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Bugfixes for ASA calculation #824

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Merged
josemduarte merged 4 commits into from
Jan 20, 2019
Merged

Bugfixes for ASA calculation #824

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9b13a29
Fixing no neighbor issue and a test
josemduarte Jan 17, 2019
2cbabae
Bugfix: case of 0-length atoms array. Also implemented suggestion fro…
josemduarte Jan 17, 2019
3c97b85
New unit test
josemduarte Jan 18, 2019
8340928
Converting to unit test
josemduarte Jan 18, 2019
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24 changes: 13 additions & 11 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -442,6 +442,13 @@ int[][] findNeighborIndicesSpatialHashing() {
nbsIndices[entry.getKey()] = indicesArray;
}

// important: some atoms might have no neighbors at all: we need to initialise to empty arrays
for (int i=0; i<nbsIndices.length; i++) {
if (nbsIndices[i] == null) {
nbsIndices[i] = new int[0];
}
}

return nbsIndices;
}

Expand All @@ -450,24 +457,19 @@ Point3d[] getAtomCoords() {
}

private List<Contact> calcContacts() {
double maxRadius = maxValue(radii);
if (atomCoords.length == 0)
return new ArrayList<>();
double maxRadius = 0;
OptionalDouble optionalDouble = Arrays.stream(radii).max();
if (optionalDouble.isPresent())
maxRadius = optionalDouble.getAsDouble();
double cutoff = maxRadius + maxRadius + probe + probe;
logger.debug("Max radius is {}, cutoff is {}", maxRadius, cutoff);
Grid grid = new Grid(cutoff);
grid.addCoords(atomCoords);
return grid.getIndicesContacts();
}

private static double maxValue(double[] array) {
double max = array[0];
for (int i = 0; i < array.length; i++) {
if (array[i] > max) {
max = array[i];
}
}
return max;
}

private double calcSingleAsa(int i) {
Point3d atom_i = atomCoords[i];

Expand Down
80 changes: 79 additions & 1 deletion biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,14 @@
*/
package org.biojava.nbio.structure.asa;

import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.AminoAcidImpl;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.AtomImpl;
import org.biojava.nbio.structure.Element;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIO;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
import static org.junit.Assert.*;
Expand Down Expand Up @@ -180,4 +187,75 @@ public void testPerformance() throws StructureException, IOException {
assertEquals(withoutSH, withSH, 0.000001);

}

@Test
public void testNoNeighborsIssue() {

Atom[] atoms = {
getAtom(1.0, 1.0, 1.0),
getAtom(10.0, 1.0, 1.0),
getAtom(13.0, 1.0, 1.0)
};

AsaCalculator asaCalc = new AsaCalculator(atoms,
AsaCalculator.DEFAULT_PROBE_SIZE,
1000, 1);

int[][] allNbsSh = asaCalc.findNeighborIndicesSpatialHashing();

int[][] allNbs = asaCalc.findNeighborIndices();

assertEquals(3, allNbs.length);
assertEquals(3, allNbsSh.length);

for (int indexToTest =0; indexToTest < asaCalc.getAtomCoords().length; indexToTest++) {
int[] nbsSh = allNbsSh[indexToTest];
int[] nbs = allNbs[indexToTest];

List<Integer> listOfMatchingIndices = new ArrayList<>();
for (int i = 0; i < nbsSh.length; i++) {
for (int j = 0; j < nbs.length; j++) {
if (nbs[j] == nbsSh[i]) {
listOfMatchingIndices.add(j);
break;
}
}
}

assertEquals(nbs.length, nbsSh.length);

assertEquals(nbs.length, listOfMatchingIndices.size());
}

// first atom should have no neighbors
assertEquals(0, allNbsSh[0].length);
}

private Atom getAtom(double x, double y, double z) {
Atom atom = new AtomImpl();
AminoAcidImpl g = new AminoAcidImpl();
g.setAminoType('A');
atom.setGroup(g);
atom.setName("CA");
atom.setElement(Element.C);
atom.setX(x);
atom.setY(y);
atom.setZ(z);
return atom;
}

@Test
public void testNoAtomsAsaCalc() {

// in case of no atoms at all, the calculation should not fail and return an empty array
Atom[] atoms = new Atom[0];

AsaCalculator asaCalc = new AsaCalculator(atoms,
AsaCalculator.DEFAULT_PROBE_SIZE,
1000, 1);
double[] asas = asaCalc.calculateAsas();
assertNotNull(asas);
assertEquals(0, asas.length);

}
}