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ASA calculation should be done per model #1107

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josemduarte merged 3 commits into from
Feb 27, 2025
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ASA calculation should be done per model #1107

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c45c3dd
Bugfix: ASA calculation was by default using all models. Now it will …
josemduarte Feb 21, 2025
324319e
Fix: first model is model index 0
josemduarte Feb 22, 2025
a5b46ab
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josemduarte Feb 22, 2025
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Bugfix: ASA calculation was by default using all models. Now it will … 
…use model 1 by default. Added new constructor to choose model.
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@josemduarte
josemduarte committed Feb 21, 2025
commit c45c3dd05beaed3f214b991526f713d9090b5e1f
34 changes: 32 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
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Expand Up @@ -126,7 +126,37 @@ static class IndexAndDistance {
* Constructs a new AsaCalculator. Subsequently call {@link #calculateAsas()}
* or {@link #getGroupAsas()} to calculate the ASAs
* Only non-Hydrogen atoms are considered in the calculation.
* @param structure the structure, all non-H atoms will be used
* @param structure the structure, all non-H atoms of given model number will be used
* @param probe the probe size
* @param nSpherePoints the number of points to be used in generating the spherical
* dot-density, the more points the more accurate (and slower) calculation
* @param nThreads the number of parallel threads to use for the calculation
* @param hetAtoms if true HET residues are considered, if false they aren't, equivalent to
* @param modelNr the model number from which we want atoms extracted
* NACCESS' -h option
*/
public AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms, int modelNr) {
this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms, modelNr);
this.atomCoords = Calc.atomsToPoints(atoms);
this.probe = probe;
this.nThreads = nThreads;

this.useSpatialHashingForNeighbors = DEFAULT_USE_SPATIAL_HASHING;

// initialising the radii by looking them up through AtomRadii
radii = new double[atomCoords.length];
for (int i=0;i<atomCoords.length;i++) {
radii[i] = getRadius(atoms[i]);
}

initSpherePoints(nSpherePoints);
}

/**
* Constructs a new AsaCalculator. Subsequently call {@link #calculateAsas()}
* or {@link #getGroupAsas()} to calculate the ASAs
* Only non-Hydrogen atoms are considered in the calculation.
* @param structure the structure, all non-H atoms of model 1 will be used
* @param probe the probe size
* @param nSpherePoints the number of points to be used in generating the spherical
* dot-density, the more points the more accurate (and slower) calculation
Expand All @@ -135,7 +165,7 @@ static class IndexAndDistance {
* NACCESS' -h option
*/
public AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms) {
this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms);
this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms, 1);
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@sbittrich sbittrich Feb 22, 2025

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Delegating to the new constructor makes this easier to maintain.

Suggested change
this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms, 1);
this(structure, probe, nSpherePoints, nThreads, hetAtoms, 1);

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@josemduarte josemduarte Feb 22, 2025

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Indeed, thanks. Now pushed

this.atomCoords = Calc.atomsToPoints(atoms);
this.probe = probe;
this.nThreads = nThreads;
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