Fix: CIF parser wasn't respecting parseCAOnly - #1156
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josemduarte wants to merge 3 commits into
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sbittrich
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September 15, 2026 06:01
sbittrich
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Sep 15, 2026
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LGTM, thanks.
Would consider moving the fixed logic though.
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| // keep only C-alpha atoms; requiring element C excludes calcium ions, whose atom name is also CA | ||
| if (!(labelAtomId.get(atomIndex).equals(StructureTools.CA_ATOM_NAME) && "C".equals(typeSymbol.get(atomIndex)))) { |
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| // keep only C-alpha atoms; requiring element C excludes calcium ions, whose atom name is also CA | |
| if (!(labelAtomId.get(atomIndex).equals(StructureTools.CA_ATOM_NAME) && "C".equals(typeSymbol.get(atomIndex)))) { | |
| for (int atomIndex = 0; atomIndex < atomSite.getRowCount(); atomIndex++) { | |
| if (params.isParseCAOnly()) { | |
| // keep only C-alpha atoms; requiring element C excludes calcium ions, whose atom name is also CA | |
| if (!(labelAtomId.get(atomIndex).equals(StructureTools.CA_ATOM_NAME) && "C".equals(typeSymbol.get(atomIndex)))) { | |
| continue; | |
| } | |
| } | |
| boolean startOfNewChain = false; |
There may be another bug here. Because the check happens this late, lots of empty groups and chains are created.
How about moving it all the way up and making it the first action in the loop?
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Indeed, good point. The empty chain/groups are actually another bug by itself. Should be fixed in 0b8427a
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Including a new unit test for it.