Package org.openscience.cdk.tools

Class SaturationChecker

java.lang.Object

org.openscience.cdk.tools.SaturationChecker

All Implemented Interfaces:

IDeduceBondOrderTool, IValencyChecker

public class SaturationChecker
extends Object
implements IValencyChecker, IDeduceBondOrderTool

Provides methods for checking whether an atoms valences are saturated with respect to a particular atom type.

Important: this class does not deal with hybridization states, which makes it fail, for example, for situations where bonds are marked as aromatic (either 1.5 or single an AROMATIC).

Author:

steinbeck, Egon Willighagen

Source code:

main

Belongs to CDK module:

valencycheck

Keywords:

saturation, atom, valency

Created on:

2001-09-04

Constructor Summary

Constructors

Constructor	Description
SaturationChecker()

Method Summary

Modifier and Type	Method	Description
boolean	allSaturated(IAtomContainer ac)
int	calculateNumberOfImplicitHydrogens(IAtom atom)
int	calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, double singleElectronSum, List<IBond> connectedBonds, boolean throwExceptionForUnknowAtom)	Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.
int	calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container)	Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.
int	calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container, boolean throwExceptionForUnknowAtom)
boolean	couldMatchAtomType(IAtomContainer atomContainer, IAtom atom, IAtomType atomType)	Determines if the atom can be of type AtomType.
protected AtomTypeFactory	getAtomTypeFactory(IChemObjectBuilder builder)
double	getCurrentMaxBondOrder(IAtom atom, IAtomContainer ac)	Returns the currently maximum formable bond order for this atom.
boolean	hasPerfectConfiguration(IAtom atom, IAtomContainer ac)
boolean	isOverSaturated(IAtom atom, IAtomContainer ac)	Checks if the current atom has exceeded its bond order sum value.
boolean	isSaturated(IAtomContainer container)	Determines of all atoms on the AtomContainer are saturated.
boolean	isSaturated(IAtom atom, IAtomContainer ac)	Checks whether an Atom is saturated by comparing it with known AtomTypes.
boolean	isSaturated(IBond bond, IAtomContainer atomContainer)	Returns whether a bond is saturated.
boolean	isUnsaturated(IBond bond, IAtomContainer atomContainer)	Returns whether a bond is unsaturated.
void	newSaturate(IAtomContainer atomContainer)	Saturates a molecule by setting appropriate bond orders.
boolean	newSaturate(IBond[] bonds, IAtomContainer atomContainer)	Saturates a set of Bonds in an AtomContainer.
boolean	newSaturate(IBond bond, IAtomContainer atomContainer)	Saturate atom by adjusting its bond orders.
void	saturate(IAtomContainer atomContainer)	The method is known to fail for certain compounds.
void	saturateRingSystems(IAtomContainer atomContainer)
void	unsaturate(IAtomContainer atomContainer)	Resets the bond orders of all atoms to 1.0.
void	unsaturateBonds(IAtomContainer container)	Resets the bond order of the Bond to 1.0.

Methods inherited from class java.lang.Object

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

Constructor Detail

SaturationChecker

public SaturationChecker()

Method Detail

getAtomTypeFactory

protected AtomTypeFactory getAtomTypeFactory(IChemObjectBuilder builder)
                                      throws CDKException

Parameters:

builder - the ChemObjectBuilder implementation used to construct the AtomType's.

Throws:

CDKException

hasPerfectConfiguration

public boolean hasPerfectConfiguration(IAtom atom,
                                       IAtomContainer ac)
                                throws CDKException

Throws:

CDKException

isSaturated

public boolean isSaturated(IAtomContainer container)
                    throws CDKException

Determines of all atoms on the AtomContainer are saturated.

Specified by:

isSaturated in interface IValencyChecker

Throws:

CDKException

allSaturated

public boolean allSaturated(IAtomContainer ac)
                     throws CDKException

Throws:

CDKException

isUnsaturated

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

Returns whether a bond is unsaturated. A bond is unsaturated if both Atoms in the bond are unsaturated.

Throws:

CDKException

isSaturated

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

Returns whether a bond is saturated. A bond is saturated if both Atoms in the bond are saturated.

Throws:

CDKException

isSaturated

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

Checks whether an Atom is saturated by comparing it with known AtomTypes.

