));
}
} catch (Exception exc) {
}
treatedAtoms.add(unplacedPartners);
if (unplacedPartners.getAtomCount() > 0) {
atomPlacer.distributePartners(
atom, sharedAtoms, centerOfRingGravity, unplacedPartners, bondLength);
}
}
}
logger.debug("RingPlacer.placeRingSubstituents() end");
return treatedAtoms;
}
/**
* The method calculates the sigma electronegativity of a given atom It is needed to call the
* addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
*
* @param atom The IAtom for which the DescriptorValue is requested
* @param ac AtomContainer
* @return return the sigma electronegativity
*/
@TestMethod(value = "testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom, IAtomContainer ac) {
IAtomContainer clone;
IAtom localAtom;
try {
clone = (IAtomContainer) ac.clone();
localAtom = clone.getAtom(ac.getAtomNumber(atom));
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(clone);
} catch (CDKException e) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(Double.NaN),
descriptorNames,
e);
} catch (CloneNotSupportedException e) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(Double.NaN),
descriptorNames,
e);
}
if (maxIterations != -1 && maxIterations != 0)
electronegativity.setMaxIterations(maxIterations);
double result = electronegativity.calculateSigmaElectronegativity(clone, localAtom);
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(result),
descriptorNames);
}
private List<List<Integer>> getAtomMappings(List bondMapping, IAtomContainer atomContainer) {
List<List<Integer>> atomMapping = new ArrayList<List<Integer>>();
// loop over each mapping
for (Object aBondMapping : bondMapping) {
List list = (List) aBondMapping;
List<Integer> tmp = new ArrayList<Integer>();
IAtom atom1 = null;
IAtom atom2 = null;
// loop over this mapping
for (Object aList : list) {
RMap map = (RMap) aList;
int bondID = map.getId1();
// get the atoms in this bond
IBond bond = atomContainer.getBond(bondID);
atom1 = bond.getAtom(0);
atom2 = bond.getAtom(1);
Integer idx1 = atomContainer.getAtomNumber(atom1);
Integer idx2 = atomContainer.getAtomNumber(atom2);
if (!tmp.contains(idx1)) tmp.add(idx1);
if (!tmp.contains(idx2)) tmp.add(idx2);
}
if (tmp.size() > 0) atomMapping.add(tmp);
// If there is only one bond, check if it matches both ways.
if (list.size() == 1 && atom1.getAtomicNumber() == atom2.getAtomicNumber()) {
List<Integer> tmp2 = new ArrayList<Integer>();
tmp2.add(tmp.get(0));
tmp2.add(tmp.get(1));
atomMapping.add(tmp2);
}
}
return atomMapping;
}
/**
* Search if the setOfAtomContainer contains the atomContainer
*
* @param set ISetOfAtomContainer object where to search
* @param atomContainer IAtomContainer to search
* @return True, if the atomContainer is contained
*/
private boolean existAC(IAtomContainerSet set, IAtomContainer atomContainer) {
IAtomContainer acClone = null;
try {
acClone = (IMolecule) atomContainer.clone();
if (!lookingSymmetry) {
/*remove all aromatic flags*/
for (IAtom atom : acClone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : acClone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
}
} catch (CloneNotSupportedException e1) {
e1.printStackTrace();
}
for (int i = 0; i < acClone.getAtomCount(); i++)
// if(acClone.getAtom(i).getID() == null)
acClone.getAtom(i).setID("" + acClone.getAtomNumber(acClone.getAtom(i)));
if (lookingSymmetry) {
try {
CDKHueckelAromaticityDetector.detectAromaticity(acClone);
} catch (CDKException e) {
e.printStackTrace();
}
} else {
if (!lookingSymmetry) {
/*remove all aromatic flags*/
for (IAtom atom : acClone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : acClone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
}
}
for (int i = 0; i < set.getAtomContainerCount(); i++) {
IAtomContainer ss = set.getAtomContainer(i);
for (int j = 0; j < ss.getAtomCount(); j++)
// if(ss.getAtom(j).getID() == null)
ss.getAtom(j).setID("" + ss.getAtomNumber(ss.getAtom(j)));
try {
if (!lookingSymmetry) {
QueryAtomContainer qAC =
QueryAtomContainerCreator.createSymbolChargeIDQueryContainer(acClone);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC)) {
QueryAtomContainer qAC2 =
QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(acClone);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC2)) return true;
}
} else {
QueryAtomContainer qAC =
QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(acClone);
CDKHueckelAromaticityDetector.detectAromaticity(ss);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC)) return true;
}
} catch (CDKException e1) {
System.err.println(e1);
logger.error(e1.getMessage());
logger.debug(e1);
}
}
return false;
}
/**
* This makes sourceAtom map1 of matching atoms out of sourceAtom map1 of matching bonds as
* produced by the get(Subgraph|Ismorphism)Map methods.
