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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
package com.actelion.research.chem;
import java.io.Serializable;
import java.text.DecimalFormat;
import java.util.Random;
/**
* Class to encapsulate 3D coordinates
*/
public final class Coordinates implements Serializable, Comparable {
public double x,y,z;
public Coordinates() {}
public Coordinates(Coordinates c) {
this(c.x, c.y, c.z);
}
public Coordinates(double x, double y, double z) {
this.x = x;
this.y = y;
this.z = z;
}
/**
* Copies x,y,z from c to this
* @param c
* @return this after copying c
*/
public Coordinates set(Coordinates c) {
set(c.x, c.y, c.z);
return this;
}
public void set(double x, double y, double z) {
this.x = x;
this.y = y;
this.z = z;
}
public double getLength() {
return dist();
}
public final double dist() {
return Math.sqrt(distSq());
}
public final double distSq() {
return x*x + y*y + z*z;
}
public final double distanceSquared(Coordinates c) {
return (c.x-x)*(c.x-x) + (c.y-y)*(c.y-y) + (c.z-z)*(c.z-z);
}
public final double distSquareTo(Coordinates c) {
return distanceSquared(c);
}
public final double distance(Coordinates c) {
return Math.sqrt(distanceSquared(c));
}
public final double dot(Coordinates c) {
return x*c.x + y*c.y + z*c.z;
}
public final Coordinates cross(Coordinates c) {
return new Coordinates(y*c.z-z*c.y, -(x*c.z-z*c.x), x*c.y-y*c.x);
}
/**
* Gets the angle formed between the 2 vectors ([0,PI])
* @param c
* @return angle in radian
*/
public final double getAngle(Coordinates c) {
double d1 = distSq();
double d2 = c.distSq();
if(d1==0 || d2==0) return 0;
double d = dot(c) / Math.sqrt(d1*d2);
if(d>=1) return 0;
if(d<=-1) return Math.PI;
return Math.acos(d);
}
/**
* Calculates the angle of the line from this location to c
* projected into the x/y plane. With Y facing upwards and X right,
* if the line points in Y direction, ten angle is 0.0 increasing
* in clockwise direction.
* @param c
* @return -PI < angle < PI
*/
public double getAngleXY(Coordinates c) {
double dx = c.x - x;
double dy = c.y - y;
if (dy == 0.0)
return (dx > 0.0) ? Math.PI/2.0 : -Math.PI/2.0;
double angle = Math.atan(dx/dy);
if (dy < 0.0)
return (dx < 0.0) ? angle - Math.PI : angle + Math.PI;
return angle;
}
public final double getDihedral(Coordinates c2, Coordinates c3, Coordinates c4) {
return getDihedral(this, c2, c3, c4);
}
public final Coordinates subC(Coordinates c) {
return new Coordinates(x-c.x, y-c.y, z-c.z);
}
public final Coordinates addC(Coordinates c) {
return new Coordinates(x+c.x, y+c.y, z+c.z);
}
public final Coordinates scaleC(double scale) {
return new Coordinates(x*scale, y*scale, z*scale);
}
/**
* @param c
* @return this after subtracting c
*/
public final Coordinates sub(Coordinates c) {
x-=c.x;
y-=c.y;
z-=c.z;
return this;
}
/**
* @param c
* @return this after subtracting c
*/
public final Coordinates add(Coordinates c) {
x+=c.x;
y+=c.y;
z+=c.z;
return this;
}
public void add(double dx, double dy, double dz) {
x += dx;
y += dy;
z += dz;
}
/**
* @param scale
* @return this after scaling this
*/
public final Coordinates scale(double scale) {
x*=scale;
y*=scale;
z*=scale;
return this;
}
public final void negate() {
x=-x;
y=-y;
z=-z;
}
/**
* @param m
* @return this after rotating it with rotation matrix m
*/
public Coordinates rotate(double[][] m) {
double x0 = x;
double y0 = y;
double z0 = z;
x = x0*m[0][0]+y0*m[1][0]+z0*m[2][0];
y = x0*m[0][1]+y0*m[1][1]+z0*m[2][1];
z = x0*m[0][2]+y0*m[1][2]+z0*m[2][2];
return this;
}
/**
* @param m
* @return new Coordinates created from this point rotated by rotation matrix m
*/
public Coordinates rotateC(double[][] m) {
return new Coordinates(x*m[0][0]+y*m[1][0]+z*m[2][0],
x*m[0][1]+y*m[1][1]+z*m[2][1],
x*m[0][2]+y*m[1][2]+z*m[2][2]);
}
public final Coordinates rotate(Coordinates normal, double theta) {
if(Math.abs(normal.x*normal.x+normal.y*normal.y+normal.z*normal.z-1)>1E-6) throw new IllegalArgumentException("normal needs to a unit vector: "+normal);
double x = normal.x;
double y = normal.y;
double z = normal.z;
double c = Math.cos(theta);
double s = Math.sin(theta);
double t = 1-c;
Coordinates opp = new Coordinates(
(t*x*x+c)*this.x + (t*x*y+s*z)*this.y + (t*x*z-s*y)*this.z,
(t*x*y-s*z)*this.x + (t*y*y+c)*this.y + (t*y*z+s*x)*this.z,
(t*x*z+s*y)*this.x + (t*z*y-s*x)*this.y + (t*z*z+c)*this.z
);
return opp;
}
/**
* @return new Coordinates with a copy of this scaled to length=1.0
*/
public final Coordinates unitC() {
double d = dist();
if(d==0) {
System.err.println("Cannot call unitC() on a null vector");
// Thread.dumpStack();
return new Coordinates(1,0,0);
}
return new Coordinates(x/d, y/d, z/d);
}
/**
* @return this after scaling it to length=1.0
*/
public final Coordinates unit() {
double d = dist();
if(d==0) {
System.err.println("Cannot call unit() on a null vector. Returned (1,0,0)");
// Thread.dumpStack();
x = 1;
y = 0;
z = 0;
// throw new IllegalArgumentException("Cannot call unit() on a null vector.");
return this;
}
x/=d;
y/=d;
z/=d;
return this;
}
/**
* Calculates the center point between this and c and sets this to the center point.
