A B C D G H I L N O S U

A

addImplicitHydrogens(IAtomContainer) - Method in class org.openscience.cdk.tools.CDKHydrogenAdder

Sets implicit hydrogen counts for all atoms in the given IAtomContainer.

addImplicitHydrogens(IAtomContainer, IAtom) - Method in class org.openscience.cdk.tools.CDKHydrogenAdder

Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.

allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

AtomTypeAwareSaturationChecker - Class in org.openscience.cdk.tools

This class tries to figure out the bond order of the bonds that has the flag SINGLE_OR_DOUBLE raised (i.e.

AtomTypeAwareSaturationChecker() - Constructor for class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker

Constructs an AtomTypeAwareSaturationChecker checker.

B

bondOrderCanBeIncreased(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker

Check if the bond order can be increased.

C

calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.

calculateNumberOfImplicitHydrogens(IAtom) - Method in class org.openscience.cdk.tools.SaturationChecker

calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.SaturationChecker

calculateNumberOfImplicitHydrogens(IAtom, double, double, List<IBond>, boolean) - Method in class org.openscience.cdk.tools.SaturationChecker

Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.

calculateNumberOfImplicitHydrogens(IAtom, double, IBond.Order, int) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

Calculates the number of hydrogens that can be added to the given atom to fullfil the atom's valency.

calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

CDKHydrogenAdder - Class in org.openscience.cdk.tools

Adds implicit hydrogens based on atom type definitions.

CDKValencyChecker - Class in org.openscience.cdk.tools

Assumes CDK atom types to be detected and adds missing hydrogens based on the atom typing.

couldMatchAtomType(IAtomContainer, IAtom, IAtomType) - Method in class org.openscience.cdk.tools.SaturationChecker

Determines if the atom can be of type AtomType.

couldMatchAtomType(IAtom, double, IBond.Order, IAtomType) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

Determines if the atom can be of type AtomType.

couldMatchAtomType(IAtomContainer, IAtom, IAtomType) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

Determines if the atom can be of type AtomType.

D

decideBondOrder(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker

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

decideBondOrder(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker

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

G

getAtomTypeFactory(IChemObjectBuilder) - Method in class org.openscience.cdk.tools.SaturationChecker

getAtomTypeFactory(IChemObjectBuilder) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

getCurrentMaxBondOrder(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Returns the currently maximum formable bond order for this atom.

getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.CDKHydrogenAdder

getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.CDKValencyChecker

getMaxNoOfBonds(IAtom) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker

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

H

hasPerfectConfiguration(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

I

IDeduceBondOrderTool - Interface in org.openscience.cdk.tools

A common interface for tools that deduce bond orders from connectivity and optionally additional information, like number of implicit or explicit hydrogens, or hybridization states.

isOverSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

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

isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker

isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker

isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.CDKValencyChecker

isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.CDKValencyChecker

isSaturated(IAtomContainer) - Method in interface org.openscience.cdk.tools.IValencyChecker

isSaturated(IAtom, IAtomContainer) - Method in interface org.openscience.cdk.tools.IValencyChecker

isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Determines of all atoms on the AtomContainer are saturated.

isSaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Returns whether a bond is saturated.

isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

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

isSaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

Returns whether a bond is saturated.

isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

Determines of all atoms on the AtomContainer are saturated.

isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

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

isUnsaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Returns whether a bond is unsaturated.

isUnsaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

Returns whether a bond is unsaturated.

IValencyChecker - Interface in org.openscience.cdk.tools

A common interface for SaturationChecker and ValencyChecker.

L

logger - Static variable in class org.openscience.cdk.tools.SmilesValencyChecker

N

newSaturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Saturates a molecule by setting appropriate bond orders.

newSaturate(IBond[], IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Saturates a set of Bonds in an AtomContainer.

newSaturate(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Saturate atom by adjusting its bond orders.

O

org.openscience.cdk.tools - package org.openscience.cdk.tools

S

saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker

saturate(IAtomContainer) - Method in interface org.openscience.cdk.tools.IDeduceBondOrderTool

saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

The method is known to fail for certain compounds.

saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

Saturates a molecule by setting appropriate bond orders.

saturate(IBond[], IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

Saturates a set of Bonds in an AtomContainer.

saturateByIncreasingBondOrder(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

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

saturateRingSystems(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

SaturationChecker - Class in org.openscience.cdk.tools

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

SaturationChecker() - Constructor for class org.openscience.cdk.tools.SaturationChecker

SmilesValencyChecker - Class in org.openscience.cdk.tools

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

SmilesValencyChecker() - Constructor for class org.openscience.cdk.tools.SmilesValencyChecker

SmilesValencyChecker(String) - Constructor for class org.openscience.cdk.tools.SmilesValencyChecker

structgenATF - Variable in class org.openscience.cdk.tools.SmilesValencyChecker

U

unsaturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Resets the bond orders of all atoms to 1.0.

unsaturateBonds(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Resets the bond order of the Bond to 1.0.

unsaturateByDecreasingBondOrder(IBond) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

A B C D G H I L N O S U