*
* @param rMapList The list produced by the getMap method.
* @param graph1 first molecule. Must not be an IQueryAtomContainer.
* @param graph2 second molecule. May be an IQueryAtomContainer.
* @return The mapping found projected on graph1. This is sourceAtom List of CDKRMap objects
* containing Ids of matching atoms.
*/
private synchronized List<List<CDKRMap>> makeAtomsMapOfBondsMap(
List<CDKRMap> rMapList, IAtomContainer graph1, IAtomContainer graph2) {
if (rMapList == null) {
return (null);
}
List<List<CDKRMap>> result;
if (rMapList.size() == 1) {
result = makeAtomsMapOfBondsMapSingleBond(rMapList, graph1, graph2);
} else {
List<CDKRMap> resultLocal = new ArrayList<CDKRMap>();
for (CDKRMap rMapList2 : rMapList) {
IBond qBond = graph1.getBond(rMapList2.getId1());
IBond tBond = graph2.getBond(rMapList2.getId2());
IAtom[] qAtoms = BondManipulator.getAtomArray(qBond);
IAtom[] tAtoms = BondManipulator.getAtomArray(tBond);
for (int j = 0; j < 2; j++) {
List<IBond> bondsConnectedToAtom1j = graph1.getConnectedBondsList(qAtoms[j]);
for (IBond bondsConnectedToAtom1j1 : bondsConnectedToAtom1j) {
if (bondsConnectedToAtom1j1 != qBond) {
IBond testBond = bondsConnectedToAtom1j1;
for (CDKRMap rMapList1 : rMapList) {
IBond testBond2;
if ((rMapList1).getId1() == graph1.getBondNumber(testBond)) {
testBond2 = graph2.getBond((rMapList1).getId2());
for (int n = 0; n < 2; n++) {
List<IBond> bondsToTest = graph2.getConnectedBondsList(tAtoms[n]);
if (bondsToTest.contains(testBond2)) {
CDKRMap map1;
if (j == n) {
map1 =
new CDKRMap(
graph1.getAtomNumber(qAtoms[0]), graph2.getAtomNumber(tAtoms[0]));
} else {
map1 =
new CDKRMap(
graph1.getAtomNumber(qAtoms[1]), graph2.getAtomNumber(tAtoms[0]));
}
if (!resultLocal.contains(map1)) {
resultLocal.add(map1);
}
CDKRMap map2;
if (j == n) {
map2 =
new CDKRMap(
graph1.getAtomNumber(qAtoms[1]), graph2.getAtomNumber(tAtoms[1]));
} else {
map2 =
new CDKRMap(
graph1.getAtomNumber(qAtoms[0]), graph2.getAtomNumber(tAtoms[1]));
}
if (!resultLocal.contains(map2)) {
resultLocal.add(map2);
}
}
}
}
}
}
}
}
}
result = new ArrayList<>();
result.add(resultLocal);
}
return result;
}
/**
* Generated coordinates for a given ring, which is fused to another ring. The rings share exactly
* one bond.