* @param c
* @return this after updating it to the center position
*/
public Coordinates center(Coordinates c) {
x = (x + c.x) / 2.0;
y = (y + c.y) / 2.0;
z = (z + c.z) / 2.0;
return this;
}
/**
* Updates this to contains the center between c1 and c2.
* @param c1
* @param c2
*/
public void center(Coordinates c1, Coordinates c2) {
x = (c1.x + c2.x) / 2.0;
y = (c1.y + c2.y) / 2.0;
z = (c1.z + c2.z) / 2.0;
}
/**
* Updates this to contain a point on the straight line through c1 and c2.
* @param c1
* @param c2
* @param f location on line 0.0 -> c1, 1.0 -> c2
* @return this after updating to be a point on the line
*/
public Coordinates between(Coordinates c1, Coordinates c2, double f) {
x = c1.x + f * (c2.x - c1.x);
y = c1.y + f * (c2.y - c1.y);
z = c1.z + f * (c2.z - c1.z);
return this;
}
public final boolean insideBounds(Coordinates[] bounds) {
return bounds!=null && bounds[0].x<=x && x<=bounds[1].x && bounds[0].y<=y && y<=bounds[1].y && bounds[0].z<=z && z<=bounds[1].z;
}
@Override
public final String toString() {
DecimalFormat df = new DecimalFormat("0.00");
return "[" + df.format(x) + ", " + df.format(y) + ", " + df.format(z) + "]";
}
public final String toStringSpaceDelimited() {
DecimalFormat df = new DecimalFormat("0.00");
return df.format(x) + " " + df.format(y) + " " + df.format(z);
}
@Override
public final boolean equals(Object o) {
if(o==null || !(o instanceof Coordinates)) return false;
Coordinates c = (Coordinates) o;
return Math.abs(c.x-x) + Math.abs(c.y-y) + Math.abs(c.z-z) < 1E-6;
}
public final boolean isNaN() {
return Double.isNaN(x) || Double.isNaN(y) || Double.isNaN(z);
}
public final Coordinates min(Coordinates c) {
return new Coordinates(Math.min(x, c.x), Math.min(y, c.y), Math.min(z, c.z));
}
public final Coordinates max(Coordinates c) {
return new Coordinates(Math.max(x, c.x), Math.max(y, c.y), Math.max(z, c.z));
}
public double cosAngle(Coordinates c) {
double d = dist() * c.dist();
if(d<=0) return 0;
return dot(c) / d;
}
/////////////////// UTILITITIES ///////////////////////////////////////
public static final Coordinates min(Coordinates[] c) {
Coordinates min = new Coordinates(c[0]);
for (int i = 1; i < c.length; i++) {
min.x = Math.min(c[i].x, min.x);
min.y = Math.min(c[i].y, min.y);
min.z = Math.min(c[i].z, min.z);
}
return min;
}
public static final Coordinates max(Coordinates[] c) {
Coordinates max = new Coordinates(c[0]);
for (int i = 1; i < c.length; i++) {
max.x = Math.max(c[i].x, max.x);
max.y = Math.max(c[i].y, max.y);
max.z = Math.max(c[i].z, max.z);
}
return max;
}
public static final Coordinates createBarycenter(Coordinates... coords) {
if(coords==null) throw new IllegalArgumentException("The coordinates are null");
Coordinates res = new Coordinates();
for(int i=0; ic1 and c3->c4 point in the same direction.
* If the projection of vector c2-c1 is rotated in clockwise direction,
* the angle increases, i.e. has a positive value.
* http://en.wikipedia.org/wiki/Dihedral_angle
* @param c1
* @param c2
* @param c3
* @param c4
* @return torsion in the range: -pi <= torsion <= pi
*/
public static final double getDihedral(Coordinates c1, Coordinates c2, Coordinates c3, Coordinates c4) {
// changed from above, because it seems a little more efficient; TLS 2-Nov-2016
Coordinates v1 = c2.subC(c1);
Coordinates v2 = c3.subC(c2);
Coordinates v3 = c4.subC(c3);
Coordinates n1 = v1.cross(v2);
Coordinates n2 = v2.cross(v3);
return -Math.atan2(v2.getLength() * v1.dot(n2), n1.dot(n2));
}
//@Override Annotation incompatible with 1.5
public int compareTo(Coordinates o) {
if(x!=o.x) return x0? Math.sqrt(sum/l): 0;
}
} © 2015 - 2025 Weber Informatics LLC | Privacy Policy