From bc9011a2d048ed0a40e44ff4cecd82796ac01eae Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 7 Dec 2017 15:09:16 -0800
Subject: [PATCH 1/4] Fix and unit test for #715

---
 .../java/org/biojava/nbio/structure/Calc.java |  5 ++
 .../org/biojava/nbio/structure/TestCalc.java  | 47 +++++++++++++++++++
 2 files changed, 52 insertions(+)

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
index 1e5f6c17c6..8d8df53284 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -579,6 +579,11 @@ public static final void transform(Chain chain, Matrix4d m) {
 			for (Atom atom : g.getAtoms()) {
 				transform(atom, m);
 			}
+			for (Group altG : g.getAltLocs()) {
+				for (Atom atom : altG.getAtoms()) {
+					transform(atom, m);
+				}				
+			}
 		}
 	}
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
index 3b48a402d8..2b85fff020 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
@@ -157,6 +157,53 @@ public void testVecmathTransformation() {
 
 		assertEquals(expected, actual);
 	}
+	
+	/**
+	 * Issue https://github.com/biojava/biojava/issues/715
+	 */
+	@Test
+	public void testChainTransform() {
+		Group g = new AminoAcidImpl();
+		Atom a = new AtomImpl();
+		a.setName("CA");
+		a.setX(1);
+		a.setY(1);
+		a.setZ(1);
+		g.addAtom(a);
+		Group altLocG = new AminoAcidImpl();
+		Atom a2 = new AtomImpl();
+		a2.setName("CA");
+		a2.setX(2);
+		a2.setY(2);
+		a2.setZ(2);
+		altLocG.addAtom(a2);
+		
+		g.addAltLoc(altLocG);
+		
+		Chain c = new ChainImpl();
+		c.addGroup(g);
+		
+		Matrix4d m = new Matrix4d(1,0,0,1, 0,1,0,0, 0,0,1,0, 0,0,0,1); // shift of 1 in x axis
+ 		Calc.transform(c, m);
+ 		
+ 		Group thegroup = c.getAtomGroup(0);
+ 		Group thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		Atom atom1 = thegroup.getAtom("CA");
+ 		Atom atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(2, atom1.getX(), 0.00001);
+ 		assertEquals(1, atom1.getY(), 0.00001);
+ 		assertEquals(1, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(3, atom2.getX(), 0.00001);
+ 		assertEquals(2, atom2.getY(), 0.00001);
+ 		assertEquals(2, atom2.getZ(), 0.00001);
+
+ 		
+	}
 
 	private static Atom getAtom(double x, double y, double z) {
 		Atom a = new AtomImpl();

From 3a1ad26c6d0df71508e58a52a114978b940b9022 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 7 Dec 2017 17:16:09 -0800
Subject: [PATCH 2/4] Fixing also Calc.transform(Structure,Matrix4d)

---
 .../java/org/biojava/nbio/structure/Calc.java | 30 +++---
 .../org/biojava/nbio/structure/TestCalc.java  | 95 ++++++++++++++++---
 2 files changed, 95 insertions(+), 30 deletions(-)

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
index 8d8df53284..70ef988e93 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -538,12 +538,13 @@ public static final void transform(Atom atom, Matrix4d m) {
 	 * @param m
 	 */
 	public static final void transform(Group group, Matrix4d m) {
-		AtomIterator iter = new AtomIterator(group);
-
-		while (iter.hasNext()) {
-			Atom atom = iter.next();
+		for (Atom atom : group.getAtoms()) {
 			transform(atom, m);
-
+		}
+		for (Group altG : group.getAltLocs()) {
+			for (Atom atom : altG.getAtoms()) {
+				transform(atom, m);
+			}				
 		}
 	}
 
@@ -556,12 +557,10 @@ public static final void transform(Group group, Matrix4d m) {
 	 * @param m
 	 */
 	public static final void transform(Structure structure, Matrix4d m) {
-		AtomIterator iter = new AtomIterator(structure);
-
-		while (iter.hasNext()) {
-			Atom atom = iter.next();
-			transform(atom, m);
-
+		for (int n=0; n<structure.nrModels();n++) {
+			for (Chain c : structure.getChains(n)) {
+				transform(c, m);
+			}
 		}
 	}
 
