Package com.actelion.research.chem.io.pdb.converter

Class MoleculeGrid

java.lang.Object

com.actelion.research.chem.io.pdb.converter.MoleculeGrid

public class MoleculeGrid
extends java.lang.Object

Class used to speed up the calculation of neighbours by creating a grid. Each atom is indexed according to its 3D coordinates.

Field Summary

Fields

Modifier and Type	Field	Description
protected java.util.Set<java.lang.Integer>[][][]	grid
protected int[]	gridSize
protected double	gridWidth
protected Coordinates	max
protected Coordinates	min
protected StereoMolecule	mol

Constructor Summary

Constructors

Constructor	Description
MoleculeGrid(StereoMolecule mol)
MoleculeGrid(StereoMolecule mol, double gridWidth, Coordinates extension)	Creates the Grid: Complexity O(nAtoms)

Method Summary

Modifier and Type	Method	Description
Coordinates	getCartCoordinates(int[] gridCoords)
int	getClosestNeighbour(Coordinates c, double maxDist)	Returns the closest neighbour.
int[]	getGridCoordinates(Coordinates c)
int[]	getGridSize()
java.util.Set<java.lang.Integer>	getNeighbours(Coordinates[] bounds, double maxDist)	Gets a Set of all neigbouring atoms.
java.util.Set<java.lang.Integer>	getNeighbours(Coordinates c, double maxDist)	Gets a Set of all neigbouring atoms.
java.util.Set<java.lang.Integer>	getNeighbours(Coordinates c, double maxDist, boolean enforceDist)
java.util.Set<java.lang.Integer>	getNeighbours(Coordinates c, double maxDist, boolean enforceDist, int requiredFlags)	Gets a Set of all neigbouring atoms.
java.util.Set<java.lang.Integer>	getNeighbours(Molecule mol, int atom, double maxDist)
java.util.Set<java.lang.Integer>	getNeighbours(Molecule mol, int atom, double maxDist, boolean enforceDist)
boolean	hasNeighbours(Coordinates c, double maxDist)
void	updateGrid(StereoMolecule mol)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

mol

protected final StereoMolecule mol

gridWidth

protected final double gridWidth

min

protected final Coordinates min

max

protected final Coordinates max

gridSize

protected final int[] gridSize

grid

protected final java.util.Set<java.lang.Integer>[][][] grid

Constructor Detail

MoleculeGrid

public MoleculeGrid(StereoMolecule mol)

MoleculeGrid

public MoleculeGrid(StereoMolecule mol,
                    double gridWidth,
                    Coordinates extension)

Creates the Grid: Complexity O(nAtoms)

Parameters:

mol -

Method Detail

getNeighbours

public java.util.Set<java.lang.Integer> getNeighbours(Coordinates c,
                                                      double maxDist)

Gets a Set of all neigbouring atoms. This class ensures that at least all atoms within maxDist are returned (+more)

Parameters:

c -

maxDist -

Returns:

getNeighbours

public java.util.Set<java.lang.Integer> getNeighbours(Coordinates c,
                                                      double maxDist,
                                                      boolean enforceDist)

getNeighbours

public java.util.Set<java.lang.Integer> getNeighbours(Coordinates c,
                                                      double maxDist,
                                                      boolean enforceDist,
                                                      int requiredFlags)

Gets a Set of all neigbouring atoms. This class ensures that at least all atoms within maxDist are returned (+more)

Parameters:

c -

maxDist -

Returns:

hasNeighbours

public boolean hasNeighbours(Coordinates c,
                             double maxDist)

getNeighbours

public java.util.Set<java.lang.Integer> getNeighbours(Coordinates[] bounds,
                                                      double maxDist)

Gets a Set of all neigbouring atoms. This class ensures that at least all atoms within maxDist are returned (+more)

Parameters:

bounds -

maxDist -

Returns:

getClosestNeighbour

public int getClosestNeighbour(Coordinates c,
                               double maxDist)

Returns the closest neighbour. maxDist has to be given to take advantage of the speed

Parameters:

c -

maxDist -

Returns:

updateGrid

public void updateGrid(StereoMolecule mol)

getNeighbours

public java.util.Set<java.lang.Integer> getNeighbours(Molecule mol,
                                                      int atom,
                                                      double maxDist)

getNeighbours

public java.util.Set<java.lang.Integer> getNeighbours(Molecule mol,
                                                      int atom,
                                                      double maxDist,
                                                      boolean enforceDist)

getGridCoordinates

public int[] getGridCoordinates(Coordinates c)

getCartCoordinates

public Coordinates getCartCoordinates(int[] gridCoords)

getGridSize

public int[] getGridSize()