*
* @param ring The ring to be placed
* @param sharedAtoms The atoms of this ring, also members of another ring, which are already
* placed
* @param sharedAtomsCenter The geometric center of these atoms
* @param ringCenterVector A vector pointing the the center of the new ring
* @param bondLength The standard bondlength
*/
public void placeFusedRing(
IRing ring,
IAtomContainer sharedAtoms,
Point2d sharedAtomsCenter,
Vector2d ringCenterVector,
double bondLength) {
logger.debug("RingPlacer.placeFusedRing() start");
Point2d ringCenter = new Point2d(sharedAtomsCenter);
double radius = getNativeRingRadius(ring, bondLength);
double newRingPerpendicular = Math.sqrt(Math.pow(radius, 2) - Math.pow(bondLength / 2, 2));
ringCenterVector.normalize();
logger.debug("placeFusedRing->: ringCenterVector.length()" + ringCenterVector.length());
ringCenterVector.scale(newRingPerpendicular);
ringCenter.add(ringCenterVector);
IAtom bondAtom1 = sharedAtoms.getAtom(0);
IAtom bondAtom2 = sharedAtoms.getAtom(1);
Vector2d bondAtom1Vector = new Vector2d(bondAtom1.getPoint2d());
Vector2d bondAtom2Vector = new Vector2d(bondAtom2.getPoint2d());
Vector2d originRingCenterVector = new Vector2d(ringCenter);
bondAtom1Vector.sub(originRingCenterVector);
bondAtom2Vector.sub(originRingCenterVector);
double occupiedAngle = bondAtom1Vector.angle(bondAtom2Vector);
double remainingAngle = (2 * Math.PI) - occupiedAngle;
double addAngle = remainingAngle / (ring.getRingSize() - 1);
logger.debug("placeFusedRing->occupiedAngle: " + Math.toDegrees(occupiedAngle));
logger.debug("placeFusedRing->remainingAngle: " + Math.toDegrees(remainingAngle));
logger.debug("placeFusedRing->addAngle: " + Math.toDegrees(addAngle));
IAtom startAtom;
double centerX = ringCenter.x;
double centerY = ringCenter.y;
double xDiff = bondAtom1.getPoint2d().x - bondAtom2.getPoint2d().x;
double yDiff = bondAtom1.getPoint2d().y - bondAtom2.getPoint2d().y;
double startAngle;
;
int direction = 1;
// if bond is vertical
if (xDiff == 0) {
logger.debug("placeFusedRing->Bond is vertical");
// starts with the lower Atom
if (bondAtom1.getPoint2d().y > bondAtom2.getPoint2d().y) {
startAtom = bondAtom1;
} else {
startAtom = bondAtom2;
}
// changes the drawing direction
if (centerX < bondAtom1.getPoint2d().x) {
direction = 1;
} else {
direction = -1;
}
}
// if bond is not vertical
else {
// starts with the left Atom
if (bondAtom1.getPoint2d().x > bondAtom2.getPoint2d().x) {
startAtom = bondAtom1;
} else {
startAtom = bondAtom2;
}
// changes the drawing direction
if (centerY - bondAtom1.getPoint2d().y
> (centerX - bondAtom1.getPoint2d().x) * yDiff / xDiff) {
direction = 1;
} else {
direction = -1;
}
}
startAngle =
GeometryTools.getAngle(
startAtom.getPoint2d().x - ringCenter.x, startAtom.getPoint2d().y - ringCenter.y);
IAtom currentAtom = startAtom;
// determine first bond in Ring
// int k = 0;
// for (k = 0; k < ring.getElectronContainerCount(); k++) {
// if (ring.getElectronContainer(k) instanceof IBond) break;
// }
IBond currentBond = sharedAtoms.getBond(0);
Vector atomsToDraw = new Vector();
for (int i = 0; i < ring.getBondCount() - 2; i++) {
currentBond = ring.getNextBond(currentBond, currentAtom);
currentAtom = currentBond.getConnectedAtom(currentAtom);
atomsToDraw.addElement(currentAtom);
}
addAngle = addAngle * direction;
try {
logger.debug("placeFusedRing->startAngle: " + Math.toDegrees(startAngle));
logger.debug("placeFusedRing->addAngle: " + Math.toDegrees(addAngle));
