chemaxon.core.util

Class BondTable

java.lang.Object

chemaxon.core.util.BondTable

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

@PublicAPI
public abstract class BondTable
extends java.lang.Object
implements java.io.Serializable, java.lang.Cloneable

Provides easy lookup of bonds between pair of atoms in a molecule graph. This class is an abstraction of the NxN square matrix for a molecule graph containing N atoms, for which matrix[i][j] and matrix[j][i] are the index of the bond between the atoms with indexes i and j, or -1 if there is no bond between the atoms.

The getMatrixArray() method returns this matrix, but the internal representation of the class is different to save memory.

Since:

Marvin 5.4

Author:

Peter Vadasz, Andras Volford, Peter Kovacs (pkovacs84)

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_VALUE The default (null) value in the matrix.

Method Summary

Modifier and Type	Method and Description
BondTable	clone()
static BondTable	cloneBondTable(BondTable bondTable) Clones the bond table.
static BondTable	createBondTable(int atomCount, int bondCount) Creates a new bond table for a molecule graph with the specified number of atoms and bonds.
int[][]	createMatrixArray() Creates the matrix array representation.
int	getAtomCount() Returns the number of atoms in the molecule this bond table represents.
abstract int	getBondIndex(int i, int j) Returns the index of the bond connecting two atoms, or -1 if the two atoms are not connected.
int[][]	getMatrixArray() Returns the matrix array representation.
void	setBondIndex(int i, int j, int bondIndex) Sets the index of the bond connecting two atoms.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_VALUE

public static final int DEFAULT_VALUE

The default (null) value in the matrix.

See Also:

Constant Field Values

Method Detail

createBondTable

public static BondTable createBondTable(int atomCount,
                                        int bondCount)

Creates a new bond table for a molecule graph with the specified number of atoms and bonds. Initially, all values are set to -1.

Parameters:

atomCount - the number of atoms (the number of rows and columns of the matrix)

bondCount - the number of bonds (required for the selection of optimized implementations)

cloneBondTable

public static BondTable cloneBondTable(BondTable bondTable)

Clones the bond table. Makes a deep copy.

Parameters:

bondTable - the matrix to copy, has to be not null.

getAtomCount

public final int getAtomCount()

Returns the number of atoms in the molecule this bond table represents. (This is the number of rows and columns of the matrix array.)

Returns:

the number of atoms (rows, columns).

getMatrixArray

public final int[][] getMatrixArray()

Returns the matrix array representation. The returned array may consume a lot of memory for (very) large molecules, so use it only if necessary.

Returns:

the matrix array representation

createMatrixArray

public int[][] createMatrixArray()

Creates the matrix array representation. This method can be overridden for efficiency reasons.

getBondIndex

public abstract int getBondIndex(int i,
                                 int j)

Returns the index of the bond connecting two atoms, or -1 if the two atoms are not connected.

Parameters:

i - the first atom index

j - the second atom index

Returns:

the connecting bond index, or -1 if there is no such bond

setBondIndex

public final void setBondIndex(int i,
                               int j,
                               int bondIndex)

Sets the index of the bond connecting two atoms. If the bond index is -1, the connection is removed.

Parameters:

i - index of the first atom

j - index of the second atom

bondIndex - index of the bond connecting atoms i and j

clone

public BondTable clone()

Overrides:

clone in class java.lang.Object