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asadasad
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Skip unchanged mapping pairs and index MCS solutions
1 parent 5aa0079 commit 7a2c638

2 files changed

Lines changed: 54 additions & 36 deletions

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‎src/main/java/com/bioinceptionlabs/reactionblast/mapping/GraphMatcher.java‎

Lines changed: 11 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -221,18 +221,19 @@ public static Collection<MCSSolution> matcher(Holder mh) throws Exception {
221221
for (int productIndex = 0; productIndex < productCount; productIndex++) {
222222
IAtomContainer educt = reactionStructureInformation.getEduct(substrateIndex);
223223
IAtomContainer product = reactionStructureInformation.getProduct(productIndex);
224-
LOGGER.debug("reactionStructureInformation.getEduct(substrateIndex).getAtomCount() " + reactionStructureInformation.getEduct(substrateIndex).getAtomCount());
225-
LOGGER.debug("reactionStructureInformation.getProduct(productIndex).getAtomCount() " + reactionStructureInformation.getProduct(productIndex).getAtomCount());
226-
if ((educt != null && product != null)
227-
&& (reactionStructureInformation.getEduct(substrateIndex).getAtomCount() > 0
228-
&& reactionStructureInformation.getProduct(productIndex).getAtomCount() > 0)
229-
|| mh.getGraphSimilarityMatrix().getValue(substrateIndex, productIndex) == -1) {
230-
// if (reactionStructureInformation.isEductModified(substrateIndex)
231-
// || reactionStructureInformation.isProductModified(productIndex)) {
232-
224+
boolean hasAtoms = educt != null && product != null
225+
&& educt.getAtomCount() > 0
226+
&& product.getAtomCount() > 0;
227+
boolean forceInitial = mh.getGraphSimilarityMatrix().getValue(substrateIndex, productIndex) == -1;
228+
boolean needsRefresh = forceInitial
229+
|| reactionStructureInformation.isEductModified(substrateIndex)
230+
|| reactionStructureInformation.isProductModified(productIndex);
231+
LOGGER.debug("educt atoms " + (educt == null ? 0 : educt.getAtomCount())
232+
+ ", product atoms " + (product == null ? 0 : product.getAtomCount())
233+
+ ", needsRefresh " + needsRefresh);
234+
if ((hasAtoms || forceInitial) && needsRefresh) {
233235
Combination c = new Combination(substrateIndex, productIndex);
234236
jobReplicatorList.add(c);
235-
// }
236237
}
237238
}
238239
}

‎src/main/java/com/bioinceptionlabs/reactionblast/mapping/algorithm/GameTheoryEngine.java‎

Lines changed: 43 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -35,6 +35,7 @@
3535
import static java.util.Collections.unmodifiableList;
3636
import java.util.Comparator;
3737
import java.util.GregorianCalendar;
38+
import java.util.HashMap;
3839
import java.util.HashSet;
3940
import java.util.LinkedList;
4041
import java.util.List;
@@ -181,6 +182,7 @@ public void UpdateMatrix(Holder mh, boolean removeHydrogen) throws InterruptedEx
181182
} catch (InterruptedException e) {
182183
LOGGER.error("Error in matching molecules, check Graph Matcher module! ", e.getMessage());
183184
}
185+
Map<ReactionContainer.Key, MCSSolution> indexedSolutions = indexSolutions(mcsSolutions);
184186
for (int substrateIndex = 0; substrateIndex < reactionStructureInformation.getEductCount(); substrateIndex++) {
185187
for (int productIndex = 0; productIndex < reactionStructureInformation.getProductCount(); productIndex++) {
186188
try {
@@ -202,7 +204,7 @@ public void UpdateMatrix(Holder mh, boolean removeHydrogen) throws InterruptedEx
202204
|| mh.getGraphSimilarityMatrix().getValue(substrateIndex, productIndex) == -1) {
203205
if (reactionStructureInformation.isEductModified(substrateIndex)
204206
|| reactionStructureInformation.isProductModified(productIndex)) {
205-
refillMatrixWithNewData(mh, substrateIndex, productIndex, mcsSolutions);
207+
refillMatrixWithNewData(mh, substrateIndex, productIndex, indexedSolutions);
206208
} else {
207209
refillMatrixWithOldData(mh, substrateIndex, productIndex);
208210
}
@@ -235,6 +237,7 @@ public void UpdateMatrix(Collection<MCSSolution> mcsSolutions, Holder mh, boolea
235237
try {
236238
LOGGER.debug("**********Updated Matrix And Calculate Similarity**************");
237239
ReactionContainer reactionStructureInformation = mh.getReactionContainer();
240+
Map<ReactionContainer.Key, MCSSolution> indexedSolutions = indexSolutions(mcsSolutions);
238241
for (int substrateIndex = 0; substrateIndex < reactionStructureInformation.getEductCount(); substrateIndex++) {
239242
for (int productIndex = 0; productIndex < reactionStructureInformation.getProductCount(); productIndex++) {
240243
IAtomContainer educt = reactionStructureInformation.getEduct(substrateIndex);
@@ -245,7 +248,7 @@ public void UpdateMatrix(Collection<MCSSolution> mcsSolutions, Holder mh, boolea
245248
|| mh.getGraphSimilarityMatrix().getValue(substrateIndex, productIndex) == -1) {
246249
if (reactionStructureInformation.isEductModified(substrateIndex)
247250
|| reactionStructureInformation.isProductModified(productIndex)) {
248-
refillMatrixWithNewData(mh, substrateIndex, productIndex, mcsSolutions);
251+
refillMatrixWithNewData(mh, substrateIndex, productIndex, indexedSolutions);
249252
} else {
250253
refillMatrixWithOldData(mh, substrateIndex, productIndex);
251254
}
@@ -268,7 +271,7 @@ public void UpdateMatrix(Collection<MCSSolution> mcsSolutions, Holder mh, boolea
268271

