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More lenient CIF parsing #1103

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Merged
josemduarte merged 1 commit into from
Jan 8, 2025
Merged

More lenient CIF parsing #1103

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8 changes: 4 additions & 4 deletions ...a-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -972,9 +972,9 @@ public void consumeStructRefSeq(StructRefSeq structRefSeq) {

DBRef dbRef = new DBRef();

dbRef.setIdCode(structRefSeq.getPdbxPDBIdCode().get(rowIndex));
dbRef.setDbAccession(structRefSeq.getPdbxDbAccession().get(rowIndex));
dbRef.setDbIdCode(structRefSeq.getPdbxDbAccession().get(rowIndex));
dbRef.setIdCode(structRefSeq.getPdbxPDBIdCode().isDefined()? structRefSeq.getPdbxPDBIdCode().get(rowIndex):null);
dbRef.setDbAccession(structRefSeq.getPdbxDbAccession().isDefined()? structRefSeq.getPdbxDbAccession().get(rowIndex):null);
dbRef.setDbIdCode(structRefSeq.getPdbxDbAccession().isDefined()? structRefSeq.getPdbxDbAccession().get(rowIndex):null);
dbRef.setChainName(structRefSeq.getPdbxStrandId().get(rowIndex));

OptionalInt structRefRowIndex = IntStream.range(0, structRef.getRowCount())
Expand Down Expand Up @@ -1330,7 +1330,7 @@ private String getEntityType(String entityId) {
private String getEntityDescription(String entityId) {
return IntStream.range(0, entity.getRowCount())
.filter(i -> entity.getId().get(i).equals(entityId))
.mapToObj(i -> entity.getPdbxDescription().get(i))
.mapToObj(i -> entity.getPdbxDescription().isDefined()? entity.getPdbxDescription().get(i):"")
.findFirst()
.orElseThrow(() -> new NoSuchElementException("could not find entity with id " + entityId));
}
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