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The protein structure modules of BioJava.
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.contact;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import javax.vecmath.Point3d;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Calc;
/**
* A grid to be used for calculating atom contacts through a spatial hashing algorithm.
*
* The grid is composed of cells of size of the cutoff so that the distances that need to be calculated
* are reduced to those within each cell and to the neighbouring cells.
*
* Usage, for generic 3D points:
*
* Point3d[] points = ...;
* Grid grid = new Grid(8.0);
* grid.addCoords(points);
* List<Contact> contacts = getIndicesContacts();
*
* Usage, for atoms:
*
* Atom[] atoms = ...;
* Grid grid = new Grid(8.0);
* grid.addCoords(atoms);
* AtomContactSet contacts = getAtomContacts();
*
*
* @author Jose Duarte
*
*/
public class Grid {
/**
* The scale: we use units of hundredths of Angstroms (thus cutoffs can be specified with a maximum precision of 0.01A)
*/
private static final int SCALE=100;
private GridCell[][][] cells;
private double cutoff;
private int cellSize;
private Point3d[] iAtoms;
private Point3d[] jAtoms;
private Atom[] iAtomObjects;
private Atom[] jAtomObjects;
// the bounds in int grid coordinates
private int[] bounds;
// the i and j bounding boxes in original double coordinates
private BoundingBox ibounds;
private BoundingBox jbounds;
private boolean noOverlap; // if the 2 sets of atoms are found not to overlap then this is set to true
/**
* Creates a Grid, the cutoff is in the same units as the coordinates
* (Angstroms if they are atom coordinates) and can
* be specified to a precision of 0.01.
* @param cutoff
*/
public Grid(double cutoff) {
this.cutoff = cutoff;
this.cellSize = (int) Math.floor(cutoff*SCALE);
this.noOverlap = false;
}
private int getFloor(double number) {
return (cellSize*((int)Math.floor(number*SCALE/cellSize)));
}
private int xintgrid2xgridindex(int xgridDim) {
return (xgridDim-bounds[0])/cellSize;
}
private int yintgrid2ygridindex(int ygridDim) {
return (ygridDim-bounds[1])/cellSize;
}
private int zintgrid2zgridindex(int zgridDim) {
return (zgridDim-bounds[2])/cellSize;
}
/**
* Adds the i and j atoms and fills the grid. Their bounds will be computed.
* Subsequent call to {@link #getIndicesContacts()} or {@link #getAtomContacts()} will produce the interatomic contacts.
* @param iAtoms
* @param jAtoms
*/
public void addAtoms(Atom[] iAtoms, Atom[] jAtoms) {
addAtoms(iAtoms, null, jAtoms, null);
}
/**
* Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima)
* This way the bounds don't need to be recomputed.
* Subsequent call to {@link #getIndicesContacts()} or {@link #getAtomContacts()} will produce the interatomic contacts.
* @param iAtoms
* @param icoordbounds
* @param jAtoms
* @param jcoordbounds
*/
public void addAtoms(Atom[] iAtoms, BoundingBox icoordbounds, Atom[] jAtoms, BoundingBox jcoordbounds) {
this.iAtoms = Calc.atomsToPoints(iAtoms);
this.iAtomObjects = iAtoms;
if (icoordbounds!=null) {
this.ibounds = icoordbounds;
} else {
this.ibounds = new BoundingBox(this.iAtoms);
}
this.jAtoms = Calc.atomsToPoints(jAtoms);
this.jAtomObjects = jAtoms;
if (jAtoms==iAtoms) {
this.jbounds=ibounds;
} else {
if (jcoordbounds!=null) {
this.jbounds = jcoordbounds;
} else {
this.jbounds = new BoundingBox(this.jAtoms);
}
}
fillGrid();
}
/**
* Adds a set of atoms, subsequent call to {@link #getIndicesContacts()} or {@link #getAtomContacts()} will produce the interatomic contacts.
* The bounding box of the atoms will be computed based on input array
* @param atoms
*/
public void addAtoms(Atom[] atoms) {
addAtoms(atoms, (BoundingBox) null);
}
/**
* Adds a set of atoms, subsequent call to {@link #getIndicesContacts()} or {@link #getAtomContacts()} will produce the interatomic contacts.
* The bounds calculated elsewhere can be passed, or if null they are computed.
* @param atoms
* @param bounds
*/
public void addAtoms(Atom[] atoms, BoundingBox bounds) {
this.iAtoms = Calc.atomsToPoints(atoms);
this.iAtomObjects = atoms;
if (bounds!=null) {
this.ibounds = bounds;
} else {
this.ibounds = new BoundingBox(iAtoms);
}
this.jAtoms = null;
this.jAtomObjects = null;
this.jbounds = null;
fillGrid();
}
/**
* Adds the i and j coordinates and fills the grid. Their bounds will be computed.
