Fix for large coordinates to avoid ',' grouping character in coordinates.

Matt Larson · Matt Larson · commit 06a20760549b · 2017-06-21T13:24:09.000-05:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
@@ -68,12 +68,14 @@ public class FileConvert {
 		d3.setMaximumIntegerDigits(4);
 		d3.setMinimumFractionDigits(3);
 		d3.setMaximumFractionDigits(3);
+		d3.setGroupingUsed(false);
 	}
 	public static DecimalFormat d2 = (DecimalFormat)NumberFormat.getInstance(Locale.US);
 	static {
 		d2.setMaximumIntegerDigits(3);
 		d2.setMinimumFractionDigits(2);
 		d2.setMaximumFractionDigits(2);
+		d2.setGroupingUsed(false);
 	}
 
 	private static final String newline = System.getProperty("line.separator");
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestWriteLargeCoordinatePDB.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestWriteLargeCoordinatePDB.java
@@ -0,0 +1,49 @@
+package org.biojava.nbio.structure.io;
+
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Group;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.junit.Test;
+
+public class TestWriteLargeCoordinatePDB {
+	
+	// This test checks that 'grouping' characters such as commas are not
+	// incorrectly introduced into formatted PDB coordinate fields.
+	// See FileConvert.d3 formatter.
+	@Test
+	public void TestWrite5D9Q() throws IOException, StructureException {
+
+		AtomCache cache = new AtomCache();
+		cache.setUseMmCif(false);
+
+		FileParsingParameters params = new FileParsingParameters();
+		params.setHeaderOnly(false);
+		cache.setFileParsingParams(params);
+
+		StructureIO.setAtomCache(cache);
+
+		// Example structure with large coordinates in PDB file.
+		Structure sPDB = StructureIO.getStructure("5D9Q");
+		
+		// If 48 column for a ATOM/HETATM has a comma, fail.
+		for (Group g : sPDB.getChain("K").getAtomGroups()) {
+			for (Atom a : g.getAtoms()) {
+				if (a.toPDB().contains(",")) {
+					fail("Comma present in ATOM/HETATM record.");
+				}
+			}
+		}
+		
+		//try (PrintWriter p = new PrintWriter(new FileWriter(new File("/tmp/test.pdb")))) {
+		//	p.print(sPDB.toPDB());
+		//}
+	}
+	
+}

Original file line number	Diff line number	Diff line change
`@@ -68,12 +68,14 @@ public class FileConvert {`
`68`	`68`	`d3.setMaximumIntegerDigits(4);`
`69`	`69`	`d3.setMinimumFractionDigits(3);`
`70`	`70`	`d3.setMaximumFractionDigits(3);`
	`71`	`+ d3.setGroupingUsed(false);`
`71`	`72`	`}`
`72`	`73`	`public static DecimalFormat d2 = (DecimalFormat)NumberFormat.getInstance(Locale.US);`
`73`	`74`	`static {`
`74`	`75`	`d2.setMaximumIntegerDigits(3);`
`75`	`76`	`d2.setMinimumFractionDigits(2);`
`76`	`77`	`d2.setMaximumFractionDigits(2);`
	`78`	`+ d2.setGroupingUsed(false);`
`77`	`79`	`}`
`78`	`80`
`79`	`81`	`private static final String newline = System.getProperty("line.separator");`