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Update Flexophore node similarity, changed threshold from 0.9 to 0.89
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-65
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+3
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‎src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/PPNodeSimilarity.java‎

Lines changed: 3 additions & 65 deletions
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,7 @@ public class PPNodeSimilarity implements IPPNodeSimilarity {
7878
7979
A similarity thresh of 0.99 allows 58 pairwise interactions.
8080
*/
81-
public static final double THRESH_SIMILARITY_HARD_MATCH = 0.9;
81+
public static final double THRESH_SIMILARITY_HARD_MATCH = 0.89;
8282

8383
public static final double HARD_MATCH_OPTIMISTIC_PERCENTILE = 0.75;
8484

@@ -105,13 +105,9 @@ public class PPNodeSimilarity implements IPPNodeSimilarity {
105105
* This constructor is used for parallel mode.
106106
*/
107107
public PPNodeSimilarity(int versionInteractionTable, int modePPNodeSimilarity){
108-
109108
maSimilarity = new Matrix(SIZE_SIM_MATRIX, SIZE_SIM_MATRIX);
110-
111109
interactionSimilarityTable = InteractionSimilarityTable.getInstance();
112-
113110
similarityMode = modePPNodeSimilarity;
114-
115111
threshSimilarityHardMatch = THRESH_SIMILARITY_HARD_MATCH;
116112
}
117113

@@ -204,28 +200,19 @@ public double getSimilarity(IPPNode query, IPPNode base) {
204200
* @throws Exception
205201
*/
206202
public double getSimilaritySimple(PPNode query, PPNode base) {
207-
208203
maSimilarity.set(0);
209-
210204
for (int i = 0; i < query.getInteractionTypeCount(); i++) {
211-
212205
int interactionTypeQuery = query.getInteractionType(i);
213-
214206
for (int j = 0; j < base.getInteractionTypeCount(); j++) {
215-
216207
int interactionTypeBase = base.getInteractionType(j);
217-
218208
double similarity = 1.0 - interactionSimilarityTable.getDistance(interactionTypeQuery, interactionTypeBase);
219-
220209
maSimilarity.set(i,j,similarity);
221210
}
222211
}
223212

224213
if(verbose) {
225214
System.out.println("PPNodeSimilarityMultiplicative");
226-
227215
TableModelString tableModelString = new TableModelString(query.getInteractionTypeCount(), base.getInteractionTypeCount());
228-
229216
for (int i = 0; i < query.getInteractionTypeCount(); i++) {
230217
int interactionType = query.getInteractionType(i);
231218
String s = InteractionAtomTypeCalculator.getString(interactionType);
@@ -237,34 +224,25 @@ public double getSimilaritySimple(PPNode query, PPNode base) {
237224
String s = InteractionAtomTypeCalculator.getString(interactionType);
238225
tableModelString.setColName(i, s);
239226
}
240-
241227
tableModelString.set(maSimilarity, 2);
242-
243228
System.out.println(tableModelString.toString());
244-
245229
}
246230

247231

248232
List<Double> liSimilarities = new ArrayList<>();
249-
250233
if(base.getInteractionTypeCount() > query.getInteractionTypeCount()) {
251-
252234
for (int col = 0; col < base.getInteractionTypeCount(); col++) {
253-
254235
double maxSimInCol = 0;
255236
for (int row = 0; row < query.getInteractionTypeCount(); row++) {
256237
if(maSimilarity.get(row,col)>maxSimInCol){
257238
maxSimInCol = maSimilarity.get(row,col);
258239
}
259240
}
260-
261241
liSimilarities.add(maxSimInCol);
262-
263242
// System.out.println("Sim maxSimInCol " + Formatter.format2(maxSimInCol) + "\t" + InteractionAtomTypeCalculator.getString(interactionTypeBase) + "\t" + InteractionAtomTypeCalculator.getString(interactionTypeQuery));
264243
}
265244
} else {
266245
for (int row = 0; row < query.getInteractionTypeCount(); row++) {
267-
268246
double maxSimInRow = 0;
269247
for (int col = 0; col < base.getInteractionTypeCount(); col++) {
270248
if(maSimilarity.get(row,col) > maxSimInRow){
@@ -285,7 +263,6 @@ public double getSimilaritySimple(PPNode query, PPNode base) {
285263
}
286264
}
287265

288-
289266
if(verbose) {
290267
System.out.println("Sim " + Formatter.format2(sim));
291268
System.out.println();
@@ -294,23 +271,15 @@ public double getSimilaritySimple(PPNode query, PPNode base) {
294271
return sim;
295272
}
296273
public double getSimilarityHardMatchMultiplicative(PPNode query, PPNode base) {
297-
298274
IPPNode queryCmp = query;
299-
300275
PPNode baseCmp = base;
301-
302276
if(base.hasHeteroAtom() && query.hasHeteroAtom()){
303-
304277
queryCmp = PPNode.getHeteroOnlyNode(query);
305-
306278
baseCmp = PPNode.getHeteroOnlyNode(base);
307-
308279
}
309280

310281
List<Double> liSimilarities = getSimilarityList((PPNode)queryCmp, baseCmp);
311-
312282
double sim = 0;
313-
314283
if(liSimilarities.size()>0) {
315284
sim = 1;
316285
for (double simPart : liSimilarities) {
@@ -379,9 +348,7 @@ public List<Double> getSimilarityList(PPNode query, PPNode base) {
379348

