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Improved ASA calculation performance #820

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Merged
sbliven merged 11 commits into from
Jan 3, 2019
Merged

Improved ASA calculation performance #820

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c213a7d
Neighbor indices now uses spatial hashing
josemduarte Jan 2, 2019
3b99afd
Supporting neighbors with and without SH
josemduarte Jan 2, 2019
a84609b
A test, demoing that SH actually performs much worse
josemduarte Jan 2, 2019
1100299
Doing all neighbor indices upfront
josemduarte Jan 2, 2019
ddeb759
Efficient neighbor index finding with SH
josemduarte Jan 2, 2019
ede5cee
Tidying up
josemduarte Jan 2, 2019
041482d
Logging, docs and some minimal optimization
josemduarte Jan 2, 2019
f42a0fa
Logging and cleanup
josemduarte Jan 2, 2019
373a407
Docs
josemduarte Jan 2, 2019
b674136
Docs
josemduarte Jan 3, 2019
8fb10fd
Should be private
josemduarte Jan 3, 2019
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Supporting neighbors with and without SH
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@josemduarte
josemduarte committed Jan 2, 2019
commit 3b99afd899a668036e5a6f4eccf1a673a9198da0
19 changes: 18 additions & 1 deletion 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 @@ -104,6 +104,8 @@ public void run() {
private double cons;
private List<Contact> contacts;

private boolean useSpatialHashingForNeighbors;

/**
* Constructs a new AsaCalculator. Subsequently call {@link #calculateAsas()}
* or {@link #getGroupAsas()} to calculate the ASAs
Expand All @@ -122,6 +124,8 @@ public AsaCalculator(Structure structure, double probe, int nSpherePoints, int n
this.probe = probe;
this.nThreads = nThreads;

this.useSpatialHashingForNeighbors = true;

// initialising the radii by looking them up through AtomRadii
radii = new double[atomCoords.length];
for (int i=0;i<atomCoords.length;i++) {
Expand Down Expand Up @@ -150,6 +154,8 @@ public AsaCalculator(Atom[] atoms, double probe, int nSpherePoints, int nThreads
this.probe = probe;
this.nThreads = nThreads;

this.useSpatialHashingForNeighbors = true;

for (Atom atom:atoms) {
if (atom.getElement()==Element.H)
throw new IllegalArgumentException("Can't calculate ASA for an array that contains Hydrogen atoms ");
Expand Down Expand Up @@ -190,6 +196,8 @@ public AsaCalculator(Point3d[] atomCoords, double probe, int nSpherePoints, int
this.probe = probe;
this.nThreads = nThreads;

this.useSpatialHashingForNeighbors = true;

// initialising the radii to the given radius for all atoms
radii = new double[atomCoords.length];
for (int i=0;i<atomCoords.length;i++) {
Expand Down Expand Up @@ -299,6 +307,10 @@ public double[] calculateAsas() {
return asas;
}

public void setUseSpatialHashingForNeighbors(boolean useSpatialHashingForNeighbors) {
this.useSpatialHashingForNeighbors = useSpatialHashingForNeighbors;
}

/**
* Returns list of 3d coordinates of points on a sphere using the
* Golden Section Spiral algorithm.
Expand Down Expand Up @@ -408,7 +420,12 @@ private static double maxValue(double[] array) {

private double calcSingleAsa(int i) {
Point3d atom_i = atomCoords[i];
Integer[] neighbor_indices = findNeighborIndicesSpatialHashing(i);
Integer[] neighbor_indices;
if (useSpatialHashingForNeighbors) {
neighbor_indices = findNeighborIndicesSpatialHashing(i);
} else {
neighbor_indices = findNeighborIndices(i);
}
int n_neighbor = neighbor_indices.length;
int j_closest_neighbor = 0;
double radius = probe + radii[i];
Expand Down