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josemduartejosemduarte
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Merge pull request #1120 from biojava/sym-edgecase
Quaternary symmetry calculation edge-case
2 parents 70e9a74 + 423cd86 commit 8edaed7

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-31
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2 files changed

+23
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‎biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java‎

Lines changed: 19 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -507,27 +507,24 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
507507
}
508508
}
509509

510-
AFPChain afp = aligner.align(this.subunits.get(this.representative)
511-
.getRepresentativeAtoms(),
512-
other.subunits.get(other.representative)
513-
.getRepresentativeAtoms());
510+
AFPChain afp = aligner.align(this.subunits.get(this.representative).getRepresentativeAtoms(),
511+
other.subunits.get(other.representative).getRepresentativeAtoms());
514512

513+
String pairName = this.subunits.get(this.representative).getName() + "-" + other.subunits.get(other.representative).getName();
515514
if (afp.getOptLength() < 1) {
516515
// alignment failed (eg if chains were too short)
517516
throw new StructureException(
518-
String.format("Subunits failed to align using %s", params.getSuperpositionAlgorithm()));
517+
String.format("Subunits %s failed to align using %s", pairName, params.getSuperpositionAlgorithm()));
519518
}
520519

521520
// Convert AFPChain to MultipleAlignment for convenience
522521
MultipleAlignment msa = new MultipleAlignmentEnsembleImpl(
523522
afp,
524523
this.subunits.get(this.representative).getRepresentativeAtoms(),
525-
other.subunits.get(other.representative)
526-
.getRepresentativeAtoms(), false)
527-
.getMultipleAlignment(0);
524+
other.subunits.get(other.representative).getRepresentativeAtoms(),
525+
false).getMultipleAlignment(0);
528526

529-
double structureCoverage = Math.min(msa.getCoverages().get(0), msa
530-
.getCoverages().get(1));
527+
double structureCoverage = Math.min(msa.getCoverages().get(0), msa.getCoverages().get(1));
531528

532529
if(params.isUseStructureCoverage() && structureCoverage < params.getStructureCoverageThreshold()) {
533530
return false;
@@ -543,8 +540,7 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
543540
return false;
544541
}
545542

546-
logger.info(String.format("SubunitClusters are structurally similar with "
547-
+ "%.2f RMSD %.2f coverage", rmsd, structureCoverage));
543+
logger.info("SubunitClusters {} are structurally similar with [ {} ] RMSD and [ {} ] coverage", pairName, String.format("%.2f", rmsd), String.format("%.2f", structureCoverage));
548544

549545
// Merge clusters
550546
List<List<Integer>> alignedRes = msa.getBlock(0).getAlignRes();
@@ -565,13 +561,18 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
565561

566562
// Only consider residues that are part of the SubunitCluster
567563
if (this.subunitEQR.get(this.representative).contains(thisIndex)
568-
&& other.subunitEQR.get(other.representative).contains(
569-
otherIndex)) {
564+
&& other.subunitEQR.get(other.representative).contains(otherIndex)) {
570565
thisAligned.add(thisIndex);
571566
otherAligned.add(otherIndex);
572567
}
573568
}
574569

570+
// this can happen in very rare cases, e.g. 9y9z when merging E_1 into the cluster D_1, OM_1, Y_1
571+
if (thisAligned.isEmpty() && otherAligned.isEmpty()) {
572+
logger.warn("No equivalent aligned atoms found between SubunitClusters {} via structure alignment. Will not merge the second one into the first.", pairName);
573+
return false;
574+
}
575+
575576
updateEquivResidues(other, thisAligned, otherAligned);
576577

577578
this.method = SubunitClustererMethod.STRUCTURE;
@@ -602,18 +603,12 @@ private void updateEquivResidues(SubunitCluster other, List<Integer> thisAligned
602603
Collections.sort(otherRemove);
603604
Collections.reverse(otherRemove);
604605

605-
for (int t = 0; t < thisRemove.size(); t++) {
606-
for (List<Integer> eqr : this.subunitEQR) {
607-
int column = thisRemove.get(t);
608-
eqr.remove(column);
609-
}
606+
for (int column : thisRemove) {
607+
this.subunitEQR.forEach(eqr -> eqr.remove(column));
610608
}
611609

612-
for (int t = 0; t < otherRemove.size(); t++) {
613-
for (List<Integer> eqr : other.subunitEQR) {
614-
int column = otherRemove.get(t);
615-
eqr.remove(column);
616-
}
610+
for (int column : otherRemove) {
611+
other.subunitEQR.forEach(eqr -> eqr.remove(column));
617612
}
618613

619614
// The representative is the longest sequence

‎biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java‎

Lines changed: 4 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -83,8 +83,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
8383
}
8484

8585
} catch (CompoundNotFoundException e) {
86-
logger.warn("Could not merge by Sequence. {}",
87-
e.getMessage());
86+
logger.info("Could not merge by Sequence. {}", e.getMessage());
8887
}
8988
}
9089
}
@@ -100,7 +99,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
10099
clusters.remove(c2);
101100
}
102101
} catch (StructureException e) {
103-
logger.warn("Could not merge by Structure. {}", e.getMessage());
102+
logger.info("Could not merge by Structure. {}", e.getMessage());
104103
}
105104
}
106105
}
@@ -112,8 +111,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
112111
try {
113112
clusters.get(c).divideInternally(params);
114113
} catch (StructureException e) {
115-
logger.warn("Error analyzing internal symmetry. {}",
116-
e.getMessage());
114+
logger.info("Error analyzing internal symmetry. {}", e.getMessage());
117115
}
118116
}
119117

@@ -125,8 +123,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
125123
if (clusters.get(c1).mergeStructure(clusters.get(c2), params))
126124
clusters.remove(c2);
127125
} catch (StructureException e) {
128-
logger.warn("Could not merge by Structure. {}",
129-
e.getMessage());
126+
logger.info("Could not merge by Structure. {}", e.getMessage());
130127
}
131128
}
132129
}

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