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A

applyAromaticityDetection(IAtomContainer, Aromaticity) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Convenience method for applying the given aromaticity model to the given molecule.

applyFiltersAndPreprocessing(IAtomContainer, Aromaticity) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Checks whether the given molecule represented by an atom container should be filtered instead of being passed on to the ErtlFunctionalGroupsFinder.find() method and if not, applies necessary preprocessing steps.

applyFiltersAndPreprocessing(IAtomContainer, Aromaticity, boolean) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Checks whether the given molecule represented by an atom container should be filtered instead of being passed on to the ErtlFunctionalGroupsFinder.find() method and if not, applies necessary preprocessing steps.

applyPreprocessing(IAtomContainer, Aromaticity) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Applies the always necessary preprocessing for functional group detection.

C

call() - Method in class org.openscience.cdk.tools.efgf.app.ExtractFunctionalGroupsTask

Applies the ErtlFunctionalGroupsFinder.find(IAtomContainer container, boolean clone) method on all given molecules (parameter clone = false) and counts the occurring exceptions.

CARBONYL_C_MARKER - Static variable in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Property name for marking carbonyl carbon atoms via IAtom properties.

containsChargedAtom(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Iterates through all atoms in the given molecule and checks whether they are charged.

containsMetalMetalloidOrPseudoAtom(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Iterates through all atoms in the given molecule and checks them for metal, metalloid, and pseudo ("R") atoms.

createPseudoSmilesCode(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Gives the pseudo SMILES code for a given molecule / functional group.

D

DEFAULT - org.openscience.cdk.tools.ErtlFunctionalGroupsFinder.Mode

Default mode including the generalization step.

E

ErtlFunctionalGroupsFinder - Class in org.openscience.cdk.tools

Finds and extracts a molecule's functional groups in a purely rule-based manner.

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

Default constructor for ErtlFunctionalGroupsFinder with functional group generalization turned ON.

ErtlFunctionalGroupsFinder(ErtlFunctionalGroupsFinder.Mode) - Constructor for class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Constructor for ErtlFunctionalGroupsFinder that allows setting the treatment of environments in the identified functional groups.

ErtlFunctionalGroupsFinder.Mode - Enum in org.openscience.cdk.tools

Defines the mode for generalizing functional group environments (default), keeping them whole, or only extracting marked atoms.

ErtlFunctionalGroupsFinderPerformanceSnapshotApp - Class in org.openscience.cdk.tools.efgf.app

An application for testing the performance of the ErtlFunctionalGroupsFinder.find() method under parallelization on multiple threads.

ErtlFunctionalGroupsFinderPerformanceSnapshotApp(String[]) - Constructor for class org.openscience.cdk.tools.efgf.app.ErtlFunctionalGroupsFinderPerformanceSnapshotApp

Instantiates and starts the application.

ErtlFunctionalGroupsFinderUtility - Class in org.openscience.cdk.tools

This class gives utility methods for using ErtlFunctionalGroupsFinder, a CDK-based implementation, published here of the Ertl algorithm for automated functional groups detection.

ExtractFunctionalGroupsTask - Class in org.openscience.cdk.tools.efgf.app

A Callable thread that extracts functional groups from all molecules in a given array using the ErtlFunctionalGroupsFinder class.

ExtractFunctionalGroupsTask(IAtomContainer[]) - Constructor for class org.openscience.cdk.tools.efgf.app.ExtractFunctionalGroupsTask

Instantiates the thread.

F

find(IAtomContainer) - Method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Find all functional groups in a molecule.

find(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Find all functional groups in a molecule.

find(IAtomContainer, boolean, boolean) - Method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Find all functional groups in a molecule.

G

getEnvMode() - Method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Returns the current setting for the treatment of functional group environments after extraction.

getFunctionalGroupHashGenerator() - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Constructs a CDK MoleculeHashGenerator that is configured to count frequencies of the functional groups returned by ErtlFunctionalGroupsFinder.

getNonmetalAtomicNumbers() - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Returns the unmodifiable set containing the atomic numbers that can be passed on to ErtlFunctionalGroupsFinder.find() if(!) input restrictions are enabled (turned off by default).