@@ -576,14 +575,7 @@ public static final void transform(Structure structure, Matrix4d m) {
 	public static final void transform(Chain chain, Matrix4d m) {
 
 		for (Group g : chain.getAtomGroups()) {
-			for (Atom atom : g.getAtoms()) {
-				transform(atom, m);
-			}
-			for (Group altG : g.getAltLocs()) {
-				for (Atom atom : altG.getAtoms()) {
-					transform(atom, m);
-				}				
-			}
+			transform(g, m);
 		}
 	}
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
index 2b85fff020..57fdfbb641 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
@@ -164,18 +164,10 @@ public void testVecmathTransformation() {
 	@Test
 	public void testChainTransform() {
 		Group g = new AminoAcidImpl();
-		Atom a = new AtomImpl();
-		a.setName("CA");
-		a.setX(1);
-		a.setY(1);
-		a.setZ(1);
+		Atom a = getAtom("CA", 1, 1, 1);
 		g.addAtom(a);
 		Group altLocG = new AminoAcidImpl();
-		Atom a2 = new AtomImpl();
-		a2.setName("CA");
-		a2.setX(2);
-		a2.setY(2);
-		a2.setZ(2);
+		Atom a2 = getAtom("CA", 2, 2, 2);
 		altLocG.addAtom(a2);
 		
 		g.addAltLoc(altLocG);
@@ -205,13 +197,94 @@ public void testChainTransform() {
  		
 	}
 
-	private static Atom getAtom(double x, double y, double z) {
+	/**
+	 * Issue https://github.com/biojava/biojava/issues/715
+	 */
+	@Test
+	public void testStructureTransform() {
+		Group g = new AminoAcidImpl();
+		Atom a = getAtom("CA", 1, 1, 1);
+		g.addAtom(a);
+		Group altLocG = new AminoAcidImpl();
+		Atom a2 = getAtom("CA", 2, 2, 2);
+		altLocG.addAtom(a2);
+		
+		g.addAltLoc(altLocG);
+		
+		Chain c1 = new ChainImpl();
+		c1.addGroup(g);
+		c1.setId("A");
+		
+		Group gc2 = new AminoAcidImpl();
+		Atom ac2 = getAtom("CA", 3, 3, 3);
+		gc2.addAtom(ac2);
+		Group altLocGc2 = new AminoAcidImpl();
+		Atom ac22 = getAtom("CA", 4, 4, 4);
+		altLocGc2.addAtom(ac22);
+		
+		gc2.addAltLoc(altLocGc2);
+		
+		Chain c2 = new ChainImpl();
+		c2.addGroup(gc2);
+		c2.setId("B");
+		
+		Structure s = new StructureImpl();
+		s.addChain(c1);
+		s.addChain(c2);
+		
+		
+		Matrix4d m = new Matrix4d(1,0,0,1, 0,1,0,0, 0,0,1,0, 0,0,0,1); // shift of 1 in x axis
+ 		Calc.transform(s, m);
+ 		
+ 		// testing 1st chain
+ 		Group thegroup = s.getChain("A").getAtomGroup(0);
+ 		Group thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		Atom atom1 = thegroup.getAtom("CA");
+ 		Atom atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(2, atom1.getX(), 0.00001);
+ 		assertEquals(1, atom1.getY(), 0.00001);
+ 		assertEquals(1, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(3, atom2.getX(), 0.00001);
+ 		assertEquals(2, atom2.getY(), 0.00001);
+ 		assertEquals(2, atom2.getZ(), 0.00001);
+
+ 		// testing 2nd chain
+ 		thegroup = s.getChain("B").getAtomGroup(0);
+ 		thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		atom1 = thegroup.getAtom("CA");
+ 		atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(4, atom1.getX(), 0.00001);
+ 		assertEquals(3, atom1.getY(), 0.00001);
+ 		assertEquals(3, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(5, atom2.getX(), 0.00001);
+ 		assertEquals(4, atom2.getY(), 0.00001);
+ 		assertEquals(4, atom2.getZ(), 0.00001);
+
+ 		
+	}
+
+	private static Atom getAtom(String name, double x, double y, double z) {
 		Atom a = new AtomImpl();
 		a.setX(x);
 		a.setY(y);
 		a.setZ(z);
+		a.setName(name);
 		return a;
 	}
+	
+	private static Atom getAtom(double x, double y, double z) {
+		return getAtom(null, x, y, z);
+	}
 
 	private static Matrix4d getSampleTransform(){
 

From 8a7e22ca406d27e3742b1df37b9be788c4c05199 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 7 Dec 2017 17:55:51 -0800
Subject: [PATCH 3/4] Fixes for translate functions, similar to #715

---
 .../java/org/biojava/nbio/structure/Calc.java |  25 ++-
 .../org/biojava/nbio/structure/TestCalc.java  | 160 +++++++++++++-----
 2 files changed, 131 insertions(+), 54 deletions(-)

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
index 70ef988e93..ce294db288 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -601,12 +601,14 @@ public static final void translate(Atom atom, Vector3d v) {
 	 * @param v
 	 */
 	public static final void translate(Group group, Vector3d v) {
-		AtomIterator iter = new AtomIterator(group);
 
-		while (iter.hasNext()) {
-			Atom atom = iter.next();
+		for (Atom atom : group.getAtoms()) {
 			translate(atom, v);
-
+		}
+		for (Group altG : group.getAltLocs()) {
+			for (Atom atom : altG.getAtoms()) {
+				translate(atom, v);
+			}				
 		}
 	}
 
