Skip to content

Commit

Permalink
added extraction of isolated double and triple bonds;
Browse files Browse the repository at this point in the history
  • Loading branch information
@Mila1004
Mila1004 committed Jul 17, 2024
1 parent cc96daa commit d04d734
Showing 1 changed file with 29 additions and 50 deletions.
79 changes: 29 additions & 50 deletions ...ava/de/unijena/cheminf/mortar/model/fragmentation/algorithm/AlkylStructureFragmenter.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -757,7 +757,10 @@ protected Object[] markConjugatedPiSystems(IAtomContainer anAtomContainer, IAtom
protected IAtomContainerSet separateDisconnectedStructures(IAtomContainer anAtomContainer) throws IllegalArgumentException{
Objects.requireNonNull(anAtomContainer,"Given IAtomContainer is null.");
try {
//should give more than two atomcontainer at the moment but only returns 2 with an error
//which also dont get presented in mortar
IAtomContainerSet tmpFragmentSet = new AtomContainerSet();
//AlkylStructureFragmenter.this.logger.log(Level.INFO, System.currentTimeMillis() + " start sD, AC size: " + anAtomContainer.getAtomCount() + ", " + anAtomContainer.getBondCount());
if (!anAtomContainer.isEmpty()) {
if (!ConnectivityChecker.isConnected(anAtomContainer)) {
IAtomContainerSet tmpContainerSet = ConnectivityChecker.partitionIntoMolecules(anAtomContainer);
Expand All @@ -771,6 +774,8 @@ protected IAtomContainerSet separateDisconnectedStructures(IAtomContainer anAtom
return tmpFragmentSet;
} catch (Exception anException) {
AlkylStructureFragmenter.this.logger.log(Level.WARNING, anException + " Connectivity Checking failed at molecule: " + anAtomContainer.getID(), anException);
//logger below for debug purpose
//AlkylStructureFragmenter.this.logger.log(Level.INFO, System.currentTimeMillis() + " start sD, AC size: " + anAtomContainer.getAtomCount() + ", " + anAtomContainer.getBondCount());
throw new IllegalArgumentException("An Error occurred during Connectivity Checking: " + anException.toString() +
": " + anAtomContainer.getProperty(Importer.MOLECULE_NAME_PROPERTY_KEY));
}
Expand Down Expand Up @@ -826,7 +831,6 @@ protected IAtomContainerSet extractFragments(IAtom[] anAtomArray, IBond[] aBondA
//<editor-fold desc="atom extraction">
//superior performance compared to normal for iteration over Array length
for (IAtom tmpAtom : anAtomArray) {
//System.out.println("atom index: " + tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_ATOM_INDEX_PROPERTY_KEY));
if (tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_FRAGMENTATION_PLACEMENT_KEY)) {
if (tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TERTIARY_CARBON_PROPERTY_KEY)) {
tmpSingleCarbonContainer.addAtom(tmpAtom);
Expand All @@ -848,11 +852,9 @@ protected IAtomContainerSet extractFragments(IAtom[] anAtomArray, IBond[] aBondA
}
//extract atoms for double/triple bonds
} else if (tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY)) {
//System.out.println("double bond: " + (int) tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_ATOM_INDEX_PROPERTY_KEY));
//tmpIsolatedMultiBondsContainer.addAtom(tmpAtom);
tmpIsolatedMultiBondsContainer.addAtom(tmpAtom);
} else if (tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY)) {
//System.out.println("triple bond: " + (int) tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_ATOM_INDEX_PROPERTY_KEY));
//tmpIsolatedMultiBondsContainer.addAtom(tmpAtom);
tmpIsolatedMultiBondsContainer.addAtom(tmpAtom);
} else {
tmpChainFragmentationContainer.addAtom(tmpAtom);
}
Expand All @@ -868,28 +870,28 @@ protected IAtomContainerSet extractFragments(IAtom[] anAtomArray, IBond[] aBondA
if (tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_FRAGMENTATION_PLACEMENT_KEY)) {
IAtom tmpBeginAtom = tmpBond.getBegin();
IAtom tmpEndAtom = tmpBond.getEnd();
boolean tmpBool = true;
if (tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY)) {
tmpIsolatedMultiBondsContainer.addAtom(tmpBeginAtom);
tmpIsolatedMultiBondsContainer.addAtom(tmpEndAtom);
tmpIsolatedMultiBondsContainer.addBond(tmpBond);
tmpBool = false;
//continue;
}
else if (tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY)) {
tmpIsolatedMultiBondsContainer.addAtom(tmpBeginAtom);
tmpIsolatedMultiBondsContainer.addAtom(tmpEndAtom);
tmpIsolatedMultiBondsContainer.addBond(tmpBond);
tmpBool = false;
//continue;
}
boolean tmpIsBeginFragPlacement = tmpBeginAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_FRAGMENTATION_PLACEMENT_KEY);
boolean tmpIsEndFragPlacement = tmpEndAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_FRAGMENTATION_PLACEMENT_KEY);
//
boolean tmpIsBeginTertiary = tmpBeginAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TERTIARY_CARBON_PROPERTY_KEY);
boolean tmpIsEndTertiary = tmpEndAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TERTIARY_CARBON_PROPERTY_KEY);
//
