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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.
*
* @author Joel Freyss
*/
package com.actelion.research.chem.io.pdb.converter;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.Molecule;
import java.util.Set;
import java.util.TreeSet;
/**
* Class used to speed up the calculation of neighbours by creating a grid.
* Each atom is indexed according to its 3D coordinates.
*
*/
public class MoleculeGrid {
protected final StereoMolecule mol;
protected final double gridWidth;
protected final Coordinates min;
protected final Coordinates max;
protected final int[] gridSize = new int[3];
protected final Set[][][] grid;
public MoleculeGrid(StereoMolecule mol) {
this(mol, 1.1,new Coordinates(0.0,0.0,0.0));
}
/**
* Creates the Grid: Complexity O(nAtoms)
* @param mol
*/
@SuppressWarnings("unchecked")
public MoleculeGrid(StereoMolecule mol, double gridWidth, Coordinates extension) {
this.mol = mol;
this.gridWidth = gridWidth;
//1. Find the Molecule's bounds
Coordinates[] bounds = GeometryCalculator.getBounds(mol);
min = bounds[0];
max = bounds[1];
min.x -= extension.x;
min.y -= extension.y;
min.z -= extension.z;
max.x += extension.x;
max.y += extension.y;
max.z += extension.z;
//2. Creates the grid
gridSize[0] = (int)((max.x-min.x)/gridWidth)+1;
gridSize[1] = (int)((max.y-min.y)/gridWidth)+1;
gridSize[2] = (int)((max.z-min.z)/gridWidth)+1;
grid = new Set[Math.max(0, gridSize[0])][Math.max(0, gridSize[1])][Math.max(0, gridSize[2])];
//3. Put each atom in the grid
int atoms = mol.getAtoms();
for (int i = 0; i < atoms; i++) {
int x = (int)((mol.getAtomX(i)-min.x)/gridWidth);
int y = (int)((mol.getAtomY(i)-min.y)/gridWidth);
int z = (int)((mol.getAtomZ(i)-min.z)/gridWidth);
if(grid[x][y][z]==null) grid[x][y][z] = new TreeSet();
grid[x][y][z].add(i);
}
}
/**
* Gets a Set of all neigbouring atoms. This class ensures that at least
* all atoms within maxDist are returned (+more)
* @param c
* @param maxDist
* @return
*/
public Set getNeighbours(Coordinates c, double maxDist) {
int radius = (int)(maxDist / gridWidth) + 1;
int x = (int)((c.x-min.x)/gridWidth);
int y = (int)((c.y-min.y)/gridWidth);
int z = (int)((c.z-min.z)/gridWidth);
Set res = new TreeSet();
for (int i = Math.max(0, x-radius); i<= Math.min(gridSize[0]-1, x+radius); i++) {
for (int j = Math.max(0, y-radius); j<= Math.min(gridSize[1]-1, y+radius); j++) {
for (int k = Math.max(0, z-radius); k<= Math.min(gridSize[2]-1, z+radius); k++) {
// int dx = i-x;
// int dy = j-y;
// int dz = k-z;
// if(dx*dx+dy*dy+dz*dz>3+radius*radius) continue;
if(grid[i][j][k]!=null) res.addAll(grid[i][j][k]);
}
}
}
return res;
}
public Set getNeighbours(Coordinates c, double maxDist, boolean enforceDist) {
return getNeighbours(c, maxDist, enforceDist, -1);
}
/**
* Gets a Set of all neigbouring atoms. This class ensures that at least
* all atoms within maxDist are returned (+more)
* @param c
* @param maxDist
* @return
*/
public Set getNeighbours(Coordinates c, double maxDist, boolean enforceDist, int requiredFlags) {
int radius = (int)(maxDist / gridWidth) + 1;
int x = (int)((c.x-min.x)/gridWidth);
int y = (int)((c.y-min.y)/gridWidth);
int z = (int)((c.z-min.z)/gridWidth);
Set res = new TreeSet();
for (int i = Math.max(0, x-radius); i<= Math.min(gridSize[0]-1, x+radius); i++) {
for (int j = Math.max(0, y-radius); j<= Math.min(gridSize[1]-1, y+radius); j++) {
for (int k = Math.max(0, z-radius); k<= Math.min(gridSize[2]-1, z+radius); k++) {
if(grid[i][j][k]!=null) {
if(enforceDist) {
for(int elt: grid[i][j][k]) {
// TODO check whether this was used somewhere