logger.debug("placeFusedRing->startAtom is: " + (molecule.getAtomNumber(startAtom) + 1));
logger.debug("AtomsToDraw: " + atomPlacer.listNumbers(molecule, atomsToDraw));
} catch (Exception exc) {
logger.debug("Caught an exception while logging in RingPlacer");
}
atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, startAngle, addAngle, radius);
}
/**
* @param atom1
* @param atom2
*/
public synchronized void put(IAtom atom1, IAtom atom2) {
mapping.put(atom1, atom2);
mappingIndex.put(query.getAtomNumber(atom1), target.getAtomNumber(atom2));
}
/**
* This makes atom map1 of matching atoms out of atom map1 of matching bonds as produced by the
* get(Subgraph|Ismorphism)Map methods. Added by Asad since CDK one doesn't pick up the correct
* changes
*
* @param list The list produced by the getMap method.
* @param sourceGraph first molecule. Must not be an IQueryAtomContainer.
* @param targetGraph second molecule. May be an IQueryAtomContainer.
* @return The mapping found projected on sourceGraph. This is atom List of CDKRMap objects
* containing Ids of matching atoms.
*/
private synchronized List<List<CDKRMap>> makeAtomsMapOfBondsMapSingleBond(
List<CDKRMap> list, IAtomContainer sourceGraph, IAtomContainer targetGraph) {
if (list == null) {
return null;
}
Map<IBond, IBond> bondMap = new HashMap<IBond, IBond>(list.size());
for (CDKRMap solBondMap : list) {
int id1 = solBondMap.getId1();
int id2 = solBondMap.getId2();
IBond qBond = sourceGraph.getBond(id1);
IBond tBond = targetGraph.getBond(id2);
bondMap.put(qBond, tBond);
}
List<CDKRMap> result1 = new ArrayList<CDKRMap>();
List<CDKRMap> result2 = new ArrayList<CDKRMap>();
for (IBond qbond : sourceGraph.bonds()) {
if (bondMap.containsKey(qbond)) {
IBond tbond = bondMap.get(qbond);
CDKRMap map00 = null;
CDKRMap map01 = null;
CDKRMap map10 = null;
CDKRMap map11 = null;
if ((qbond.getAtom(0).getSymbol().equals(tbond.getAtom(0).getSymbol()))
&& (qbond.getAtom(1).getSymbol().equals(tbond.getAtom(1).getSymbol()))) {
map00 =
new CDKRMap(
sourceGraph.getAtomNumber(qbond.getAtom(0)),
targetGraph.getAtomNumber(tbond.getAtom(0)));
map11 =
new CDKRMap(
sourceGraph.getAtomNumber(qbond.getAtom(1)),
targetGraph.getAtomNumber(tbond.getAtom(1)));
if (!result1.contains(map00)) {
result1.add(map00);
}
if (!result1.contains(map11)) {
result1.add(map11);
}
}
if ((qbond.getAtom(0).getSymbol().equals(tbond.getAtom(1).getSymbol()))
&& (qbond.getAtom(1).getSymbol().equals(tbond.getAtom(0).getSymbol()))) {
map01 =
new CDKRMap(
sourceGraph.getAtomNumber(qbond.getAtom(0)),
targetGraph.getAtomNumber(tbond.getAtom(1)));
map10 =
new CDKRMap(
sourceGraph.getAtomNumber(qbond.getAtom(1)),
targetGraph.getAtomNumber(tbond.getAtom(0)));
if (!result2.contains(map01)) {
result2.add(map01);
}
if (!result2.contains(map10)) {
result2.add(map10);
}
}
}
}
List<List<CDKRMap>> result = new ArrayList<List<CDKRMap>>();
if (result1.size() == result2.size()) {
result.add(result1);
result.add(result2);
} else if (result1.size() > result2.size()) {
result.add(result1);
} else {
result.add(result2);
}
return result;
}
@TestMethod(value = "testCalculate_IAtomContainer")
public DescriptorValue calculate(
IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset) {
IAtomContainer varAtomContainer;
try {
varAtomContainer = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e);
}
int atomPosition = atomContainer.getAtomNumber(atom);
