Java Code Examples for org.openscience.cdk.interfaces.IAtomContainer#getConnectedBondsList()
The following examples show how to use
org.openscience.cdk.interfaces.IAtomContainer#getConnectedBondsList() .
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Example 1
| Source File: CaseHandler.java From ReactionDecoder with GNU Lesser General Public License v3.0 | 5 votes |
|
private boolean findAndChipBond(IAtomContainer container, IAtomContainer referenceContainer) {
boolean flag = false;
if (container != null) {
for (IBond bond : container.bonds()) {
if ((bond.getAtom(0).getSymbol().equalsIgnoreCase("O")
&& bond.getAtom(1).getSymbol().equalsIgnoreCase("C"))
|| (bond.getAtom(0).getSymbol().equalsIgnoreCase("C")
&& bond.getAtom(1).getSymbol().equalsIgnoreCase("O"))) {
if (!bond.getAtom(0).getFlag(ISAROMATIC)
&& !bond.getAtom(1).getFlag(ISAROMATIC)) {
if (referenceContainer.contains(bond)) {
IAtom atom = bond.getAtom(0).getSymbol().equalsIgnoreCase("C") ? bond.getAtom(0) : bond.getAtom(1);
List<IBond> neighbourhoodBonds = referenceContainer.getConnectedBondsList(atom);
flag = false;
for (IBond neighbourhoodBond : neighbourhoodBonds) {
if (neighbourhoodBond.contains(atom) && !neighbourhoodBond.getFlag(ISINRING)) {
if ((neighbourhoodBond.getAtom(0).getSymbol().equalsIgnoreCase("O")
&& neighbourhoodBond.getAtom(1).getSymbol().equalsIgnoreCase("C"))
|| (neighbourhoodBond.getAtom(0).getSymbol().equalsIgnoreCase("C")
&& neighbourhoodBond.getAtom(1).getSymbol().equalsIgnoreCase("O"))) {
flag = true;
}
}
}
if (flag) {
referenceContainer.removeBond(bond);
break;
}
}
}
}
}
}
return flag;
}
Example 2
| Source File: CaseHandler.java From ReactionDecoder with GNU Lesser General Public License v3.0 | 5 votes |
|
private boolean findAndChipBondPhophate(IAtomContainer container) {
boolean flag = false;
for (IBond bond : container.bonds()) {
IAtom atomE = bond.getAtom(0);
IAtom atomP = bond.getAtom(1);
if ((atomE.getSymbol().equals("O") && atomP.getSymbol().equals("P"))
|| (atomE.getSymbol().equals("P") && atomP.getSymbol().equals("O"))) {
if (bond.getOrder().equals(SINGLE)) {
IAtom oxygen = atomE.getSymbol().equals("O") ? atomE : atomP;
List<IBond> neighbourBonds = container.getConnectedBondsList(oxygen);
if (neighbourBonds.size() == 2) {
neighbourBonds.stream().filter((b) -> (b.getAtom(0).getSymbol().equals("O")
|| b.getAtom(0).getSymbol().equals("P"))).filter((b) -> (b.getAtom(1).getSymbol().equals("O")
|| b.getAtom(1).getSymbol().equals("P"))).map((b) -> {
container.removeBond(b);
return b;
}).filter((b) -> (DEBUG)).map((b) -> {
out.println("bondToBeChipped " + b.getAtom(0).getSymbol());
return b;
}).map((b) -> {
out.println("bondToBeChipped " + b.getAtom(1).getSymbol());
return b;
}).forEach((_item) -> {
out.println("removeBond o-p ");
});
return true;
}
}
}
}
return flag;
}
Example 3
| Source File: CDKCentreProvider.java From ReactionDecoder with GNU Lesser General Public License v3.0 | 5 votes |
|
private boolean onlyConnectedToSingleBonds(IBond bond, IAtom atom, IAtomContainer container) {
for (IBond connected : container.getConnectedBondsList(atom)) {
if (!SINGLE.equals(connected.getOrder()) && !connected.equals(bond)) {
return FALSE;
}
}
return TRUE;
}
Example 4
| Source File: CDKCentreProvider.java From ReactionDecoder with GNU Lesser General Public License v3.0 | 5 votes |
|
private boolean hasVariableBond(IAtomContainer container, IAtom atom) {
for (IBond bond : container.getConnectedBondsList(atom)) {
IBond.Stereo stereo = bond.getStereo();
if (UP_OR_DOWN.equals(stereo)
|| UP_OR_DOWN_INVERTED.equals(stereo)) {
return TRUE;
}
}
return FALSE;
}
Example 5
| Source File: CDKCentreProvider.java From ReactionDecoder with GNU Lesser General Public License v3.0 | 5 votes |
|
private boolean hasStereoBonds(IAtomContainer container, IAtom atom) {
for (IBond bond : container.getConnectedBondsList(atom)) {
IBond.Stereo stereo = bond.getStereo();
if (UP.equals(stereo)
|| DOWN.equals(stereo)
|| UP_INVERTED.equals(stereo)
|| DOWN_INVERTED.equals(stereo)) {
return TRUE;
}
}
return FALSE;
}
Example 6
| Source File: CDKMCS.java From ReactionDecoder with GNU Lesser General Public License v3.0 | 4 votes |
|
/**
* This makes a map of matching atoms out of a map of matching bonds as
* produced by the get(Subgraph|Ismorphism)Map methods.