I

isAtomOrBondCountZero(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Checks whether the atom count or bond count of the given molecule is zero.

isCharged(IAtom) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Checks whether a given atom is charged.

isMetalMetalloidOrPseudoAtom(IAtom) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Checks whether a given atom is a metal, metalloid, or pseudo atom judging by its atomic number.

isStructureUnconnected(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Checks whether the given molecule consists of two or more unconnected structures, e.g.

isValidArgumentForFindMethod(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Checks whether the given molecule represented by an atom container can be passed on to the ErtlFunctionalGroupsFinder.find() method without problems if(!) strict input restrictions are turned on (turned off by default).

isValidArgumentForFindMethod(IAtomContainer, boolean) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Checks whether the given molecule represented by an atom container can be passed on to the ErtlFunctionalGroupsFinder.find() method without problems if(!) strict input restrictions are turned on (turned off by default).

isValidInputMoleculeWithRestrictionsTurnedOn(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Checks whether the given molecule represented by an atom container can be passed on to the ErtlFunctionalGroupsFinder.find() method without problems even if(!) the input restrictions are turned on (turned off by default).

L

LOGGING_TOOL - Static variable in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

CDK logging tool instance for this class.

M

main(String[]) - Static method in class org.openscience.cdk.tools.efgf.app.Main

Starts the application.

Main - Class in org.openscience.cdk.tools.efgf.app

Main class for starting application.

N

neutralizeCharges(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Neutralizes charged atoms in the given atom container by zeroing the formal atomic charges and filling up free valences with implicit hydrogen atoms (according to the CDK atom types).

neutralizeCharges(IAtom, IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Neutralizes a charged atom in the given parent atom container by zeroing the formal atomic charge and filling up free valences with implicit hydrogen atoms (according to the CDK atom types).

newErtlFunctionalGroupsFinderFullEnvironmentMode() - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Constructs a new ErtlFunctionalGroupsFinder instance with generalization of returned functional groups turned OFF.

newErtlFunctionalGroupsFinderGeneralizingMode() - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Constructs a new ErtlFunctionalGroupsFinder instance with generalization of returned functional groups turned ON.

newErtlFunctionalGroupsFinderOnlyMarkedAtomsMode() - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Constructs a new ErtlFunctionalGroupsFinder instance that extracts only the marked atoms of the functional groups, no attached environmental atoms.

NO_GENERALIZATION - org.openscience.cdk.tools.ErtlFunctionalGroupsFinder.Mode

Skips the generalization step.

NONMETAL_ATOMIC_NUMBERS - Static variable in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Set of atomic numbers of nonmetal elements, namely hydrogen, carbon, nitrogen, oxygen, phosphorus, sulfur, selenium, halogens (fluorine, chlorine, bromine, iodine), and noble gases (helium, neon, argon, krypton, xenon, radon).

O

ONLY_MARKED_ATOMS - org.openscience.cdk.tools.ErtlFunctionalGroupsFinder.Mode

Functional groups will only consist of atoms marked according to the conditions defined by Ertl, environments will be completely ignored.

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

org.openscience.cdk.tools.efgf.app - package org.openscience.cdk.tools.efgf.app

P

perceiveAtomTypesAndConfigureAtoms(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDK AtomContainerManipulator or rather the CDKAtomTypeMatcher.

R

restoreOriginalEnvironmentalCarbons(List<IAtomContainer>, IAtomContainer, boolean, boolean, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Replaces the environmental carbon or pseudo-atoms (new IAtom objects) inserted by the EFGF in an identified functional group with the carbon IAtom objects from the original molecule object.

S

selectBiggestUnconnectedComponent(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Returns the biggest unconnected component/structure of the given atom container, judging by the atom count.

setEnvMode(ErtlFunctionalGroupsFinder.Mode) - Method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinder

Allows setting the treatment of functional group environments after extraction.

shouldBeFiltered(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Checks whether the given molecule represented by an atom container should NOT be passed on to the ErtlFunctionalGroupsFinder.find() method but instead be filtered if(!) strict input restrictions are turned on (turned off by default).

shouldBeFiltered(IAtomContainer, boolean) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Checks whether the given molecule represented by an atom container should NOT be passed on to the ErtlFunctionalGroupsFinder.find() method but instead be filtered if(!) strict input restrictions are turned on (turned off by default).

shouldBePreprocessed(IAtomContainer) - Static method in class org.openscience.cdk.tools.ErtlFunctionalGroupsFinderUtility

Checks whether the given molecule represented by an atom container needs to be preprocessed before it is passed on to the ErtlFunctionalGroupsFinder.find() method because it is unconnected or contains charged atoms if(!) strict input restrictions are turned on (turned off by default).

V

valueOf(String) - Static method in enum org.openscience.cdk.tools.ErtlFunctionalGroupsFinder.Mode

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.openscience.cdk.tools.ErtlFunctionalGroupsFinder.Mode

Returns an array containing the constants of this enum type, in the order they are declared.

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