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WIP! on methods to create deep copies of atoms and bonds;
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@Mila1004
Mila1004 committed Nov 22, 2024
1 parent b7b6d78 commit 99f1167
Showing 1 changed file with 69 additions and 27 deletions.
96 changes: 69 additions & 27 deletions ...ava/de/unijena/cheminf/mortar/model/fragmentation/algorithm/AlkylStructureFragmenter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.ringsearch.RingSearch;
Expand Down Expand Up @@ -216,7 +217,7 @@ public class AlkylStructureFragmenter implements IMoleculeFragmenter{
*/
private static final Logger logger = Logger.getLogger(AlkylStructureFragmenter.class.getName());
//WIP
private IAtomContainer builderInstanceAtomContainer;
private IChemObjectBuilder chemObjectBuilderInstance;
//</editor-fold>
//
//<editor-fold desc="Constructor">
Expand Down Expand Up @@ -608,8 +609,8 @@ public List<IAtomContainer> fragmentMolecule(IAtomContainer aMolecule)
//<editor-fold desc="Molecule Cloning, Property and Arrays Set" defaultstate="collapsed">
IAtomContainer tmpClone = aMolecule.clone();
//WIP
this.builderInstanceAtomContainer = null;
this.builderInstanceAtomContainer = tmpClone.getBuilder().newInstance(IAtomContainer.class);
this.chemObjectBuilderInstance = null;
this.chemObjectBuilderInstance = tmpClone.getBuilder();
//IAtomContainer tmpBuilderAtomContainer = tmpClone.getBuilder().newInstance(IAtomContainer.class);
int tmpPreFragmentationAtomCount = 0;
for (IAtom tmpAtom: tmpClone.atoms()) {
Expand Down Expand Up @@ -1053,7 +1054,7 @@ protected IAtomContainerSet extractFragments(IAtom[] anAtomArray, IBond[] aBondA
//<editor-fold desc="Extraction">
IAtomContainerSet tmpExtractionSet = new AtomContainerSet();
//WIP
IAtomContainer tmpRingFragmentationContainer = this.builderInstanceAtomContainer.clone();
IAtomContainer tmpRingFragmentationContainer = this.chemObjectBuilderInstance.newAtomContainer();
//IAtomContainer tmpRingFragmentationContainer = new AtomContainer();
IAtomContainer tmpChainFragmentationContainer = new AtomContainer();
IAtomContainer tmpIsolatedMultiBondsContainer = new AtomContainer();
Expand All @@ -1067,7 +1068,7 @@ protected IAtomContainerSet extractFragments(IAtom[] anAtomArray, IBond[] aBondA
if (!((boolean) tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_RING_MARKER_KEY)
|| (boolean) tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_CONJ_PI_MARKER_KEY))) {
if (tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TERTIARY_CARBON_PROPERTY_KEY)) {
tmpRingFragmentationContainer.addAtom(tmpAtom);
tmpRingFragmentationContainer.addAtom(this.deepCopyAtom(tmpAtom));
//System.out.println("tert atom added");
if (this.altHandlingSingleTertQuatCarbonsSetting.get()) {
for (int i = 0; i < 3; i++) {
Expand All @@ -1077,7 +1078,7 @@ protected IAtomContainerSet extractFragments(IAtom[] anAtomArray, IBond[] aBondA
}
}
} else if (tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_QUATERNARY_CARBON_PROPERTY_KEY)) {
tmpRingFragmentationContainer.addAtom(tmpAtom);
tmpRingFragmentationContainer.addAtom(this.deepCopyAtom(tmpAtom));
//System.out.println("quart atom added");
if (this.altHandlingSingleTertQuatCarbonsSetting.get()) {
for (int i = 0; i < 4; i++) {
Expand All @@ -1100,43 +1101,43 @@ else if (tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_M
boolean tmpBegin = tmpDoubleToRingBond.getBegin().getProperty(AlkylStructureFragmenter.INTERNAL_ASF_RING_MARKER_KEY);
boolean tmpEnd = tmpDoubleToRingBond.getEnd().getProperty(AlkylStructureFragmenter.INTERNAL_ASF_RING_MARKER_KEY);
if (tmpBegin || tmpEnd) {
tmpRingFragmentationContainer.addAtom(tmpAtom);
//WIP
tmpRingFragmentationContainer.addAtom(this.deepCopyAtom(tmpAtom));
//System.out.println("double bond to ring atom added");
} else {
tmpIsolatedMultiBondsContainer.addAtom(tmpAtom);
tmpIsolatedMultiBondsContainer.addAtom(this.deepCopyAtom(tmpAtom));
//System.out.println("double bond atom added");
}
}
}
} else if (tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY)) {
tmpIsolatedMultiBondsContainer.addAtom(tmpAtom);
tmpIsolatedMultiBondsContainer.addAtom(this.deepCopyAtom(tmpAtom));
//System.out.println("triple bond atom added");
}
//extract neighbor atoms of tertiary or quaternary carbon atoms
else if (tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_NEIGHBOR_MARKER_KEY)) {
if (this.altHandlingSingleTertQuatCarbonsSetting.get()) {continue;}
tmpRingFragmentationContainer.addAtom(tmpAtom);
tmpRingFragmentationContainer.addAtom(this.deepCopyAtom(tmpAtom));
//System.out.println("neighbor atom added");
}
//extract residue atoms as linear chain atoms
else {
tmpChainFragmentationContainer.addAtom(tmpAtom);
tmpChainFragmentationContainer.addAtom(this.deepCopyAtom(tmpAtom));
//System.out.println("chain residue atom added");
}
} else {
if (!this.keepRingsSetting.get()) {
ArrayList<Integer> tmpList = tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_RING_ATOM_LIST_KEY);
if (tmpList.size() > 1) {
tmpSpiroCarbonContainer.addAtom(tmpAtom);
tmpSpiroCarbonContainer.addAtom(this.deepCopyAtom(tmpAtom));
} /*
else {
tmpSpiroResidueContainer.addAtom(tmpAtom);
}
*/
tmpRingFragmentationContainer.addAtom(tmpAtom);
tmpRingFragmentationContainer.addAtom(this.deepCopyAtom(tmpAtom));
} else {
tmpRingFragmentationContainer.addAtom(tmpAtom);
tmpRingFragmentationContainer.addAtom(this.deepCopyAtom(tmpAtom));
//System.out.println("ring atom list: " + tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_RING_ATOM_LIST_KEY));
//System.out.println("ring atom added");
}
Expand Down Expand Up @@ -1176,31 +1177,31 @@ else if (tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_NEIGHBOR_MARK

