org.openscience.cdk.tools

Class SmilesValencyChecker

java.lang.Object

org.openscience.cdk.tools.SmilesValencyChecker

All Implemented Interfaces:

IDeduceBondOrderTool, IValencyChecker

public class SmilesValencyChecker
extends Object
implements IValencyChecker, IDeduceBondOrderTool

Small customization of ValencyHybridChecker suggested by Todd Martin specially tuned for SMILES parsing.

Author:

Egon Willighagen

Source code:

master

Belongs to CDK module:

valencycheck

Keywords:

atom, valency

Created on:

2004-06-12

Field Summary

Fields

Modifier and Type	Field and Description
protected static ILoggingTool	logger
protected AtomTypeFactory	structgenATF

Constructor Summary

Constructors

Constructor and Description
SmilesValencyChecker()
SmilesValencyChecker(String atomTypeList)

Method Summary

Modifier and Type	Method and Description
boolean	allSaturated(IAtomContainer ac)
int	calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, IBond.Order maxBondOrder, int neighbourCount) Calculates the number of hydrogens that can be added to the given atom to fullfil the atom's valency.
int	calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container)
boolean	couldMatchAtomType(IAtomContainer container, IAtom atom, IAtomType type) Determines if the atom can be of type AtomType.
boolean	couldMatchAtomType(IAtom atom, double bondOrderSum, IBond.Order maxBondOrder, IAtomType type) Determines if the atom can be of type AtomType.
protected AtomTypeFactory	getAtomTypeFactory(IChemObjectBuilder builder)
boolean	isSaturated(IAtomContainer container) Determines of all atoms on the AtomContainer are saturated.
boolean	isSaturated(IAtom atom, IAtomContainer container) 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	saturate(IAtomContainer atomContainer) Saturates a molecule by setting appropriate bond orders.
boolean	saturate(IBond[] bonds, IAtomContainer atomContainer) Saturates a set of Bonds in an AtomContainer.
boolean	saturateByIncreasingBondOrder(IBond bond, IAtomContainer atomContainer) Tries to saturate a bond by increasing its bond orders by 1.0.
boolean	unsaturateByDecreasingBondOrder(IBond bond)

Methods inherited from class java.lang.Object

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

Field Detail

structgenATF

protected AtomTypeFactory structgenATF

logger

protected static ILoggingTool logger

Constructor Detail

SmilesValencyChecker

public SmilesValencyChecker()

SmilesValencyChecker

public SmilesValencyChecker(String atomTypeList)

Method Detail

saturate

public void saturate(IAtomContainer atomContainer)
              throws CDKException

Saturates a molecule by setting appropriate bond orders.

Specified by:

saturate in interface IDeduceBondOrderTool

Throws:

CDKException

Keywords:

bond order, calculation

Created on:

2003-10-03

saturate

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

Saturates a set of Bonds in an AtomContainer.

Throws:

CDKException

unsaturateByDecreasingBondOrder

public boolean unsaturateByDecreasingBondOrder(IBond bond)

isUnsaturated

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

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

Throws:

CDKException

saturateByIncreasingBondOrder

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

Tries to saturate a bond by increasing its bond orders by 1.0.

Returns:

true if the bond could be increased

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(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

couldMatchAtomType

public boolean couldMatchAtomType(IAtom atom,
                                  double bondOrderSum,
                                  IBond.Order maxBondOrder,
                                  IAtomType type)

Determines if the atom can be of type AtomType. That is, it sees if this AtomType only differs in bond orders, or implicit hydrogen count.

calculateNumberOfImplicitHydrogens

public int calculateNumberOfImplicitHydrogens(IAtom atom,
                                              double bondOrderSum,
                                              IBond.Order maxBondOrder,
                                              int neighbourCount)
                                       throws CDKException

Calculates the number of hydrogens that can be added to the given atom to fullfil the atom's valency. It will return 0 for PseudoAtoms, and for atoms for which it does not have an entry in the configuration file.

Throws:

CDKException

isSaturated

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

Checks whether an Atom is saturated by comparing it with known AtomTypes. It returns true if the atom is an PseudoAtom and when the element is not in the list.

Specified by:

isSaturated in interface IValencyChecker

Throws:

CDKException

calculateNumberOfImplicitHydrogens

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

Throws:

CDKException

getAtomTypeFactory

protected AtomTypeFactory getAtomTypeFactory(IChemObjectBuilder builder)
                                      throws CDKException

Throws:

CDKException

couldMatchAtomType

public boolean couldMatchAtomType(IAtomContainer container,
                                  IAtom atom,
                                  IAtomType type)

Determines if the atom can be of type AtomType.