package org.biojava.nbio.structure.geometry;
import javax.vecmath.Matrix4d;
import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;
import org.biojava.nbio.structure.jama.Matrix;
/**
* Utility operations on Point3d.
*
* @author Aleix Lafita
* @since 5.0.0
*
*/
public class CalcPoint {
/** Prevent instantiation */
private CalcPoint() {
}
/**
* Center a cloud of points. This means subtracting the {@lin
* #centroid(Point3d[])} of the cloud to each point.
*
* @param x
* array of points. Point objects will be modified
*/
public static void center(Point3d[] x) {
Point3d center = centroid(x);
center.negate();
translate(new Vector3d(center), x);
}
/**
* Calculate the centroid of the point cloud.
*
* @param x
* array of points. Point objects will not be modified
* @return centroid as Point3d
*/
public static Point3d centroid(Point3d[] x) {
Point3d center = new Point3d();
for (Point3d p : x) {
center.add(p);
}
center.scale(1.0 / x.length);
return center;
}
/**
* Transform all points with a 4x4 transformation matrix.
*
* @param rotTrans
* 4x4 transformation matrix
* @param x
* array of points. Point objects will be modified
*/
public static void transform(Matrix4d rotTrans, Point3d[] x) {
for (Point3d p : x) {
rotTrans.transform(p);
}
}
/**
* Translate all points with a translation vector.
*
* @param trans
* the translation vector to apply
* @param x
* array of points. Point objects will be modified
*/
public static void translate(Vector3d trans, Point3d[] x) {
for (Point3d p : x) {
p.add(trans);
}
}
/**
* Clone an array of points.
*
* @param x
* original array of points. Point objects will not be modified
* @return new array of points, identical clone of x
*/
public static Point3d[] clonePoint3dArray(Point3d[] x) {
Point3d[] clone = new Point3d[x.length];
for (int i = 0; i < x.length; i++) {
clone[i] = new Point3d(x[i]);
}
return clone;
}
/*
* Peter can you document this method? TODO
*
* @param moved
* @param fixed
* @return
*/
public static Matrix formMatrix(Point3d[] a, Point3d[] b) {
double xx = 0.0, xy = 0.0, xz = 0.0;
double yx = 0.0, yy = 0.0, yz = 0.0;
double zx = 0.0, zy = 0.0, zz = 0.0;
for (int i = 0; i < a.length; i++) {
xx += a[i].x * b[i].x;
xy += a[i].x * b[i].y;
xz += a[i].x * b[i].z;
yx += a[i].y * b[i].x;
yy += a[i].y * b[i].y;
yz += a[i].y * b[i].z;
zx += a[i].z * b[i].x;
zy += a[i].z * b[i].y;
zz += a[i].z * b[i].z;
}
double[][] f = new double[4][4];
f[0][0] = xx + yy + zz;
f[0][1] = zy - yz;
f[1][0] = f[0][1];
f[1][1] = xx - yy - zz;
f[0][2] = xz - zx;
f[2][0] = f[0][2];
f[1][2] = xy + yx;
f[2][1] = f[1][2];
f[2][2] = yy - zz - xx;
f[0][3] = yx - xy;
f[3][0] = f[0][3];
f[1][3] = zx + xz;
f[3][1] = f[1][3];
f[2][3] = yz + zy;
f[3][2] = f[2][3];
f[3][3] = zz - xx - yy;
return new Matrix(f);
}
/**
* Returns the TM-Score for two superimposed sets of coordinates Yang Zhang
* and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics
* 57:702–710 (2004)
*
* @param x
* coordinate set 1
* @param y
* coordinate set 2
* @param lengthNative
* total length of native sequence
* @return
*/
public static double TMScore(Point3d[] x, Point3d[] y, int lengthNative) {
if (x.length != y.length) {
throw new IllegalArgumentException(
"Point arrays are not of the same length.");
}
double d0 = 1.24 * Math.cbrt(x.length - 15.0) - 1.8;
double d0Sq = d0 * d0;
double sum = 0;
for (int i = 0; i < x.length; i++) {
sum += 1.0 / (1.0 + x[i].distanceSquared(y[i]) / d0Sq);
}
return sum / lengthNative;
}
/*
* Needs documentation!
*
* @param x
*
* @param y
*
* @return
*/
public static double GTSlikeScore(Point3d[] x, Point3d[] y) {
if (x.length != y.length) {
throw new IllegalArgumentException(
"Point arrays are not of the same length.");
}
int contacts = 0;
for (Point3d px : x) {
double minDist = Double.MAX_VALUE;
for (Point3d py : y) {
minDist = Math.min(minDist, px.distanceSquared(py));
}
if (minDist > 64)
continue;
contacts++;
if (minDist > 16)
continue;
contacts++;
if (minDist > 4)
continue;
contacts++;
if (minDist > 1)
continue;
contacts++;
}
return contacts * 25.0 / x.length;
}
/**
* Calculate the RMSD of two point arrays, already superposed.
*
* @param x
* array of points superposed to y
* @param y
* array of points superposed to x
* @return RMSD
*/
public static double rmsd(Point3d[] x, Point3d[] y) {
if (x.length != y.length) {
throw new IllegalArgumentException(
"Point arrays are not of the same length.");
}
double sum = 0.0;
for (int i = 0; i < x.length; i++) {
sum += x[i].distanceSquared(y[i]);
}
return Math.sqrt(sum / x.length);
}
/*
* Needs documentation!
*
* @param x
*
* @param y
*
* @return
*/
public static double rmsdMin(Point3d[] x, Point3d[] y) {
if (x.length != y.length) {
throw new IllegalArgumentException(
"Point arrays are not of the same length.");
}
double sum = 0.0;
for (int i = 0; i < x.length; i++) {
double minDist = Double.MAX_VALUE;
for (int j = 0; j < y.length; j++) {
minDist = Math.min(minDist, x[i].distanceSquared(y[j]));
}
sum += minDist;
}
return Math.sqrt(sum / x.length);
}
/*
* Needs documentation!
*
* @param x
*
* @param y
*
* @param maxDistance
*
* @return
*/
public static int contacts(Point3d[] x, Point3d[] y, double maxDistance) {
int contacts = 0;
for (int i = 0; i < x.length; i++) {
double minDist = Double.MAX_VALUE;
for (int j = 0; j < y.length; j++) {
minDist = Math.min(minDist, x[i].distanceSquared(y[j]));
}
if (minDist < maxDistance * maxDistance) {
contacts++;
}
}
return contacts;
}
}