@@ -620,9 +622,7 @@ public static final void translate(Group group, Vector3d v) {
 	public static final void translate(Chain chain, Vector3d v) {
 
 		for (Group g : chain.getAtomGroups()) {
-			for (Atom atom : g.getAtoms()) {
-				translate(atom, v);
-			}
+			translate(g, v);
 		}
 	}
 
@@ -634,12 +634,11 @@ public static final void translate(Chain chain, Vector3d v) {
 	 * @param v
 	 */
 	public static final void translate(Structure structure, Vector3d v) {
-		AtomIterator iter = new AtomIterator(structure);
-
-		while (iter.hasNext()) {
-			Atom atom = iter.next();
-			translate(atom, v);
-
+		
+		for (int n=0; n<structure.nrModels();n++) {
+			for (Chain c : structure.getChains(n)) {
+				translate(c, v);
+			}
 		}
 	}
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
index 57fdfbb641..c834b22a61 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
@@ -24,6 +24,7 @@
 
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
+import javax.vecmath.Vector3d;
 
 import org.biojava.nbio.structure.geometry.Matrices;
 import org.biojava.nbio.structure.jama.Matrix;
@@ -163,17 +164,8 @@ public void testVecmathTransformation() {
 	 */
 	@Test
 	public void testChainTransform() {
-		Group g = new AminoAcidImpl();
-		Atom a = getAtom("CA", 1, 1, 1);
-		g.addAtom(a);
-		Group altLocG = new AminoAcidImpl();
-		Atom a2 = getAtom("CA", 2, 2, 2);
-		altLocG.addAtom(a2);
-		
-		g.addAltLoc(altLocG);
 		
-		Chain c = new ChainImpl();
-		c.addGroup(g);
+		Chain c = createDummyChain();
 		
 		Matrix4d m = new Matrix4d(1,0,0,1, 0,1,0,0, 0,0,1,0, 0,0,0,1); // shift of 1 in x axis
  		Calc.transform(c, m);
@@ -184,12 +176,12 @@ public void testChainTransform() {
  		Atom atom1 = thegroup.getAtom("CA");
  		Atom atom2 = thealtlocgroup.getAtom("CA");
  		
- 		// x should be shitfted by 1
+ 		// x should be shifted by 1
  		assertEquals(2, atom1.getX(), 0.00001);
  		assertEquals(1, atom1.getY(), 0.00001);
  		assertEquals(1, atom1.getZ(), 0.00001);
  		
- 		// x should be shitfted by 1
+ 		// x should be shifted by 1
  		assertEquals(3, atom2.getX(), 0.00001);
  		assertEquals(2, atom2.getY(), 0.00001);
  		assertEquals(2, atom2.getZ(), 0.00001);
@@ -202,36 +194,8 @@ public void testChainTransform() {
 	 */
 	@Test
 	public void testStructureTransform() {
-		Group g = new AminoAcidImpl();
-		Atom a = getAtom("CA", 1, 1, 1);
-		g.addAtom(a);
-		Group altLocG = new AminoAcidImpl();
-		Atom a2 = getAtom("CA", 2, 2, 2);
-		altLocG.addAtom(a2);
-		
-		g.addAltLoc(altLocG);
-		
-		Chain c1 = new ChainImpl();
-		c1.addGroup(g);
-		c1.setId("A");
-		
-		Group gc2 = new AminoAcidImpl();
-		Atom ac2 = getAtom("CA", 3, 3, 3);
-		gc2.addAtom(ac2);
-		Group altLocGc2 = new AminoAcidImpl();
-		Atom ac22 = getAtom("CA", 4, 4, 4);
-		altLocGc2.addAtom(ac22);
-		
-		gc2.addAltLoc(altLocGc2);
-		
-		Chain c2 = new ChainImpl();
-		c2.addGroup(gc2);
-		c2.setId("B");
-		
-		Structure s = new StructureImpl();
-		s.addChain(c1);
-		s.addChain(c2);
 		
+		Structure s = createDummyStructure();
 		
 		Matrix4d m = new Matrix4d(1,0,0,1, 0,1,0,0, 0,0,1,0, 0,0,0,1); // shift of 1 in x axis
  		Calc.transform(s, m);
@@ -272,6 +236,72 @@ public void testStructureTransform() {
 