*
* @param l The list produced by the getMap method.
* @param g1 first molecule. Must not be an {@link IQueryAtomContainer}.
* @param g2 second molecule. May be an {@link IQueryAtomContainer}.
* @return The mapping found projected on g1. This is a {@link List} of
* {@link CDKRMap} objects containing Ids of matching atoms.
*/
private static List<CDKRMap> makeAtomsMapOfBondsMap(List<CDKRMap> l, IAtomContainer g1, IAtomContainer g2) {
if (l == null) {
return (l);
}
List<CDKRMap> result = new ArrayList<>();
for (int i = 0; i < l.size(); i++) {
IBond bond1 = g1.getBond(l.get(i).getId1());
IBond bond2 = g2.getBond(l.get(i).getId2());
IAtom[] atom1 = BondManipulator.getAtomArray(bond1);
IAtom[] atom2 = BondManipulator.getAtomArray(bond2);
for (int j = 0; j < 2; j++) {
List<IBond> bondsConnectedToAtom1j = g1.getConnectedBondsList(atom1[j]);
for (int k = 0; k < bondsConnectedToAtom1j.size(); k++) {
if (bondsConnectedToAtom1j.get(k) != bond1) {
IBond testBond = bondsConnectedToAtom1j.get(k);
for (int m = 0; m < l.size(); m++) {
IBond testBond2;
if (l.get(m).getId1() == g1.indexOf(testBond)) {
testBond2 = g2.getBond(l.get(m).getId2());
for (int n = 0; n < 2; n++) {
List<IBond> bondsToTest = g2.getConnectedBondsList(atom2[n]);
if (bondsToTest.contains(testBond2)) {
CDKRMap map;
if (j == n) {
map = new CDKRMap(g1.indexOf(atom1[0]), g2.indexOf(atom2[0]));
} else {
map = new CDKRMap(g1.indexOf(atom1[1]), g2.indexOf(atom2[0]));
}
if (!result.contains(map)) {
result.add(map);
}
CDKRMap map2;
if (j == n) {
map2 = new CDKRMap(g1.indexOf(atom1[1]), g2.indexOf(atom2[1]));
} else {
map2 = new CDKRMap(g1.indexOf(atom1[0]), g2.indexOf(atom2[1]));
}
if (!result.contains(map2)) {
result.add(map2);
}
}
}
}
}
}
}
}
}
return result;
}
Example 7
| Source File: MappingHandler.java From ReactionDecoder with GNU Lesser General Public License v3.0 | 4 votes |
|
/**
* This makes a map of matching atoms out of a map of matching bonds as
* produced by the get(Subgraph|Ismorphism)Map methods.
*
* @param l The list produced by the getMap method.
* @param g1 first molecule. Must not be an {@link IQueryAtomContainer}.
* @param g2 second molecule. May be an {@link IQueryAtomContainer}.
* @param shouldMatchRings
* @param matchAtomTypes
* @return The mapping found projected on g1. This is a {@link List} of
* {@link RMap} objects containing Ids of matching atoms.
