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E

ExhaustiveFragmenter - Class in org.openscience.cdk.fragment

Generate fragments exhaustively.

ExhaustiveFragmenter() - Constructor for class org.openscience.cdk.fragment.ExhaustiveFragmenter

Instantiate fragmenter with default minimum fragment size.

ExhaustiveFragmenter(int) - Constructor for class org.openscience.cdk.fragment.ExhaustiveFragmenter

Instantiate fragmenter with user specified minimum fragment size.

F

FragmentUtils - Class in org.openscience.cdk.fragment

Helper methods for fragmentation algorithms.

FragmentUtils() - Constructor for class org.openscience.cdk.fragment.FragmentUtils

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generateFragments(IAtomContainer) - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter

Generate fragments for the input molecule.

generateFragments(IAtomContainer) - Method in interface org.openscience.cdk.fragment.IFragmenter

Generate fragments for the input molecule.

generateFragments(IAtomContainer) - Method in class org.openscience.cdk.fragment.MurckoFragmenter

Perform the fragmentation procedure.

getFragments() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter

Get the fragments generated as SMILES strings.

getFragments() - Method in interface org.openscience.cdk.fragment.IFragmenter

Get the fragments generated as SMILES strings.

getFragments() - Method in class org.openscience.cdk.fragment.MurckoFragmenter

This returns the frameworks and ring systems from a Murcko fragmentation.

getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter

Get the fragments generated as IAtomContainer objects..

getFragmentsAsContainers() - Method in interface org.openscience.cdk.fragment.IFragmenter

Get fragments generated as IAtomContainer objects.

getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter

Get all frameworks and ring systems as IAtomContainer objects.

getFrameworks() - Method in class org.openscience.cdk.fragment.MurckoFragmenter

Get frameworks as SMILES strings.

getFrameworksAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter

Get frameworks as IAtomContainer as objects.

getRingSystems() - Method in class org.openscience.cdk.fragment.MurckoFragmenter

Get the ring system fragments as SMILES strings.

getRingSystemsAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter

Get rings systems as IAtomContainer objects.

I

IFragmenter - Interface in org.openscience.cdk.fragment

An interface for classes implementing fragmentation algorithms.

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makeAtomContainer(IAtom, List<IBond>, IAtom) - Static method in class org.openscience.cdk.fragment.FragmentUtils

MurckoFragmenter - Class in org.openscience.cdk.fragment

An implementation of the Murcko fragmenation method [Bemis, G.W. and Murcko, M.A. . Journal of Medicinal Chemistry. 1996. 39].

MurckoFragmenter() - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter

Instantiate Murcko fragmenter.

MurckoFragmenter(boolean, int) - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter

Instantiate Murcko fragmenter.

MurckoFragmenter(boolean, int, MoleculeHashGenerator) - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter

Instantiate Murcko fragmenter.

O

org.openscience.cdk.fragment - package org.openscience.cdk.fragment

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scaffold(IAtomContainer) - Static method in class org.openscience.cdk.fragment.MurckoFragmenter

Computes the Murcko Scaffold for the provided molecule in linear time.

setComputeRingFragments(boolean) - Method in class org.openscience.cdk.fragment.MurckoFragmenter

Sets whether to calculate ring fragments (true by default).

setMinimumFragmentSize(int) - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter

Set the minimum fragment size.

splitMolecule(IAtomContainer, IBond) - Static method in class org.openscience.cdk.fragment.FragmentUtils

Non destructively split a molecule into two parts at the specified bond.

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traverse(IAtomContainer, IAtom, List<IBond>) - Static method in class org.openscience.cdk.fragment.FragmentUtils

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