IAtom clonedAtom = varAtomContainer.getAtom(atomPosition);
DoubleArrayResult rdfProtonCalculatedValues = new DoubleArrayResult(gsr_desc_length);
if (!atom.getSymbol().equals("H")) {
return getDummyDescriptorValue(new CDKException("Invalid atom specified"));
}
///////////////////////// FIRST SECTION OF MAIN METHOD: DEFINITION OF MAIN VARIABLES
///////////////////////// AND AROMATICITY AND PI-SYSTEM AND RINGS DETECTION
Molecule mol = new Molecule(varAtomContainer);
if (varAtomContainer != acold) {
acold = varAtomContainer;
// DETECTION OF pi SYSTEMS
varAtomContainerSet = ConjugatedPiSystemsDetector.detect(mol);
if (precalculatedringset == null)
try {
varRingSet = (new AllRingsFinder()).findAllRings(varAtomContainer);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
else varRingSet = precalculatedringset;
try {
GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges();
peoe.assignGasteigerMarsiliSigmaPartialCharges(mol, true);
} catch (Exception ex1) {
return getDummyDescriptorValue(ex1);
}
}
if (checkAromaticity) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(varAtomContainer);
CDKHueckelAromaticityDetector.detectAromaticity(varAtomContainer);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
}
IRingSet rsAtom;
Ring ring;
IRingSet ringsWithThisBond;
// SET ISINRING FLAGS FOR BONDS
Iterator<IBond> bondsInContainer = varAtomContainer.bonds().iterator();
while (bondsInContainer.hasNext()) {
IBond bond = bondsInContainer.next();
ringsWithThisBond = varRingSet.getRings(bond);
if (ringsWithThisBond.getAtomContainerCount() > 0) {
bond.setFlag(CDKConstants.ISINRING, true);
}
}
// SET ISINRING FLAGS FOR ATOMS
IRingSet ringsWithThisAtom;
for (int w = 0; w < varAtomContainer.getAtomCount(); w++) {
ringsWithThisAtom = varRingSet.getRings(varAtomContainer.getAtom(w));
if (ringsWithThisAtom.getAtomContainerCount() > 0) {
varAtomContainer.getAtom(w).setFlag(CDKConstants.ISINRING, true);
}
}
IAtomContainer detected = varAtomContainerSet.getAtomContainer(0);
// neighboors[0] is the atom joined to the target proton:
List<IAtom> neighboors = mol.getConnectedAtomsList(clonedAtom);
IAtom neighbour0 = neighboors.get(0);
// 2', 3', 4', 5', 6', and 7' atoms up to the target are detected:
List<IAtom> atomsInSecondSphere = mol.getConnectedAtomsList(neighbour0);
List<IAtom> atomsInThirdSphere;
List<IAtom> atomsInFourthSphere;
List<IAtom> atomsInFifthSphere;
List<IAtom> atomsInSixthSphere;
List<IAtom> atomsInSeventhSphere;
// SOME LISTS ARE CREATED FOR STORING OF INTERESTING ATOMS AND BONDS DURING DETECTION
ArrayList<Integer> singles = new ArrayList<Integer>(); // list of any bond not rotatable
ArrayList<Integer> doubles = new ArrayList<Integer>(); // list with only double bonds
ArrayList<Integer> atoms = new ArrayList<Integer>(); // list with all the atoms in spheres
// atoms.add( Integer.valueOf( mol.getAtomNumber(neighboors[0]) ) );
ArrayList<Integer> bondsInCycloex =
new ArrayList<Integer>(); // list for bonds in cycloexane-like rings
// 2', 3', 4', 5', 6', and 7' bonds up to the target are detected:
IBond secondBond; // (remember that first bond is proton bond)
IBond thirdBond; //
IBond fourthBond; //
IBond fifthBond; //
IBond sixthBond; //
IBond seventhBond; //
// definition of some variables used in the main FOR loop for detection of interesting atoms and
// bonds:
boolean theBondIsInA6MemberedRing; // this is like a flag for bonds which are in cycloexane-like
// rings (rings with more than 4 at.)
