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Fixing issue with Calc.transform(Chain,Matrix4d) #716

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Merged
josemduarte merged 4 commits into from
Dec 12, 2017
Merged

Fixing issue with Calc.transform(Chain,Matrix4d) #716

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bc9011a
Fix and unit test for #715
josemduarte Dec 7, 2017
3a1ad26
Fixing also Calc.transform(Structure,Matrix4d)
josemduarte Dec 8, 2017
8a7e22c
Fixes for translate functions, similar to #715
josemduarte Dec 8, 2017
e0c031b
Recursive transform for group
josemduarte Dec 9, 2017
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46 changes: 19 additions & 27 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
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Original file line number Diff line number Diff line change
Expand Up @@ -538,12 +538,11 @@ 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()) {
transform(altG, m);
}
}

Expand All @@ -556,12 +555,10 @@ 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);
}
}
}

Expand All @@ -576,9 +573,7 @@ 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);
}
transform(g, m);
}
}

Expand All @@ -604,12 +599,12 @@ 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()) {
translate(altG, v);
}
}

Expand All @@ -623,9 +618,7 @@ 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);
}
}

Expand All @@ -637,12 +630,11 @@ 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);
}
}
}

Expand Down
200 changes: 199 additions & 1 deletion biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -157,14 +158,163 @@ public void testVecmathTransformation() {

assertEquals(expected, actual);
}

/**
* Issue https://github.com/biojava/biojava/issues/715
*/
@Test
public void testChainTransform() {

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);

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);


}

private static Atom getAtom(double x, double y, double z) {
/**
* Issue https://github.com/biojava/biojava/issues/715
*/
@Test
public void testStructureTransform() {

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);

// 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);


}

@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();
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(){

Expand All @@ -174,5 +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;
}

}