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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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Fix and unit test for #715
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@josemduarte
josemduarte committed Dec 7, 2017
commit bc9011a2d048ed0a40e44ff4cecd82796ac01eae
5 changes: 5 additions & 0 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 @@ -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);
}
}
}
}

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47 changes: 47 additions & 0 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
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Expand Up @@ -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();
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