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Quaternary symmetry calculation edge-case #1120

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Merged
josemduarte merged 1 commit into from
Dec 10, 2025
Merged

Quaternary symmetry calculation edge-case #1120

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43 changes: 19 additions & 24 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
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Original file line number Diff line number Diff line change
Expand Up @@ -507,27 +507,24 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
}
}

AFPChain afp = aligner.align(this.subunits.get(this.representative)
.getRepresentativeAtoms(),
other.subunits.get(other.representative)
.getRepresentativeAtoms());
AFPChain afp = aligner.align(this.subunits.get(this.representative).getRepresentativeAtoms(),
other.subunits.get(other.representative).getRepresentativeAtoms());

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

// Convert AFPChain to MultipleAlignment for convenience
MultipleAlignment msa = new MultipleAlignmentEnsembleImpl(
afp,
this.subunits.get(this.representative).getRepresentativeAtoms(),
other.subunits.get(other.representative)
.getRepresentativeAtoms(), false)
.getMultipleAlignment(0);
other.subunits.get(other.representative).getRepresentativeAtoms(),
false).getMultipleAlignment(0);

double structureCoverage = Math.min(msa.getCoverages().get(0), msa
.getCoverages().get(1));
double structureCoverage = Math.min(msa.getCoverages().get(0), msa.getCoverages().get(1));

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

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

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

// Only consider residues that are part of the SubunitCluster
if (this.subunitEQR.get(this.representative).contains(thisIndex)
&& other.subunitEQR.get(other.representative).contains(
otherIndex)) {
&& other.subunitEQR.get(other.representative).contains(otherIndex)) {
thisAligned.add(thisIndex);
otherAligned.add(otherIndex);
}
}

// this can happen in very rare cases, e.g. 9y9z when merging E_1 into the cluster D_1, OM_1, Y_1
if (thisAligned.isEmpty() && otherAligned.isEmpty()) {
logger.warn("No equivalent aligned atoms found between SubunitClusters {} via structure alignment. Will not merge the second one into the first.", pairName);
return false;
}
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@josemduarte josemduarte Dec 8, 2025

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This is the fix. The rest are formatting and logging improvements.


updateEquivResidues(other, thisAligned, otherAligned);

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

for (int t = 0; t < thisRemove.size(); t++) {
for (List<Integer> eqr : this.subunitEQR) {
int column = thisRemove.get(t);
eqr.remove(column);
}
for (int column : thisRemove) {
this.subunitEQR.forEach(eqr -> eqr.remove(column));
}

for (int t = 0; t < otherRemove.size(); t++) {
for (List<Integer> eqr : other.subunitEQR) {
int column = otherRemove.get(t);
eqr.remove(column);
}
for (int column : otherRemove) {
other.subunitEQR.forEach(eqr -> eqr.remove(column));
}

// The representative is the longest sequence
Expand Down
11 changes: 4 additions & 7 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -83,8 +83,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
}

} catch (CompoundNotFoundException e) {
logger.warn("Could not merge by Sequence. {}",
e.getMessage());
logger.info("Could not merge by Sequence. {}", e.getMessage());
}
}
}
Expand All @@ -100,7 +99,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
clusters.remove(c2);
}
} catch (StructureException e) {
logger.warn("Could not merge by Structure. {}", e.getMessage());
logger.info("Could not merge by Structure. {}", e.getMessage());
}
}
}
Expand All @@ -112,8 +111,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
try {
clusters.get(c).divideInternally(params);
} catch (StructureException e) {
logger.warn("Error analyzing internal symmetry. {}",
e.getMessage());
logger.info("Error analyzing internal symmetry. {}", e.getMessage());
}
}

Expand All @@ -125,8 +123,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
if (clusters.get(c1).mergeStructure(clusters.get(c2), params))
clusters.remove(c2);
} catch (StructureException e) {
logger.warn("Could not merge by Structure. {}",
e.getMessage());
logger.info("Could not merge by Structure. {}", e.getMessage());
}
}
}
Expand Down