Merge pull request #1107 from josemduarte/asafix-multimodel

josemduarte · web-flow · commit e0e7904daa04 · 2025-02-27T09:41:12.000-08:00
ASA calculation should be done per model
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -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;
@@ -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.