* Subsequent call to {@link #getIndicesContacts()} will produce the
* contacts, i.e. the set of points within distance cutoff.
*
* Subsequent calls to method {@link #getAtomContacts()} will produce a NullPointerException
* since this only adds coordinates and no atom information.
* @param iAtoms
* @param jAtoms
*/
public void addCoords(Point3d[] iAtoms, Point3d[] jAtoms) {
addCoords(iAtoms, null, jAtoms, null);
}
/**
* Adds the i and j coordinates and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima)
* This way the bounds don't need to be recomputed.
* Subsequent call to {@link #getIndicesContacts()} will produce the
* contacts, i.e. the set of points within distance cutoff.
*
* Subsequent calls to method {@link #getAtomContacts()} will produce a NullPointerException
* since this only adds coordinates and no atom information.
* @param iAtoms
* @param icoordbounds
* @param jAtoms
* @param jcoordbounds
*/
public void addCoords(Point3d[] iAtoms, BoundingBox icoordbounds, Point3d[] jAtoms, BoundingBox jcoordbounds) {
this.iAtoms = iAtoms;
this.iAtomObjects = null;
if (icoordbounds!=null) {
this.ibounds = icoordbounds;
} else {
this.ibounds = new BoundingBox(this.iAtoms);
}
this.jAtoms = jAtoms;
this.jAtomObjects = null;
if (jAtoms==iAtoms) {
this.jbounds=ibounds;
} else {
if (jcoordbounds!=null) {
this.jbounds = jcoordbounds;
} else {
this.jbounds = new BoundingBox(this.jAtoms);
}
}
fillGrid();
}
/**
* Adds a set of coordinates, subsequent call to {@link #getIndicesContacts()} will produce the
* contacts, i.e. the set of points within distance cutoff.
* The bounding box of the atoms will be computed based on input array.
* Subsequent calls to method {@link #getAtomContacts()} will produce a NullPointerException
* since this only adds coordinates and no atom information.
* @param atoms
*/
public void addCoords(Point3d[] atoms) {
addCoords(atoms, (BoundingBox) null);
}
/**
* Adds a set of coordinates, subsequent call to {@link #getIndicesContacts()} will produce the
* contacts, i.e. the set of points within distance cutoff.
* The bounds calculated elsewhere can be passed, or if null they are computed.
* Subsequent calls to method {@link #getAtomContacts()} will produce a NullPointerException
* since this only adds coordinates and no atom information.
* @param atoms
* @param bounds
*/
public void addCoords(Point3d[] atoms, BoundingBox bounds) {
this.iAtoms = atoms;
this.iAtomObjects = null;
if (bounds!=null) {
this.ibounds = bounds;
} else {
this.ibounds = new BoundingBox(iAtoms);
}
this.jAtoms = null;
this.jAtomObjects = null;
this.jbounds = null;
fillGrid();
}
/**
* Creates the grid based on the boundaries defined by all atoms given (iAtoms and jAtoms)
* and places the atoms in their corresponding grid cells.
* Checks also if the i and j grid overlap, i.e. the enclosing bounds of
* the 2 grids (i and j) are no more than one cell size apart. If they don't
* overlap then they are too far apart so there's nothing to calculate, we set
* the noOverlap flag and then {@link #getIndicesContacts()} will do no calculation at all.
*/
private void fillGrid() {
if (jbounds!=null && !ibounds.overlaps(jbounds, cutoff)) {
//System.out.print("-");
noOverlap = true;
return;
}
findFullGridIntBounds();
cells = new GridCell[1+(bounds[3]-bounds[0])/cellSize]
[1+(bounds[4]-bounds[1])/cellSize]
[1+(bounds[5]-bounds[2])/cellSize];
int i = 0;
for (Point3d atom:iAtoms) {
int xind = xintgrid2xgridindex(getFloor(atom.x));
int yind = yintgrid2ygridindex(getFloor(atom.y));
int zind = zintgrid2zgridindex(getFloor(atom.z));
if (cells[xind][yind][zind]==null) {
cells[xind][yind][zind] = new GridCell(this);
}
cells[xind][yind][zind].addIindex(i);
i++;
}
if (jAtoms==null) return;
int j = 0;
for (Point3d atom:jAtoms) {
int xind = xintgrid2xgridindex(getFloor(atom.x));
int yind = yintgrid2ygridindex(getFloor(atom.y));
int zind = zintgrid2zgridindex(getFloor(atom.z));
if (cells[xind][yind][zind]==null) {
cells[xind][yind][zind] = new GridCell(this);
}
cells[xind][yind][zind].addJindex(j);
j++;
}
}
/**