269272
private void refillMatrixWithNewData(
270273
Holder holder, int substrateIndex, int productIndex,
271-
Collection<MCSSolution> mcsSolutions) {
274+
Map<ReactionContainer.Key, MCSSolution> solutionIndex) {
272275
LOGGER.debug("**********Generate NEW MCS And Calculate Similarity**************");
273276
try {
274277
ReactionContainer reactionContainer = holder.getReactionContainer();
@@ -286,7 +289,7 @@ private void refillMatrixWithNewData(
286289
MCSSolution atomatomMapping = getMappings(
287290
holder.getReactionID(),
288291
holder.getTheory() == null ? "UNKNOWN" : holder.getTheory().name(),
289-
substrateIndex, productIndex, educt, product, mcsSolutions);
292+
substrateIndex, productIndex, educt, product, solutionIndex);
290293
if (atomatomMapping == null) {
291294
clearScores(holder, substrateIndex, productIndex);
292295
return;
@@ -339,33 +342,47 @@ private MCSSolution getMappings(
339342
String reactionId, String algorithmName,
340343
int queryPosition, int targetPosition,
341344
IAtomContainer educt, IAtomContainer product,
342-
Collection<MCSSolution> mcsSolutions) throws CDKException {
343-
if (mcsSolutions.isEmpty()) {
345+
Map<ReactionContainer.Key, MCSSolution> solutionIndex) throws CDKException {
346+
if (solutionIndex == null || solutionIndex.isEmpty()) {
344347
return quickMapping(reactionId, algorithmName, educt, product, queryPosition, targetPosition);
345348
}
346-
for (MCSSolution solution : mcsSolutions) {
347-
if (solution.getQueryPosition() == queryPosition
348-
&& solution.getTargetPosition() == targetPosition) {
349-
if (solution.getAtomAtomMapping().isEmpty()) {
350-
Set<String> atomMaps = new HashSet<>();
351-
for (IAtom a : educt.atoms()) {
352-
atomMaps.add(a.getSymbol());
353-
}
354-
boolean mappingPossible = false;
355-
for (IAtom a : product.atoms()) {
356-
if (atomMaps.contains(a.getSymbol())) {
357-
mappingPossible = true;
358-
}
359-
}
360-
atomMaps.clear();
361-
if (mappingPossible) {
362-
return quickMapping(reactionId, algorithmName, educt, product, queryPosition, targetPosition);
363-
}
349+
MCSSolution solution = solutionIndex.get(new ReactionContainer.Key(queryPosition, targetPosition));
350+
if (solution == null) {
351+
return null;
352+
}
353+
if (solution.getAtomAtomMapping().isEmpty()) {
354+
Set<String> atomMaps = new HashSet<>();
355+
for (IAtom a : educt.atoms()) {
356+
atomMaps.add(a.getSymbol());
357+
}
358+
boolean mappingPossible = false;
359+
for (IAtom a : product.atoms()) {
360+
if (atomMaps.contains(a.getSymbol())) {
361+
mappingPossible = true;
364362
}
365-
return solution;
363+
}
364+
atomMaps.clear();
365+
if (mappingPossible) {
366+
return quickMapping(reactionId, algorithmName, educt, product, queryPosition, targetPosition);
366367
}
367368
}
368-
return null;
369+
return solution;
370+
}
371+
372+
private Map<ReactionContainer.Key, MCSSolution> indexSolutions(Collection<MCSSolution> mcsSolutions) {
373+
Map<ReactionContainer.Key, MCSSolution> indexedSolutions = new HashMap<>();
374+
if (mcsSolutions == null) {
375+
return indexedSolutions;
376+
}
377+
for (MCSSolution solution : mcsSolutions) {
378+
if (solution == null) {
379+
continue;
380+
}
381+
indexedSolutions.put(
382+
new ReactionContainer.Key(solution.getQueryPosition(), solution.getTargetPosition()),
383+
solution);
384+
}
385+
return indexedSolutions;
369386
}
370387

371388
private MCSSolution quickMapping(String reactionId, String algorithmName,

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