Specified by:

isSaturated in interface IValencyChecker

Throws:

CDKException

isOverSaturated

public boolean isOverSaturated(IAtom atom,
                               IAtomContainer ac)
                        throws CDKException

Checks if the current atom has exceeded its bond order sum value.

Parameters:

atom - The Atom to check

ac - The atomcontainer context

Returns:

oversaturated or not

Throws:

CDKException

getCurrentMaxBondOrder

public double getCurrentMaxBondOrder(IAtom atom,
                                     IAtomContainer ac)
                              throws CDKException

Returns the currently maximum formable bond order for this atom.

Parameters:

atom - The atom to be checked

ac - The AtomContainer that provides the context

Returns:

the currently maximum formable bond order for this atom

Throws:

CDKException

unsaturate

public void unsaturate(IAtomContainer atomContainer)

Resets the bond orders of all atoms to 1.0.

unsaturateBonds

public void unsaturateBonds(IAtomContainer container)

Resets the bond order of the Bond to 1.0.

newSaturate

public void newSaturate(IAtomContainer atomContainer)
                 throws CDKException

Saturates a molecule by setting appropriate bond orders. This method is known to fail, especially on pyrolle-like compounds. Consider using import org.openscience.cdk.smiles.DeduceBondSystemTool, which should work better

Throws:

CDKException

Keywords:

bond order, calculation

Created on:

2003-10-03

newSaturate

public boolean newSaturate(IBond[] bonds,
                           IAtomContainer atomContainer)
                    throws CDKException

Saturates a set of Bonds in an AtomContainer. This method is known to fail, especially on pyrolle-like compounds. Consider using import org.openscience.cdk.smiles.DeduceBondSystemTool, which should work better

Throws:

CDKException

newSaturate

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

Saturate atom by adjusting its bond orders. This method is known to fail, especially on pyrolle-like compounds. Consider using import org.openscience.cdk.smiles.DeduceBondSystemTool, which should work better

Throws:

CDKException

couldMatchAtomType

public boolean couldMatchAtomType(IAtomContainer atomContainer,
                                  IAtom atom,
                                  IAtomType atomType)

Determines if the atom can be of type AtomType.

saturate

public void saturate(IAtomContainer atomContainer)
              throws CDKException

The method is known to fail for certain compounds. For more information, see cdk.test.limitations package. This method is known to fail, especially on pyrolle-like compounds. Consider using import org.openscience.cdk.smiles.DeduceBondSystemTool, which should work better

Specified by:

saturate in interface IDeduceBondOrderTool

Throws:

CDKException

saturateRingSystems

public void saturateRingSystems(IAtomContainer atomContainer)
                         throws CDKException

Throws:

CDKException

calculateNumberOfImplicitHydrogens

public int calculateNumberOfImplicitHydrogens(IAtom atom,
                                              IAtomContainer container)
                                       throws CDKException

Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds. Charges are included in the calculation. The number of expected bonds is defined by the AtomType generated with the AtomTypeFactory.

Parameters:

atom - Description of the Parameter

container - Description of the Parameter

Returns:

Description of the Return Value

Throws:

CDKException

See Also:

AtomTypeFactory

calculateNumberOfImplicitHydrogens

public int calculateNumberOfImplicitHydrogens(IAtom atom)
                                       throws CDKException

Throws:

CDKException

calculateNumberOfImplicitHydrogens

public int calculateNumberOfImplicitHydrogens(IAtom atom,
                                              IAtomContainer container,
                                              boolean throwExceptionForUnknowAtom)
                                       throws CDKException

Throws:

CDKException

calculateNumberOfImplicitHydrogens

public int calculateNumberOfImplicitHydrogens(IAtom atom,
                                              double bondOrderSum,
                                              double singleElectronSum,
                                              List<IBond> connectedBonds,
                                              boolean throwExceptionForUnknowAtom)
                                       throws CDKException

Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds. Charges are included in the calculation. The number of expected bonds is defined by the AtomType generated with the AtomTypeFactory.

Parameters:

atom - Description of the Parameter

throwExceptionForUnknowAtom - Should an exception be thrown if an unknown atomtype is found or 0 returned ?

Returns:

Description of the Return Value

Throws:

CDKException

See Also:

AtomTypeFactory