org.openscience.cdk.tools

Class AtomTypeAwareSaturationChecker

java.lang.Object

org.openscience.cdk.tools.AtomTypeAwareSaturationChecker

All Implemented Interfaces:

IDeduceBondOrderTool, IValencyChecker

public class AtomTypeAwareSaturationChecker
extends Object
implements IValencyChecker, IDeduceBondOrderTool

This class tries to figure out the bond order of the bonds that has the flag SINGLE_OR_DOUBLE raised (i.e. set to true).
The code is written with the assumption that the properties of the atoms in the molecule has configured with the help of AtomContainerManipulator. This class uses the SaturationChecker internally.
If it can't find a solution where all atoms in the molecule are saturated, it gives a "best guess", i.e. the solution with most saturated atoms. If not all atoms are saturated then it will be noticed as a warning in the log.

Author:

Klas Jönsson, Egon Willighagen

Source code:

master

Belongs to CDK module:

valencycheck

Keywords:

bond order

Created on:

2012-04-13

Constructor Summary

Constructors

Constructor and Description
AtomTypeAwareSaturationChecker() Constructs an AtomTypeAwareSaturationChecker checker.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	bondOrderCanBeIncreased(IBond bond, IAtomContainer atomContainer) Check if the bond order can be increased.
void	decideBondOrder(IAtomContainer atomContainer) This method decides the bond order on bonds that has the SINGLE_OR_DOUBLE-flag raised.
void	decideBondOrder(IAtomContainer atomContainer, boolean atomsSaturated) This method decides the bond order on bonds that has the SINGLE_OR_DOUBLE-flag raised.
double	getMaxNoOfBonds(IAtom atom) This method calculates the number of bonds that an IAtom can have.
boolean	isSaturated(IAtomContainer container)
boolean	isSaturated(IAtom atom, IAtomContainer container)
void	saturate(IAtomContainer container)

Methods inherited from class java.lang.Object

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

Constructor Detail

AtomTypeAwareSaturationChecker

public AtomTypeAwareSaturationChecker()

Constructs an AtomTypeAwareSaturationChecker checker.

Method Detail

decideBondOrder

public void decideBondOrder(IAtomContainer atomContainer,
                   boolean atomsSaturated)
                     throws CDKException

This method decides the bond order on bonds that has the SINGLE_OR_DOUBLE-flag raised.

Parameters:

atomContainer - The molecule to investigate

atomsSaturated - Set to true if you want to make sure that all atoms are saturated.

Throws:

CDKException

decideBondOrder

public void decideBondOrder(IAtomContainer atomContainer)
                     throws CDKException

This method decides the bond order on bonds that has the SINGLE_OR_DOUBLE-flag raised.

Parameters:

atomContainer - The molecule to investigate.

Throws:

CDKException

bondOrderCanBeIncreased

public boolean bondOrderCanBeIncreased(IBond bond,
                              IAtomContainer atomContainer)
                                throws CDKException

Check if the bond order can be increased. This method assumes that the bond is between only two atoms.

Parameters:

bond - The bond to check

atomContainer - The IAtomContainer that the bond belongs to

Returns:

True if it is possibly to increase the bond order

Throws:

CDKException

getMaxNoOfBonds

public double getMaxNoOfBonds(IAtom atom)
                       throws CDKException

This method calculates the number of bonds that an IAtom can have.

Parameters:

atom - The IAtom to be investigated

Returns:

The max number of bonds the IAtom can have

Throws:

CDKException - when the atom's valency is not set

saturate

public void saturate(IAtomContainer container)
              throws CDKException

Specified by:

saturate in interface IDeduceBondOrderTool

Throws:

CDKException

isSaturated

public boolean isSaturated(IAtomContainer container)
                    throws CDKException

Specified by:

isSaturated in interface IValencyChecker

Throws:

CDKException

isSaturated

public boolean isSaturated(IAtom atom,
                  IAtomContainer container)
                    throws CDKException

Specified by:

isSaturated in interface IValencyChecker

Throws:

CDKException