//</editor-fold>
if (tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY)) {

//WIP
boolean tmpBegin = tmpBond.getBegin().getProperty(AlkylStructureFragmenter.INTERNAL_ASF_RING_MARKER_KEY);
boolean tmpEnd = tmpBond.getEnd().getProperty(AlkylStructureFragmenter.INTERNAL_ASF_RING_MARKER_KEY);
if (tmpBegin || tmpEnd) {
tmpRingFragmentationContainer.addBond(tmpBond);
tmpRingFragmentationContainer.addBond(this.deepCopyBond(tmpBond, tmpRingFragmentationContainer));
//System.out.println("double bond to ring added");
} else {
tmpIsolatedMultiBondsContainer.addBond(tmpBond);
tmpIsolatedMultiBondsContainer.addBond(this.deepCopyBond(tmpBond, tmpIsolatedMultiBondsContainer));
//System.out.println("double bond added");
}
}
else if (tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY)) {
tmpIsolatedMultiBondsContainer.addBond(tmpBond);
else if ((boolean) tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY)) {
tmpIsolatedMultiBondsContainer.addBond(this.deepCopyBond(tmpBond, tmpIsolatedMultiBondsContainer));
//System.out.println("triple bond added");
}
else if ((boolean) tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_NEIGHBOR_MARKER_KEY)
&& !((tmpIsBeginRing && tmpIsBeginTertiary) || (tmpIsEndRing && tmpIsEndTertiary)
|| (tmpIsBeginRing && tmpIsBeginQuaternary) || (tmpIsEndRing && tmpIsEndQuaternary))) {
tmpRingFragmentationContainer.addBond(tmpBond);
tmpRingFragmentationContainer.addBond(this.deepCopyBond(tmpBond, tmpRingFragmentationContainer));
//System.out.println("neighbor bond added");
}
if (!(tmpIsBeginRing && tmpIsEndRing && tmpIsBeginConjPi && tmpIsEndConjPi)
&& !(tmpIsBeginDouble || tmpIsEndDouble || tmpIsBeginTriple || tmpIsEndTriple)) {
if (!(tmpIsBeginTertiary || tmpIsEndTertiary || tmpIsBeginQuaternary || tmpIsEndQuaternary || tmpIsBeginNeighbor || tmpIsEndNeighbor)) {
tmpChainFragmentationContainer.addBond(tmpBond);
tmpChainFragmentationContainer.addBond(this.deepCopyBond(tmpBond, tmpChainFragmentationContainer));
//System.out.println("chain residue bond added");
}
}
Expand All @@ -1219,10 +1220,10 @@ else if ((boolean) tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_NEI
tmpIsEndSpiro = true;
}
if (!tmpIsBeginSpiro && !tmpIsEndSpiro) {
tmpRingFragmentationContainer.addBond(tmpBond);
tmpRingFragmentationContainer.addBond(this.deepCopyBond(tmpBond, tmpRingFragmentationContainer));
}
} else {
tmpRingFragmentationContainer.addBond(tmpBond);
tmpRingFragmentationContainer.addBond(this.deepCopyBond(tmpBond, tmpRingFragmentationContainer));
//System.out.println("ring bond added");
}
}
