A test for CRYST1 parsing issue

josemduarte · josemduarte · commit 126d3cfae5e8 · 2018-03-06T15:14:06.000-08:00
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java
@@ -23,6 +23,7 @@
 import static org.junit.Assert.*;
 
 import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
@@ -408,6 +409,23 @@ public void testWaterOnlyChainCif() throws IOException {
 		assertSame(c, cAsymId);
 		
 	}
+	
+	/**
+	 * Some PDB files coming from phenix or other software can have a CRYST1 line without z and not padded with white-spaces 
+	 * for the space group column.
+	 * @throws Exception
+	 * @since 5.0.0
+	 */
+	@Test
+	public void testCryst1Parsing() throws Exception {
+		String cryst1Line = "CRYST1   11.111   11.111  111.111  70.00  80.00  60.00 P 1";
+		Structure s;
+		PDBFileParser pdbPars = new PDBFileParser();
+		try(InputStream is = new ByteArrayInputStream(cryst1Line.getBytes()) ) {
+			s = pdbPars.parsePDBFile(is);
+		}
+		assertEquals("P 1", s.getPDBHeader().getCrystallographicInfo().getSpaceGroup().getShortSymbol());
+	}
 
 	
 	private static int[] countEntityTypes(List<EntityInfo> entities) {