boolean tmpIsBeginQuaternary = tmpBeginAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_QUATERNARY_CARBON_PROPERTY_KEY);
boolean tmpIsEndQuaternary = tmpEndAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_QUATERNARY_CARBON_PROPERTY_KEY);
if (tmpIsBeginFragPlacement && tmpIsEndFragPlacement && tmpBool) {
//
boolean tmpIsBeginDouble = tmpBeginAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY);
boolean tmpIsEndDouble = tmpEndAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY);
//
boolean tmpIsBeginTriple = tmpBeginAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY);
boolean tmpIsEndTriple = tmpEndAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY);
//
if (tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY)) {
tmpIsolatedMultiBondsContainer.addBond(tmpBond);
}
else if (tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY)) {
tmpIsolatedMultiBondsContainer.addBond(tmpBond);
}
if (tmpIsBeginFragPlacement && tmpIsEndFragPlacement && !(tmpIsBeginDouble || tmpIsEndDouble || tmpIsBeginTriple || tmpIsEndTriple)) {
if (!(tmpIsBeginTertiary || tmpIsEndTertiary || tmpIsBeginQuaternary || tmpIsEndQuaternary)) {
tmpChainFragmentationContainer.addBond(tmpBond);
}
Expand All @@ -913,9 +915,7 @@ else if (tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_M
//remnants after ring, conj. system and tertiary/quaternary carbon extractions
//expected to be only linear carbohydrates
if (!tmpIsolatedMultiBondsContainer.isEmpty()) {
//System.out.println(tmpIsolatedMultiBondsContainer.getAtomCount());
tmpExtractionSet.add(this.separateDisconnectedStructures(tmpIsolatedMultiBondsContainer));
//System.out.println(tmpExtractionSet.getAtomContainerCount());
}
IAtomContainerSet tmpChainACSet = this.separateDisconnectedStructures(tmpChainFragmentationContainer);
//ACSet for dissected chains
Expand All @@ -925,7 +925,6 @@ else if (tmpBond.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_M
//check maxchainlength
switch (tmpMaxChainLengthInteger) {
default -> {
//down
//restrictions > 1
for (IAtomContainer tmpAtomContainer : tmpChainACSet.atomContainers()) {
tmpDissectedChainACSet.add(this.separateDisconnectedStructures(this.dissectLinearChain(tmpAtomContainer,
Expand Down Expand Up @@ -1006,7 +1005,9 @@ protected Object[] markMultiBonds(IAtom[] anAtomArray, IBond[] aBondArray) {
int tmpEndIndex = tmpArrayBond.getEnd().getProperty(AlkylStructureFragmenter.INTERNAL_ASF_ATOM_INDEX_PROPERTY_KEY);
for (IAtom tmpAtom: anAtomArray) {
int tmpAtomIndex = tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_ATOM_INDEX_PROPERTY_KEY);
if ( tmpAtomIndex == tmpBeginIndex || tmpAtomIndex == tmpEndIndex) {
if (tmpAtomIndex == tmpBeginIndex) {
tmpAtom.setProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY, true);
} else if (tmpAtomIndex == tmpEndIndex) {
tmpAtom.setProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY, true);
}
}
Expand All @@ -1016,36 +1017,14 @@ protected Object[] markMultiBonds(IAtom[] anAtomArray, IBond[] aBondArray) {
int tmpEndIndex = tmpArrayBond.getEnd().getProperty(AlkylStructureFragmenter.INTERNAL_ASF_ATOM_INDEX_PROPERTY_KEY);
for (IAtom tmpAtom: anAtomArray) {
int tmpAtomIndex = tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_ATOM_INDEX_PROPERTY_KEY);
if ( tmpAtomIndex == tmpBeginIndex || tmpAtomIndex == tmpEndIndex) {
if ( tmpAtomIndex == tmpBeginIndex) {
tmpAtom.setProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY, true);
} else if (tmpAtomIndex == tmpEndIndex) {
tmpAtom.setProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY, true);
}
}
}
}
/*
for (IAtom tmpAtom: anAtomArray) {
System.out.println("max bond order: " + tmpAtom.getMaxBondOrder().numeric() + " at atom: " + tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_ATOM_INDEX_PROPERTY_KEY));
if (tmpAtom.getMaxBondOrder().numeric() == 2) {
tmpAtom.setProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY, true);
for (IBond tmpBond: tmpAtom.bonds()) {
if (tmpBond.getOrder().numeric() == 2) {
tmpBond.setProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY, true);
//tmpBond.getBegin().setProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY, true);
//tmpBond.getEnd().setProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_MARKER_KEY, true);
}
}
} else if (tmpAtom.getMaxBondOrder().numeric() == 3) {
tmpAtom.setProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY, true);
for (IBond tmpBond: tmpAtom.bonds()) {
if (tmpBond.getOrder().numeric() == 3) {
tmpBond.setProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY, true);
//tmpBond.getBegin().setProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY, true);
//tmpBond.getEnd().setProperty(AlkylStructureFragmenter.INTERNAL_ASF_TRIPLE_BOND_MARKER_KEY, true);
}
}
}
}
*/
Object[] tmpObject = new Object[2];
tmpObject[0] = anAtomArray;
tmpObject[1] = aBondArray;
Expand Down

0 comments on commit d04d734

Please sign in to comment.