Expand Down Expand Up @@ -1310,15 +1311,15 @@ protected IAtomContainer dissectLinearChain(IAtomContainer anAC, int aLength) {
IBond tmpBond = tmpBondIterator.next();
if (tmpCounter == aLength) {
if (!tmpBondIterator.hasNext()) {
tmpReturnAC.addAtom(tmpBond.getEnd());
tmpReturnAC.addAtom(this.deepCopyAtom(tmpBond.getEnd()));
}
tmpCounter = 1;
} else {
IAtom tmpBeginAtom = tmpBond.getBegin();
IAtom tmpEndAtom = tmpBond.getEnd();
tmpReturnAC.addAtom(tmpBeginAtom);
tmpReturnAC.addAtom(tmpEndAtom);
tmpReturnAC.addBond(tmpBond);
tmpReturnAC.addAtom(this.deepCopyAtom(tmpBeginAtom));
tmpReturnAC.addAtom(this.deepCopyAtom(tmpEndAtom));
tmpReturnAC.addBond(this.deepCopyBond(tmpBond, tmpReturnAC));
tmpCounter++;
}
}
Expand Down Expand Up @@ -1367,6 +1368,47 @@ protected Object[] markMultiBonds(IAtom[] anAtomArray, IBond[] aBondArray) {
tmpObject[1] = aBondArray;
return tmpObject;
}
//WIP

/**
* Method to create a deeper copy of a given atom, meant to replace the default addAtom() method of IAtomContainer
* in which only the reference is added to the atomcontainer instead of a new atom.
*
* @param anAtomToCopy the atom to create a deep copy of
* @return the deep copy of the given atom
*/
protected IAtom deepCopyAtom(IAtom anAtomToCopy) {
IAtom tmpNewAtom = this.chemObjectBuilderInstance.newAtom();
tmpNewAtom.setAtomicNumber(anAtomToCopy.getAtomicNumber());
tmpNewAtom.setImplicitHydrogenCount(anAtomToCopy.getImplicitHydrogenCount());
tmpNewAtom.setProperties(anAtomToCopy.getProperties());
return tmpNewAtom;
}

/**
* Method to create a deep copy of a given bond, meant to replace the default addBond() method of IAtomContainer
*
* @param aBondToCopy the bond to create a deep copy of
* @param aBondIncludingAtomContainer the atomcontainer in which the bond's atoms are placed in
* @return the deep copy of the given bond
*/
protected IBond deepCopyBond(IBond aBondToCopy, IAtomContainer aBondIncludingAtomContainer) {
IBond tmpNewBond = this.chemObjectBuilderInstance.newBond();
tmpNewBond.setOrder(aBondToCopy.getOrder());
IAtom tmpBeginAtom = this.deepCopyAtom(aBondToCopy.getBegin());
IAtom tmpEndAtom = this.deepCopyAtom(aBondToCopy.getEnd());
for (IAtom tmpAtom: aBondIncludingAtomContainer.atoms()) {
if (tmpAtom.equals(tmpBeginAtom)) {
tmpNewBond.setAtom(tmpAtom, 0);
} else if (tmpAtom.equals(tmpEndAtom)) {
tmpNewBond.setAtom(tmpAtom, 1);
}
}
//sets the atoms from bond to copy for new bond
//tmpNewBond.setAtom(aBondToCopy.getAtom(0), 0);
//tmpNewBond.setAtom(aBondToCopy.getAtom(1), 1);
return tmpNewBond;
}
//</editor-fold>
//
}

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