  		
 	}
+	
+	@Test
+	public void testChainTranslate() {
+		Chain c = createDummyChain();
+
+		Vector3d translation = new Vector3d(1, 0, 0);
+ 		Calc.translate(c, translation);
+ 		
+ 		Group thegroup = c.getAtomGroup(0);
+ 		Group thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		Atom atom1 = thegroup.getAtom("CA");
+ 		Atom atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shifted by 1
+ 		assertEquals(2, atom1.getX(), 0.00001);
+ 		assertEquals(1, atom1.getY(), 0.00001);
+ 		assertEquals(1, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shifted by 1
+ 		assertEquals(3, atom2.getX(), 0.00001);
+ 		assertEquals(2, atom2.getY(), 0.00001);
+ 		assertEquals(2, atom2.getZ(), 0.00001);
+	}
+	
+	@Test
+	public void testStructureTranslate() {
+		Structure s = createDummyStructure();
+		
+		Vector3d translation = new Vector3d(1, 0, 0);
+ 		Calc.translate(s, translation);
+ 		
+ 		// testing 1st chain
+ 		Group thegroup = s.getChain("A").getAtomGroup(0);
+ 		Group thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		Atom atom1 = thegroup.getAtom("CA");
+ 		Atom atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(2, atom1.getX(), 0.00001);
+ 		assertEquals(1, atom1.getY(), 0.00001);
+ 		assertEquals(1, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(3, atom2.getX(), 0.00001);
+ 		assertEquals(2, atom2.getY(), 0.00001);
+ 		assertEquals(2, atom2.getZ(), 0.00001);
+
+ 		// testing 2nd chain
+ 		thegroup = s.getChain("B").getAtomGroup(0);
+ 		thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		atom1 = thegroup.getAtom("CA");
+ 		atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(4, atom1.getX(), 0.00001);
+ 		assertEquals(3, atom1.getY(), 0.00001);
+ 		assertEquals(3, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(5, atom2.getX(), 0.00001);
+ 		assertEquals(4, atom2.getY(), 0.00001);
+ 		assertEquals(4, atom2.getZ(), 0.00001);
+	}
 
 	private static Atom getAtom(String name, double x, double y, double z) {
 		Atom a = new AtomImpl();
@@ -294,5 +324,53 @@ private static Matrix4d getSampleTransform(){
 		                                0.0,0.0,0.0,1.0});
 		return sample;
 	}
+	
+	private static Chain createDummyChain() {
+		Group g = new AminoAcidImpl();
+		Atom a = getAtom("CA", 1, 1, 1);
+		g.addAtom(a);
+		Group altLocG = new AminoAcidImpl();
+		Atom a2 = getAtom("CA", 2, 2, 2);
+		altLocG.addAtom(a2);
+		
+		g.addAltLoc(altLocG);
+		
+		Chain c = new ChainImpl();
+		c.addGroup(g);
+		return c;
+	}
+	
+	private static Structure createDummyStructure() {
+		Group g = new AminoAcidImpl();
+		Atom a = getAtom("CA", 1, 1, 1);
+		g.addAtom(a);
+		Group altLocG = new AminoAcidImpl();
+		Atom a2 = getAtom("CA", 2, 2, 2);
+		altLocG.addAtom(a2);
+		
+		g.addAltLoc(altLocG);
+		
+		Chain c1 = new ChainImpl();
+		c1.addGroup(g);
+		c1.setId("A");
+		
+		Group gc2 = new AminoAcidImpl();
+		Atom ac2 = getAtom("CA", 3, 3, 3);
+		gc2.addAtom(ac2);
+		Group altLocGc2 = new AminoAcidImpl();
+		Atom ac22 = getAtom("CA", 4, 4, 4);
+		altLocGc2.addAtom(ac22);
+		
+		gc2.addAltLoc(altLocGc2);
+		
+		Chain c2 = new ChainImpl();
+		c2.addGroup(gc2);
+		c2.setId("B");
+		
+		Structure s = new StructureImpl();
+		s.addChain(c1);
+		s.addChain(c2);
+		return s;
+	}
 
 }

From e0c031b62420d86c9a3657eab440326852660ec2 Mon Sep 17 00:00:00 2001
From: Jose Duarte <jose.m.duarte@gmail.com>
Date: Sat, 9 Dec 2017 07:51:52 -0800
Subject: [PATCH 4/4] Recursive transform for group

---
 .../src/main/java/org/biojava/nbio/structure/Calc.java    | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

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
index ce294db288..f68a4b8ed9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -542,9 +542,7 @@ public static final void transform(Group group, Matrix4d m) {
 			transform(atom, m);
 		}
 		for (Group altG : group.getAltLocs()) {
-			for (Atom atom : altG.getAtoms()) {
-				transform(atom, m);
-			}				
+			transform(altG, m);
 		}
 	}
 
@@ -606,9 +604,7 @@ public static final void translate(Group group, Vector3d v) {
 			translate(atom, v);
 		}
 		for (Group altG : group.getAltLocs()) {
-			for (Atom atom : altG.getAtoms()) {
-				translate(atom, v);
-			}				
+			translate(altG, v);
 		}
 	}