IBond.Order bondOrder;
int bondNumber;
int sphere;
// THIS MAIN FOR LOOP DETECT RIGID BONDS IN 7 SPHERES:
for (IAtom curAtomSecond : atomsInSecondSphere) {
secondBond = mol.getBond(neighbour0, curAtomSecond);
if (mol.getAtomNumber(curAtomSecond) != atomPosition
&& getIfBondIsNotRotatable(mol, secondBond, detected)) {
sphere = 2;
bondOrder = secondBond.getOrder();
bondNumber = mol.getBondNumber(secondBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSecond),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInThirdSphere = mol.getConnectedAtomsList(curAtomSecond);
if (atomsInThirdSphere.size() > 0) {
for (IAtom curAtomThird : atomsInThirdSphere) {
thirdBond = mol.getBond(curAtomThird, curAtomSecond);
// IF THE ATOMS IS IN THE THIRD SPHERE AND IN A CYCLOEXANE-LIKE RING, IT IS STORED IN
// THE PROPER LIST:
if (mol.getAtomNumber(curAtomThird) != atomPosition
&& getIfBondIsNotRotatable(mol, thirdBond, detected)) {
sphere = 3;
bondOrder = thirdBond.getOrder();
bondNumber = mol.getBondNumber(thirdBond);
theBondIsInA6MemberedRing = false;
// if the bond is in a cyclohexane-like ring (a ring with 5 or more atoms, not
// aromatic)
// the boolean "theBondIsInA6MemberedRing" is set to true
if (!thirdBond.getFlag(CDKConstants.ISAROMATIC)) {
if (!curAtomThird.equals(neighbour0)) {
rsAtom = varRingSet.getRings(thirdBond);
for (int f = 0; f < rsAtom.getAtomContainerCount(); f++) {
ring = (Ring) rsAtom.getAtomContainer(f);
if (ring.getRingSize() > 4 && ring.contains(thirdBond)) {
theBondIsInA6MemberedRing = true;
}
}
}
}
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomThird),
atoms,
sphere,
theBondIsInA6MemberedRing);
theBondIsInA6MemberedRing = false;
atomsInFourthSphere = mol.getConnectedAtomsList(curAtomThird);
if (atomsInFourthSphere.size() > 0) {
for (IAtom curAtomFourth : atomsInFourthSphere) {
fourthBond = mol.getBond(curAtomThird, curAtomFourth);
if (mol.getAtomNumber(curAtomFourth) != atomPosition
&& getIfBondIsNotRotatable(mol, fourthBond, detected)) {
sphere = 4;
bondOrder = fourthBond.getOrder();
bondNumber = mol.getBondNumber(fourthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomFourth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInFifthSphere = mol.getConnectedAtomsList(curAtomFourth);
if (atomsInFifthSphere.size() > 0) {
for (IAtom curAtomFifth : atomsInFifthSphere) {
fifthBond = mol.getBond(curAtomFifth, curAtomFourth);
if (mol.getAtomNumber(curAtomFifth) != atomPosition
&& getIfBondIsNotRotatable(mol, fifthBond, detected)) {
sphere = 5;
bondOrder = fifthBond.getOrder();
bondNumber = mol.getBondNumber(fifthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomFifth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInSixthSphere = mol.getConnectedAtomsList(curAtomFifth);
if (atomsInSixthSphere.size() > 0) {
for (IAtom curAtomSixth : atomsInSixthSphere) {
sixthBond = mol.getBond(curAtomFifth, curAtomSixth);
if (mol.getAtomNumber(curAtomSixth) != atomPosition
&& getIfBondIsNotRotatable(mol, sixthBond, detected)) {
sphere = 6;
bondOrder = sixthBond.getOrder();