380349

381350
private static double [] getTopValues(Matrix maSimilarity, int rows, int cols, double thresh){
382-
383351
double [] arrTopSim = new double[Math.max(rows, cols)];
384-
385352
if(rows==1 && cols==1){
386353
arrTopSim[0]=maSimilarity.get(0,0);
387354
return arrTopSim;
@@ -477,11 +444,8 @@ public List<Double> getSimilarityList(PPNode query, PPNode base) {
477444

478445
public double getSimilarityHardMatchAverage(PPNode query, PPNode base) {
479446
List<Double> liSimilarities = getSimilarityList(query, base);
480-
481447
double sumSim = 0;
482-
483448
if(liSimilarities.size()>0) {
484-
485449
for (double simPart : liSimilarities) {
486450
if(simPart< threshSimilarityHardMatch){
487451
sumSim = 0;
@@ -492,7 +456,6 @@ public double getSimilarityHardMatchAverage(PPNode query, PPNode base) {
492456
}
493457

494458
double sim = sumSim/liSimilarities.size();
495-
496459
if(verbose) {
497460
System.out.println("Sim " + Formatter.format2(sim));
498461
System.out.println();
@@ -525,11 +488,8 @@ public double getSimilarityHardMatchOptimistic(PPNode query, PPNode base) {
525488
}
526489

527490
public double getSimilarityExtraCarbonConsideration(PPNode query, PPNode base) {
528-
529491
maSimilarity.set(0);
530-
531492
final double valNoInteraction = -1;
532-
533493
boolean lowCarbonFractionQuery = (query.getFractionCarbonInteractions()< THRESH_CARBON_INTERACTIONS)?true:false;
534494
boolean lowCarbonFractionBase = (base.getFractionCarbonInteractions()< THRESH_CARBON_INTERACTIONS)?true:false;
535495

@@ -540,7 +500,6 @@ public double getSimilarityExtraCarbonConsideration(PPNode query, PPNode base) {
540500
// }
541501
// }
542502

543-
544503
for (int i = 0; i < query.getInteractionTypeCount(); i++) {
545504

546505
int interactionTypeQuery = query.getInteractionType(i);
@@ -598,38 +557,27 @@ public double getSimilarityExtraCarbonConsideration(PPNode query, PPNode base) {
598557

599558
}
600559

601-
602560
List<Double> liSimilarities = new ArrayList<>();
603-
604561
if(base.getInteractionTypeCount() > query.getInteractionTypeCount()) {
605-
606562
for (int col = 0; col < base.getInteractionTypeCount(); col++) {
607-
608563
int interactionTypeQuery=-1;
609564
int interactionTypeBase=-1;
610-
611565
double maxSimInCol = valNoInteraction;
612566
for (int row = 0; row < query.getInteractionTypeCount(); row++) {
613567
if(maSimilarity.get(row,col)>maxSimInCol){
614568
maxSimInCol = maSimilarity.get(row,col);
615-
616569
interactionTypeBase = base.getInteractionType(col);
617570
interactionTypeQuery = query.getInteractionType(row);
618571
}
619572
}
620-
621-
622573
if(Math.abs(maxSimInCol-valNoInteraction)<TINY){
623574
continue;
624575
}
625-
626576
liSimilarities.add(maxSimInCol);
627-
628577
// System.out.println("Sim maxSimInCol " + Formatter.format2(maxSimInCol) + "\t" + InteractionAtomTypeCalculator.getString(interactionTypeBase) + "\t" + InteractionAtomTypeCalculator.getString(interactionTypeQuery));
629578
}
630579
} else {
631580
for (int row = 0; row < query.getInteractionTypeCount(); row++) {
632-
633581
int interactionTypeQuery=-1;
634582
int interactionTypeBase=-1;
635583

@@ -643,45 +591,35 @@ public double getSimilarityExtraCarbonConsideration(PPNode query, PPNode base) {
643591
}
644592
}
645593
// System.out.println("Sim maxSimInRow " + Formatter.format2(maxSimInRow) + "\t" + InteractionAtomTypeCalculator.getString(interactionTypeBase) + "\t" + InteractionAtomTypeCalculator.getString(interactionTypeQuery));
646-
647-
648594
if(Math.abs(maxSimInRow-valNoInteraction)<TINY){
649595
continue;
650596
}
651-
652-
liSimilarities.add(maxSimInRow); }
597+
liSimilarities.add(maxSimInRow);
598+
}
653599
}
654-
655-
656600
double sim = 0;
657-
658601
if(liSimilarities.size()>0) {
659602
sim = 1;
660603
for (Double simPart : liSimilarities) {
661604
sim *= simPart;
662605
}
663606
}
664-
665-
666607
if(verbose) {
667608
System.out.println("Sim " + Formatter.format2(sim));
668609
System.out.println();
669610
}
670-
671611
return sim;
672612
}
673613

674614

675615
public boolean isValidType(int type){
676616
boolean valid = true;
677-
678617
try {
679618
int key = InteractionDistanceStatistics.getInstance().getKey(type);
680619
interactionSimilarityTable.getDistance(key, key);
681620
} catch (Exception e) {
682621
valid = false;
683622
}
684-
685623
return valid;
686624
}
687625

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