*/
public static Map<Integer, Integer> makeAtomsMapOfBondsMap(
Map<Integer, Integer> l, IAtomContainer g1, IAtomContainer g2,
AtomMatcher am, BondMatcher bm) {
if (l == null) {
return (new TreeMap<>());
}
Map<Integer, Integer> result = new TreeMap<>();
for (Map.Entry<Integer, Integer> map : l.entrySet()) {
IBond bond1 = g1.getBond(map.getKey());
IBond bond2 = g2.getBond(map.getValue());
IAtom[] atom1 = BondManipulator.getAtomArray(bond1);
IAtom[] atom2 = BondManipulator.getAtomArray(bond2);
for (int j = 0; j < 2; j++) {
List<IBond> bondsConnectedToAtom1j = g1.getConnectedBondsList(atom1[j]);
for (int k = 0; k < bondsConnectedToAtom1j.size(); k++) {
if (!bondsConnectedToAtom1j.get(k).equals(bond1)) {
IBond testBond = (IBond) bondsConnectedToAtom1j.get(k);
for (Map.Entry<Integer, Integer> m : l.entrySet()) {
IBond testBond2;
if (m.getKey() == g1.indexOf(testBond)) {
testBond2 = g2.getBond(m.getValue());
for (int n = 0; n < 2; n++) {
List<IBond> bondsToTest = g2.getConnectedBondsList(atom2[n]);
if (bondsToTest.contains(testBond2)) {
if (j == n) {
if (!result.containsKey(g1.indexOf(atom1[0]))
&& !result.containsValue(g2.indexOf(atom2[0]))) {
result.put(g1.indexOf(atom1[0]), g2.indexOf(atom2[0]));
}
} else {
if (!result.containsKey(g1.indexOf(atom1[1]))
&& !result.containsValue(g2.indexOf(atom2[0]))) {
result.put(g1.indexOf(atom1[1]), g2.indexOf(atom2[0]));
}
}
if (j == n) {
if (!result.containsKey(g1.indexOf(atom1[1]))
&& !result.containsValue(g2.indexOf(atom2[1]))) {
result.put(g1.indexOf(atom1[1]), g2.indexOf(atom2[1]));
}
} else {
if (!result.containsKey(g1.indexOf(atom1[0]))
&& !result.containsValue(g2.indexOf(atom2[1]))) {
result.put(g1.indexOf(atom1[0]), g2.indexOf(atom2[1]));
}
}
}
}
}
}
}
}
}
}
if (result.isEmpty() && l.size() == 1) {
result = SingleMappingCase(l, g1, g2, am, bm);
}
return result;
}
Example 8
| Source File: CaseHandler.java From ReactionDecoder with GNU Lesser General Public License v3.0 | 4 votes |
|
private boolean findAndChipBondBetweenRings(IAtomContainer container) {
if (DEBUG) {
out.println("Find and Chip Bond Between Rings");
}
List<IBond> bond_to_be_removed = new ArrayList<>();
for (IAtom atom : container.atoms()) {
if (atom.getSymbol().equals("O") && !atom.isAromatic()) {
int number_of_rings = ((Integer) atom.getProperty(RING_CONNECTIONS));
if (DEBUG) {
out.println("number_of_rings " + number_of_rings);
}
List<IBond> bonds = container.getConnectedBondsList(atom);
if (DEBUG) {
out.println("number_of_bonds " + bonds.size());
bonds.stream().forEach((bond) -> {
out.println("BONDS "
+ " B0 " + bond.getAtom(0).getSymbol()
+ " B1 " + bond.getAtom(1).getSymbol());
});
}
if (bonds.size() == 2 && number_of_rings == 2) {
IBond bondToBeChipped = bonds.iterator().next();
bond_to_be_removed.add(bondToBeChipped);
}
}
}
bond_to_be_removed.stream().map((bond) -> {
container.removeBond(bond);
return bond;
}).filter((bond) -> (DEBUG)).forEach((bond) -> {
try {
out.println("CHIPPING BONDS "
+ " B0 " + bond.getAtom(0).getSymbol()
+ " B1 " + bond.getAtom(1).getSymbol());
out.println("CHIPPED SM " + new SmilesGenerator(SmiFlavor.Generic).create(container));
} catch (CDKException ex) {
LOGGER.error(SEVERE, "Clipping Bonds: ", ex.getMessage());
}
});
return !bond_to_be_removed.isEmpty();
}
