Documentation and minor fix

lafita · lafita · commit a8828cacf2b4 · 2016-09-19T17:40:21.000+02:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -998,7 +998,7 @@ public static final Atom createVirtualCBAtom(AminoAcid amino)
 
 		SuperPositionSVD svd = new SuperPositionSVD(false);
 
-		Matrix4d transform = svd.superpose(arr1, arr2);
+		Matrix4d transform = svd.superpose(Calc.atomsToPoints(arr1), Calc.atomsToPoints(arr2));
 		Matrix rotMatrix = Matrices.getRotationJAMA(transform);
 		Atom tranMatrix = getTranslationVector(transform);
 		
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -1361,6 +1361,14 @@ public static void shiftCA2(AFPChain afpChain, Atom[] ca2,  Matrix m, Atom shift
 		}
 	}
 	
+	/**
+	 * Fill the aligned Atom arrays with the equivalent residues in the afpChain.
+	 * @param afpChain
+	 * @param ca1
+	 * @param ca2
+	 * @param ca1aligned
+	 * @param ca2aligned
+	 */
 	public static void fillAlignedAtomArrays(AFPChain afpChain, Atom[] ca1, 
 			Atom[] ca2, Atom[] ca1aligned, Atom[] ca2aligned) {
 		

Original file line number	Diff line number	Diff line change
`@@ -1361,6 +1361,14 @@ public static void shiftCA2(AFPChain afpChain, Atom[] ca2, Matrix m, Atom shift`
`1361`	`1361`	`}`
`1362`	`1362`	`}`
`1363`	`1363`
	`1364`	`+ /**`
	`1365`	`+ * Fill the aligned Atom arrays with the equivalent residues in the afpChain.`
	`1366`	`+ * @param afpChain`
	`1367`	`+ * @param ca1`
	`1368`	`+ * @param ca2`
	`1369`	`+ * @param ca1aligned`
	`1370`	`+ * @param ca2aligned`
	`1371`	`+ */`
`1364`	`1372`	`public static void fillAlignedAtomArrays(AFPChain afpChain, Atom[] ca1,`
`1365`	`1373`	`Atom[] ca2, Atom[] ca1aligned, Atom[] ca2aligned) {`
`1366`	`1374`