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Parsing PDB-IHM CIF files #1108

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Merged
josemduarte merged 6 commits into from
Mar 5, 2025
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Parsing PDB-IHM CIF files #1108

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a6723d4
Deal with some missing fields in IHM
josemduarte Feb 28, 2025
8286260
Dealing with struct_ref_seq_dif strand_id by referencing through stru…
josemduarte Feb 28, 2025
58136fe
Logging
josemduarte Feb 28, 2025
fdf9864
Revert "Dealing with struct_ref_seq_dif strand_id by referencing thro…
josemduarte Feb 28, 2025
2841770
Deal with missing strand_id
josemduarte Feb 28, 2025
48cb462
Update biojava-structure/src/main/java/org/biojava/nbio/structure/io/…
josemduarte Mar 4, 2025
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Update biojava-structure/src/main/java/org/biojava/nbio/structure/io/… 
…cif/CifStructureConsumerImpl.java

Co-authored-by: Sebastian Bittrich <sebastian.bittrich@rcsb.org>
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@josemduarte @sbittrich
josemduarte and sbittrich authored Mar 4, 2025
commit 48cb462e137a17d5161f390bbf265a11bc4f48ee
4 changes: 2 additions & 2 deletions ...a-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
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Expand Up @@ -1311,8 +1311,8 @@ public void finish() {
seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null);
seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex));

String strandId = structRefSeqDif.getPdbxPdbStrandId().isDefined()? structRefSeqDif.getPdbxPdbStrandId().get(rowIndex) : null;
if (strandId == null) continue;
if (!structRefSeqDif.getPdbxPdbStrandId().isDefined()) continue;
String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex);
List<SeqMisMatch> seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>());
seqMisMatches.add(seqMisMatch);
}
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