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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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Lenient to missing atom_site.occupancy
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@josemduarte
josemduarte committed Feb 21, 2025
commit 65d3dcde9a49b3b3f36750815c2c2b3e0d501d5a
2 changes: 1 addition & 1 deletion ...a-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
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Expand Up @@ -333,7 +333,7 @@ public void consumeAtomSite(AtomSite atomSite) {
atom.setY(cartnY.get(atomIndex));
atom.setZ(cartnZ.get(atomIndex));

atom.setOccupancy((float) occupancy.get(atomIndex));
atom.setOccupancy((float) (occupancy.isDefined()? occupancy.get(atomIndex) : 1.0));
atom.setTempFactor((float) bIsoOrEquiv.get(atomIndex));

if (altLocation == null || altLocation.isEmpty() || ".".equals(altLocation)) {
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