bondNumber = mol.getBondNumber(sixthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSixth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInSeventhSphere = mol.getConnectedAtomsList(curAtomSixth);
if (atomsInSeventhSphere.size() > 0) {
for (IAtom curAtomSeventh : atomsInSeventhSphere) {
seventhBond = mol.getBond(curAtomSeventh, curAtomSixth);
if (mol.getAtomNumber(curAtomSeventh) != atomPosition
&& getIfBondIsNotRotatable(mol, seventhBond, detected)) {
sphere = 7;
bondOrder = seventhBond.getOrder();
bondNumber = mol.getBondNumber(seventhBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSeventh),
atoms,
sphere,
theBondIsInA6MemberedRing);
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
// Variables
double[] values; // for storage of results of other methods
double distance;
double sum;
double smooth = -20;
double partial;
int position;
double limitInf;
double limitSup;
double step;
//////////////////////// THE FOUTH DESCRIPTOR IS gS(r), WHICH TAKES INTO ACCOUNT SINGLE BONDS IN
// RIGID SYSTEMS
Vector3d a_a = new Vector3d();
Vector3d a_b = new Vector3d();
Vector3d b_a = new Vector3d();
Vector3d b_b = new Vector3d();
Point3d middlePoint = new Point3d();
double angle = 0;
if (singles.size() > 0) {
double dist0;
double dist1;
IAtom singleBondAtom0;
IAtom singleBondAtom1;
distance = 0;
position = 0;
IBond theSingleBond = null;
limitInf = 0;
limitSup = Math.PI / 2;
step = (limitSup - limitInf) / 7;
smooth = -1.15;
int counter = 0;
for (double ghs = 0; ghs < limitSup; ghs = ghs + step) {
sum = 0;
for (int sing = 0; sing < singles.size(); sing++) {
angle = 0;
partial = 0;
Integer thisSingleBond = singles.get(sing);
position = thisSingleBond;
theSingleBond = mol.getBond(position);
middlePoint = theSingleBond.get3DCenter();
singleBondAtom0 = theSingleBond.getAtom(0);
singleBondAtom1 = theSingleBond.getAtom(1);
dist0 = calculateDistanceBetweenTwoAtoms(singleBondAtom0, atom);
dist1 = calculateDistanceBetweenTwoAtoms(singleBondAtom1, atom);
a_a.set(middlePoint.x, middlePoint.y, middlePoint.z);
if (dist1 > dist0)
a_b.set(
singleBondAtom0.getPoint3d().x,
singleBondAtom0.getPoint3d().y,
singleBondAtom0.getPoint3d().z);
else
a_b.set(
singleBondAtom1.getPoint3d().x,
singleBondAtom1.getPoint3d().y,
singleBondAtom1.getPoint3d().z);
b_a.set(middlePoint.x, middlePoint.y, middlePoint.z);
b_b.set(atom.getPoint3d().x, atom.getPoint3d().y, atom.getPoint3d().z);
values = calculateDistanceBetweenAtomAndBond(atom, theSingleBond);
angle = calculateAngleBetweenTwoLines(a_a, a_b, b_a, b_b);
// System.out.println("ANGLe: "+angle+ " "+ mol.getAtomNumber(atomsInSingleBond[0]) +" "
// +mol.getAtomNumber(atomsInSingleBond[1]));
partial =
(1 / (Math.pow(values[0], 2))) * Math.exp(smooth * (Math.pow((ghs - angle), 2)));
sum += partial;
}
// gSr_function.add(new Double(sum));
rdfProtonCalculatedValues.add(sum);
logger.debug("RDF gSr prob.: " + sum + " at distance " + ghs);
counter++;
}
} else {
return getDummyDescriptorValue(new CDKException("Some error occurred. Please report"));
}
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
rdfProtonCalculatedValues,
getDescriptorNames());
}
/**
* Initiates the process for the given mechanism. The atoms to apply are mapped between reactants
* and products.
