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Fix CE-Symm bug with short repeats #1101

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Merged
sbliven merged 5 commits into from
Sep 4, 2024
Merged

Fix CE-Symm bug with short repeats #1101

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403241f
Fix some typos
sbliven Aug 30, 2024
e9e0f00
Add test for rcsb/symmetry#118
sbliven Aug 30, 2024
57a487d
Fix CE-Symm bug relating to short subunits.
sbliven Aug 30, 2024
bfbe710
Fix test result.
sbliven Aug 30, 2024
5b35c70
Add additional error checks to QuatSymmetry functions
sbliven Aug 30, 2024
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Add test for rcsb/symmetry#118
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@sbliven
sbliven committed Aug 30, 2024
commit e9e0f007298c8c90c9b78a906b9f37b5e6dd72b8
25 changes: 24 additions & 1 deletion biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestCeSymm.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@

import static org.junit.Assert.*;
import static org.junit.Assume.assumeNotNull;
import static org.junit.jupiter.api.Assertions.assertNotNull;

import java.io.IOException;
import java.io.InputStream;
Expand Down Expand Up @@ -60,7 +61,7 @@ public void testEasyCases() throws IOException, StructureException {
CeSymmResult result = CeSymm.analyze(atoms);

assertTrue(result.isSignificant());
assertEquals(result.getNumRepeats(), orders[i]);
assertEquals(orders[i], result.getNumRepeats());
}
}

Expand All @@ -75,4 +76,26 @@ public void testAlphafold() throws IOException, StructureException {
CeSymmResult result = CeSymm.analyze(atoms);
assertNotNull(result);
}

@Test
public void testShort() throws IOException, StructureException {
// ERIC2_c35200, a near-perfect 15 residue beta-solenoid
// At 15 residues this should reliably trigger rcsb/symmetry#118
URL url = this.getClass().getResource("/AF-V9WDR2-F1-model_v4.cif");
assumeNotNull(url);
String file = url.getPath();
Structure s = StructureIO.getStructure(file);
assertNull(s.getPdbId());
Atom[] atoms = StructureTools.getRepresentativeAtomArray(s);
CESymmParameters params = new CESymmParameters();
params.setMinCoreLength(10); // Ensure it gets refined (should be 15 long)
CeSymmResult result = CeSymm.analyze(atoms, params);
assertNotNull(result);
assertTrue(result.isSignificant());
assertEquals(9, result.getNumRepeats());
assertEquals("R",result.getSymmGroup());
assertNotNull(result.getAxes());
assertNotEquals("Error", result.getReason());

}
}
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