Merge remote-tracking branch 'upstream/master'

sbittrich · sbittrich · commit 3c83e8b037b3 · 2023-04-03T16:24:06.000-07:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestCrystallographicMetadata.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestCrystallographicMetadata.java
@@ -52,8 +52,8 @@ public void test4hhb() throws Exception {
 
 		Structure s = StructureIO.getStructure("4hhb");
 
-		// 4hhb is one of the few entries that aren't in the standard coordinate frame convention
-		assertTrue(s.getCrystallographicInfo().isNonStandardCoordFrameConvention());
+		// 4hhb was one of the few entries in a non-standard coordinate frame convention: but after a remediation in early 2023 it was finally fixed
+		assertFalse(s.getCrystallographicInfo().isNonStandardCoordFrameConvention());
 
 		// 4hhn has a standard SG
 		assertFalse(s.getCrystallographicInfo().isNonStandardSg());
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/xtal/TestCrystalBuilder.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/xtal/TestCrystalBuilder.java
@@ -173,22 +173,4 @@ public void test2H2Z() throws IOException, StructureException {
 
 	}
 
-	@Test
-	public void test4HHB() throws IOException, StructureException {
-
-		// 4hhb is a very old entry with a non-standard coordinate frame convention, we should calculate only AU contacts
-
-		AtomCache cache = new AtomCache();
-
-		StructureIO.setAtomCache(cache);
-
-		cache.setFiletype(StructureFiletype.CIF);
-		Structure s1 = StructureIO.getStructure("4HHB");
-		CrystalBuilder cb = new CrystalBuilder(s1);
-		StructureInterfaceList interfaces = cb.getUniqueInterfaces(5.5);
-		// 5 interfaces in the AU: the 4 of the tetramer + 1 cross-interface
-		assertEquals(5, interfaces.size());
-
-	}
-
 }
diff --git a/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/symmetry/TestJmolSymmetryScriptGenerator.java b/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/symmetry/TestJmolSymmetryScriptGenerator.java
@@ -39,6 +39,7 @@
 import org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod;
 import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
 
 /**
@@ -50,6 +51,7 @@ public class TestJmolSymmetryScriptGenerator {
     public void setUp() {
     }
 
+    @Ignore("This test is broken since 4hhb remediation in early 2023. In any case, the comparison to the hard-coded polyhedron coordinates wasn't a very good way to test.")
     @Test
     public void testPolygon() throws IOException, StructureException {
         Structure struc = StructureIO.getStructure("4hhb");
