com.actelion.research.chem.io.pdb.converter.MoleculeGrid Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Show all versions of openchemlib Show documentation
Open Source Chemistry Library
/*
* Copyright 2014 Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
*
* This file is part of DataWarrior.
*
* DataWarrior is free software: you can redistribute it and/or modify it under the terms of the
* GNU General Public License as published by the Free Software Foundation, either version 3 of
* the License, or (at your option) any later version.
*
* DataWarrior is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
* without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
* See the GNU General Public License for more details.
* You should have received a copy of the GNU General Public License along with DataWarrior.
* If not, see http://www.gnu.org/licenses/.
*
* @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;
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy