chem comp parsing errors & missing crystal translation

sbittrich · sbittrich · commit 85b6c6b3e779 · 2021-01-26T10:39:34.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
@@ -5,6 +5,7 @@
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.biojava.nbio.structure.io.LocalPDBDirectory;
 import org.biojava.nbio.structure.io.cif.ChemCompConverter;
+import org.rcsb.cif.ParsingException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -217,8 +218,14 @@ public ChemComp getChemComp(String recordName) {
         if (haveFile) {
             String filename = getLocalFileName(recordName);
             try {
-                ChemicalComponentDictionary dict = ChemCompConverter.fromPath(Paths.get(filename));
-                ChemComp chemComp = dict.getChemComp(recordName);
+                ChemComp chemComp;
+                try {
+                    ChemicalComponentDictionary dict = ChemCompConverter.fromPath(Paths.get(filename));
+                    chemComp = dict.getChemComp(recordName);
+                } catch (ParsingException e) {
+                    // happens for corrupt files
+                    chemComp = null;
+                }
 
                 // May be null if the file was corrupt. Fall back on ReducedChemCompProvider in that case
                 if (chemComp != null) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/ChemCompConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/ChemCompConverter.java
@@ -1,6 +1,5 @@
 package org.biojava.nbio.structure.io.cif;
 
-import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.chem.ChemicalComponentDictionary;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.rcsb.cif.CifIO;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/StructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/StructureConsumerImpl.java
@@ -1377,14 +1377,17 @@ private void setStructNcsOps() {
                 operator.setElement(0, 0, structNcsOper.getMatrix11().get(rowIndex));
                 operator.setElement(0, 1, structNcsOper.getMatrix12().get(rowIndex));
                 operator.setElement(0, 2, structNcsOper.getMatrix13().get(rowIndex));
+                operator.setElement(0, 3, structNcsOper.getVector1().get(rowIndex));
 
                 operator.setElement(1, 0, structNcsOper.getMatrix21().get(rowIndex));
                 operator.setElement(1, 1, structNcsOper.getMatrix22().get(rowIndex));
                 operator.setElement(1, 2, structNcsOper.getMatrix23().get(rowIndex));
+                operator.setElement(1, 3, structNcsOper.getVector2().get(rowIndex));
 
                 operator.setElement(2, 0, structNcsOper.getMatrix31().get(rowIndex));
                 operator.setElement(2, 1, structNcsOper.getMatrix32().get(rowIndex));
                 operator.setElement(2, 2, structNcsOper.getMatrix33().get(rowIndex));
+                operator.setElement(2, 3, structNcsOper.getVector3().get(rowIndex));
 
                 operator.setElement(3, 0, 0);
                 operator.setElement(3, 1, 0);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java
@@ -220,45 +220,32 @@ public void testFetchObsolete() throws IOException, StructureException {
 
 	}
 
-
 	@Test
 	public void testSettingFileParsingType(){
-
 		AtomCache cache = new AtomCache();
 
 		//test defaults
-
 		// first is mmtf, second is mmcif
-		testFlags(cache,true,false);
+		testFlags(cache, false, false, true);
 
 		// now change the values
-
 		cache.setFiletype(StructureFiletype.CIF);
-
-		testFlags(cache,false,true);
+		testFlags(cache, false, true, false);
 
 		cache.setFiletype(StructureFiletype.MMTF);
-
-		testFlags(cache,true,false);
+		testFlags(cache, true, false, false);
 
 		// this sets to use PDB!
 		cache.setFiletype(StructureFiletype.PDB);
+		testFlags(cache, false, false, false);
 
-		testFlags(cache,false,false);
-
-		// back to defaults
+		// back to MMTF
 		cache.setFiletype(StructureFiletype.MMTF);
-
-		testFlags(cache,true,false);
-
+		testFlags(cache, true, false, false);
 
 		// back to parsing PDB
 		cache.setFiletype(StructureFiletype.PDB);
-
-		testFlags(cache,false,false);
-
-
-
+		testFlags(cache, false, false, false);
 	}
 
 
@@ -268,15 +255,12 @@ public void testSettingFileParsingType(){
 	 * @param useMmTf
 	 * @param useMmCif
 	 */
-	private void testFlags(AtomCache cache ,boolean useMmTf, boolean useMmCif) {
-
+	private void testFlags(AtomCache cache ,boolean useMmTf, boolean useMmCif, boolean useBcif) {
 		assertEquals("flag for parsing mmtf is set to " + cache.getFiletype() + " but should be " + useMmTf,
 				cache.getFiletype() == StructureFiletype.MMTF, useMmTf);
 		assertEquals("flag for parsing mmcif is set to " + cache.getFiletype() + " but should be set to " + useMmCif,
 				cache.getFiletype() == StructureFiletype.CIF, useMmCif);
-
-
-
+		assertEquals("flag for parsing bcif is set to " + cache.getFiletype() + " but should be set to " + useBcif,
+				cache.getFiletype() == StructureFiletype.BCIF, useBcif);
 	}
-
 }