*
* @param atomContainerSet
* @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms. The
* first atom is the atom which contains the ISingleElectron and the second third is the atom
* which will be removed the first atom
* @param bondList The list of bonds taking part in the mechanism. Only allowed one bond. It is
* the bond which is moved
* @return The Reaction mechanism
*/
@TestMethod(value = "testInitiate_IAtomContainerSet_ArrayList_ArrayList")
public IReaction initiate(
IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
throws CDKException {
CDKAtomTypeMatcher atMatcher = CDKAtomTypeMatcher.getInstance(atomContainerSet.getBuilder());
if (atomContainerSet.getAtomContainerCount() != 1) {
throw new CDKException("RadicalSiteIonizationMechanism only expects one IMolecule");
}
if (atomList.size() != 3) {
throw new CDKException("RadicalSiteIonizationMechanism expects three atoms in the ArrayList");
}
if (bondList.size() != 2) {
throw new CDKException(
"RadicalSiteIonizationMechanism only expect one bond in the ArrayList");
}
IAtomContainer molecule = atomContainerSet.getAtomContainer(0);
IAtomContainer reactantCloned;
try {
reactantCloned = (IAtomContainer) molecule.clone();
} catch (CloneNotSupportedException e) {
throw new CDKException("Could not clone IMolecule!", e);
}
IAtom atom1 = atomList.get(0); // Atom containing the ISingleElectron
IAtom atom1C = reactantCloned.getAtom(molecule.getAtomNumber(atom1));
IAtom atom2 = atomList.get(1); // Atom
IAtom atom2C = reactantCloned.getAtom(molecule.getAtomNumber(atom2));
IAtom atom3 = atomList.get(2); // Atom to be saved
IAtom atom3C = reactantCloned.getAtom(molecule.getAtomNumber(atom3));
IBond bond1 = bondList.get(0); // Bond to increase the order
int posBond1 = molecule.getBondNumber(bond1);
IBond bond2 = bondList.get(1); // Bond to remove
int posBond2 = molecule.getBondNumber(bond2);
BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1));
reactantCloned.removeBond(reactantCloned.getBond(posBond2));
List<ISingleElectron> selectron = reactantCloned.getConnectedSingleElectronsList(atom1C);
reactantCloned.removeSingleElectron(selectron.get(selectron.size() - 1));
atom1C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, atom1C);
if (type == null) return null;
atom2C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.findMatchingAtomType(reactantCloned, atom2C);
if (type == null) return null;
reactantCloned.addSingleElectron(new SingleElectron(atom3C));
atom3C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.findMatchingAtomType(reactantCloned, atom3C);
if (type == null) return null;
IReaction reaction = DefaultChemObjectBuilder.getInstance().newInstance(IReaction.class);
reaction.addReactant(molecule);
/* mapping */
for (IAtom atom : molecule.atoms()) {
IMapping mapping =
DefaultChemObjectBuilder.getInstance()
.newInstance(
IMapping.class, atom, reactantCloned.getAtom(molecule.getAtomNumber(atom)));
reaction.addMapping(mapping);
}
IAtomContainerSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
for (int z = 0; z < moleculeSetP.getAtomContainerCount(); z++)
reaction.addProduct((IAtomContainer) moleculeSetP.getAtomContainer(z));
return reaction;
}