* Calculates an int array of size 6 into member variable bounds:
* - elements 0,1,2: minimum x,y,z of the iAtoms and jAtoms
* - elements 3,4,5: maximum x,y,z of the iAtoms and jAtoms
*/
private void findFullGridIntBounds() {
int[] iIntBounds = getIntBounds(ibounds);
bounds = new int[6];
if (jbounds==null) {
bounds = iIntBounds;
} else {
int[] jIntBounds = getIntBounds(jbounds);
bounds[0] = Math.min(iIntBounds[0],jIntBounds[0]);
bounds[1] = Math.min(iIntBounds[1],jIntBounds[1]);
bounds[2] = Math.min(iIntBounds[2],jIntBounds[2]);
bounds[3] = Math.max(iIntBounds[3],jIntBounds[3]);
bounds[4] = Math.max(iIntBounds[4],jIntBounds[4]);
bounds[5] = Math.max(iIntBounds[5],jIntBounds[5]);
}
}
/**
* Returns an int array of size 6 :
* - elements 0,1,2: minimum x,y,z (in grid int coordinates) of the given atoms
* - elements 3,4,5: maximum x,y,z (in grid int coordinates) of the given atoms
* @return
*/
private int[] getIntBounds(BoundingBox coordbounds) {
int[] bs = new int[6];
bs[0] = getFloor(coordbounds.xmin);
bs[1] = getFloor(coordbounds.ymin);
bs[2] = getFloor(coordbounds.zmin);
bs[3] = getFloor(coordbounds.xmax);
bs[4] = getFloor(coordbounds.ymax);
bs[5] = getFloor(coordbounds.zmax);
return bs;
}
/**
* Returns all contacts, i.e. all atoms that are within the cutoff distance.
* If both iAtoms and jAtoms are defined then contacts are between iAtoms and jAtoms,
* if jAtoms is null, then contacts are within the iAtoms.
* @return
*/
public AtomContactSet getAtomContacts() {
AtomContactSet contacts = new AtomContactSet(cutoff);
List list = getIndicesContacts();
if (jAtomObjects == null) {
for (Contact cont : list) {
contacts.add(new AtomContact(new Pair(iAtomObjects[cont.getI()],iAtomObjects[cont.getJ()]),cont.getDistance()));
}
} else {
for (Contact cont : list) {
contacts.add(new AtomContact(new Pair(iAtomObjects[cont.getI()],jAtomObjects[cont.getJ()]),cont.getDistance()));
}
}
return contacts;
}
/**
* Returns all contacts, i.e. all atoms that are within the cutoff distance.
* If both iAtoms and jAtoms are defined then contacts are between iAtoms and jAtoms,
* if jAtoms is null, then contacts are within the iAtoms.
* @return
* @deprecated use {@link #getAtomContacts()} instead
*/
@Deprecated
public AtomContactSet getContacts() {
return getAtomContacts();
}
/**
* Returns all contacts, i.e. all atoms that are within the cutoff distance, as simple Contact objects containing the atom indices pairs and the distance.
* If both iAtoms and jAtoms are defined then contacts are between iAtoms and jAtoms,
* if jAtoms is null, then contacts are within the iAtoms.
* @return
*/
public List getIndicesContacts() {
List list = new ArrayList<>();
// if the 2 sets of atoms are not overlapping they are too far away and no need to calculate anything
// this won't apply if there's only one set of atoms (iAtoms), where we would want all-to-all contacts
if (noOverlap) return list;
for (int xind=0;xind=0 && x=0 && y=0 && z atoms) {
for(Point3d atom : atoms) {
// Calculate Grid cell for the atom
int xind = xintgrid2xgridindex(getFloor(atom.x));
int yind = yintgrid2ygridindex(getFloor(atom.y));
int zind = zintgrid2zgridindex(getFloor(atom.z));
// Consider 3x3x3 grid of cells around point
for (int x=xind-1;x<=xind+1;x++) {
if( x<0 || cells.length<=x) continue;
for (int y=yind-1;y<=yind+1;y++) {
if( y<0 || cells[x].length<=y ) continue;
for (int z=zind-1;z<=zind+1;z++) {
if( z<0 || cells[x][y].length<=z ) continue;
GridCell cell = cells[x][y][z];
// Check for contacts in this cell
if(cell != null && cell.hasContactToAtom(iAtoms, jAtoms, atom, cutoff)) {
return true;
}
}
}
}
}
return false;
}
public double getCutoff() {
return cutoff;
}
/**
* Tells whether (after having added atoms to grid) the i and j grids are not overlapping.
* Overlap is defined as enclosing bounds of the 2 grids being no more than one cell size apart.
* @return true if the 2 grids don't overlap, false if they do
*/
public boolean isNoOverlap() {
return noOverlap;
}
protected Point3d[] getIAtoms() {
return iAtoms;
}
protected Point3d[] getJAtoms() {
return jAtoms;
}
}