// if(requiredFlags>=0 && !mol.isAtomFlag(elt, requiredFlags)) continue;
if(mol.getCoordinates(elt).distSquareTo(c)>maxDist*maxDist ) continue;
res.add(elt);
}
} else {
res.addAll(grid[i][j][k]);
}
}
}
}
}
return res;
}
public boolean hasNeighbours(Coordinates c, double maxDist) {
int radius = (int)(maxDist / gridWidth) + 1;
int x = (int)((c.x-min.x)/gridWidth);
int y = (int)((c.y-min.y)/gridWidth);
int z = (int)((c.z-min.z)/gridWidth);
for (int i = Math.max(0, x-radius); i<= Math.min(gridSize[0]-1, x+radius); i++) {
for (int j = Math.max(0, y-radius); j<= Math.min(gridSize[1]-1, y+radius); j++) {
for (int k = Math.max(0, z-radius); k<= Math.min(gridSize[2]-1, z+radius); k++) {
if(grid[i][j][k]!=null) {
for(int a : grid[i][j][k]) {
if(mol.getCoordinates(a).distSquareTo(c)<=maxDist*maxDist ) {
return true;
}
}
}
}
}
}
return false;
}
/**
* Gets a Set of all neigbouring atoms. This class ensures that at least
* all atoms within maxDist are returned (+more)
* @param bounds
* @param maxDist
* @return
*/
public Set getNeighbours(Coordinates[] bounds, double maxDist) {
int radius = (int)(maxDist / gridWidth) + 1;
int x1 = (int)((bounds[0].x-min.x)/gridWidth);
int y1 = (int)((bounds[0].y-min.y)/gridWidth);
int z1 = (int)((bounds[0].z-min.z)/gridWidth);
int x2 = (int)((bounds[1].x-min.x)/gridWidth);
int y2 = (int)((bounds[1].y-min.y)/gridWidth);
int z2 = (int)((bounds[1].z-min.z)/gridWidth);
int xMin = Math.min(x1, x2);
int xMax = Math.max(x1, x2);
int yMin = Math.min(y1, y2);
int yMax = Math.max(y1, y2);
int zMin = Math.min(z1, z2);
int zMax = Math.max(z1, z2);
Set res = new TreeSet();
for (int i = Math.max(0, xMin-radius); i<= Math.min(gridSize[0]-1, xMax+radius); i++) {
for (int j = Math.max(0, yMin-radius); j<= Math.min(gridSize[1]-1, yMax+radius); j++) {
for (int k = Math.max(0, zMin-radius); k<= Math.min(gridSize[2]-1, zMax+radius); k++) {
//int dx = i-x;
//int dy = j-y;
//int dz = k-z;
//if(dx*dx+dy*dy+dz*dz>gridWidth+radius*radius) continue;
if(grid[i][j][k]!=null) res.addAll(grid[i][j][k]);
}
}
}
return res;
}
/**
* Returns the closest neighbour. maxDist has to be given to take advantage of the speed
* @param c
* @param maxDist
* @return
*/
public int getClosestNeighbour(Coordinates c, double maxDist) {
Set set = getNeighbours(c, maxDist);
int closest = -1;
double bestDist = maxDist;
for (int a : set) {
double d = mol.getCoordinates(a).distanceSquared(c);
if(d();
if(grid[x][y][z].contains(i))
continue;
else {
removeAtom(i);
grid[x][y][z].add(i);
}
}
}
private void removeAtom(int index) {
int l = Math.max(0, gridSize[0]);
int m = Math.max(0, gridSize[1]);
int n = Math.max(0, gridSize[2]);
for(int i=0;i getNeighbours(Molecule mol, int atom, double maxDist) {
return getNeighbours(mol, atom, maxDist, false);
}
public Set getNeighbours(Molecule mol, int atom, double maxDist, boolean enforceDist) {
Set res = getNeighbours(mol.getCoordinates(atom), maxDist, enforceDist);
res.remove(Integer.valueOf(atom));
return res;
}
public int[] getGridCoordinates(Coordinates c) {
int[] gridCoords = new int[3];
gridCoords[0] = (int)((c.x-min.x)/gridWidth);
gridCoords[1] = (int)((c.y-min.y)/gridWidth);
gridCoords[2] = (int)((c.z-min.z)/gridWidth);
return gridCoords;
}
public Coordinates getCartCoordinates(int[] gridCoords) {
int gridX = gridCoords[0];
int gridY = gridCoords[1];
int gridZ = gridCoords[2];
Coordinates cartCoords = new Coordinates();
cartCoords.x = min.x + gridX*gridWidth;
cartCoords.y = min.y + gridY*gridWidth;
cartCoords.z = min.z + gridZ*gridWidth;
return cartCoords;
}
public int[] getGridSize() {
return gridSize;
}
}