Merge pull request biojava#434 from abradle/master

andreasprlic · andreasprlic · commit 084cd4acc007 · 2016-03-11T18:49:39.000-08:00
Fixed a bug where nucleotide bonds were not being generated. Added a …
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
@@ -165,8 +165,8 @@ private void formNucleotideBonds() {
 					continue;
 				}
 
-				Atom phosphorous = tail.getP();
-				Atom oThreePrime = head.getO3Prime();
+				Atom phosphorous = head.getP();
+				Atom oThreePrime = tail.getO3Prime();
 
 				if (phosphorous == null || oThreePrime == null) {
 					continue;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java
@@ -21,6 +21,8 @@
 package org.biojava.nbio.structure;
 
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
@@ -138,6 +140,38 @@ public void testLigandBonds() throws StructureException, IOException {
 		assertTrue(areBonded(phosphateP, phosphateO));
 	}
 
+ 	/**
+ 	 * Test whether nucleotide bonds are being generated
+ 	 * @throws IOException
+ 	 * @throws StructureException
+ 	 */
+ 	@Test 
+ 	public void testNucleotideBonds() throws IOException, StructureException {
+ 		Structure bio = StructureIO.getStructure("4y60");
+ 		for( Chain c : bio.getChains()) {
+ 			int groupCounter = 0;
+ 			List<Group> currentGroups = c.getAtomGroups();
+ 			for ( Group g : currentGroups) {
+ 				if(groupCounter!=0 && groupCounter<currentGroups.size()) {
+ 					List<Atom> atoms = g.getAtoms();
+ 					for ( Atom a : atoms) {
+ 						if ( a.getName().equals("P")){
+ 							// Check to see if one of the phosphate atoms has bonding to something
+ 							// outside of the group.
+ 							List<Integer> indexList = new ArrayList<>();
+ 							for (Bond b : a.getBonds()){
+ 								indexList.add(atoms.indexOf(b.getOther(a)));
+ 							}
+ 							assertTrue(indexList.contains(-1));
+ 						}
+ 					}
+ 				}
+ 				groupCounter++;
+ 			}
+ 
+ 		}
+ 	}
+
 	private boolean areBonded(Atom a, Atom b) {
 		for (Bond bond : a.getBonds()) {
 			if (bond.getOther(a) == b) {

Original file line number	Diff line number	Diff line change
`@@ -165,8 +165,8 @@ private void formNucleotideBonds() {`
`165`	`165`	`continue;`
`166`	`166`	`}`
`167`	`167`
`168`		`- Atom phosphorous = tail.getP();`
`169`		`- Atom oThreePrime = head.getO3Prime();`
	`168`	`+ Atom phosphorous = head.getP();`
	`169`	`+ Atom oThreePrime = tail.getO3Prime();`
`170`	`170`
`171`	`171`	`if (phosphorous == null \|\| oThreePrime == null) {`
`172`	`172`	`continue;`