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More on lenient PDBx/mmCIF parsing #1106

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Merged
josemduarte merged 3 commits into from
Feb 27, 2025
+35 −26
Merged

More on lenient PDBx/mmCIF parsing #1106

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93c1c8f
Handle more missing fields in struct_ref_seq
josemduarte Feb 21, 2025
65d3dcd
Lenient to missing atom_site.occupancy
josemduarte Feb 21, 2025
12dcb2c
Another safeguard, that applies to some PDB-IHM entries
josemduarte Feb 21, 2025
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Another safeguard, that applies to some PDB-IHM entries
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@josemduarte
josemduarte committed Feb 21, 2025
commit 12dcb2ce3c1a03d67798311ca7cf6fd26e12563f
4 changes: 4 additions & 0 deletions ...a-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
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Expand Up @@ -1819,6 +1819,10 @@ private void initMaps() {

String[] chainNames = entityPoly.getPdbxStrandId().get(rowIndex).split(",");
List<String> asymIds = entityId2asymId.get(entityPoly.getEntityId().get(rowIndex));
if (asymIds == null) {
logger.warn("No asym ids found for entity {} in _struct_asym. Can't provide a mapping from asym ids to author chain ids for this entity", entityPoly.getEntityId().get(rowIndex));
break;
}
if (chainNames.length != asymIds.size()) {
logger.warn("The list of asym ids (from _struct_asym) and the list of author ids (from _entity_poly) " +
"for entity {} have different lengths! Can't provide a mapping from asym ids to author chain " +
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