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ASA calculation should be done per model #1107

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Merged
josemduarte merged 3 commits into from
Feb 27, 2025
Merged

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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23 changes: 20 additions & 3 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 @@ -126,16 +126,17 @@ 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) {
this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms);
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;
Expand All @@ -151,6 +152,22 @@ public AsaCalculator(Structure structure, double probe, int nSpherePoints, int n
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
* @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
* NACCESS' -h option
*/
public AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms) {
this(structure, probe, nSpherePoints, nThreads, hetAtoms, 0);
}

/**
* Constructs a new AsaCalculator. Subsequently call {@link #calculateAsas()}
* or {@link #getGroupAsas()} to calculate the ASAs.
Expand Down