Uses of Class
org.openscience.cdk.isomorphism.Pattern

Packages that use Pattern

Package	Description
org.openscience.cdk.isomorphism
org.openscience.cdk.layout
org.openscience.cdk.smarts
org.openscience.cdk.smiles.smarts

Uses of Pattern in org.openscience.cdk.isomorphism

Subclasses of Pattern in org.openscience.cdk.isomorphism

Modifier and Type	Class	Description
class	DfPattern	The depth-first (DF) backtracking sub-structure matching algorithm so named because it matches the molecule in a depth-first manner (bond by bond).
class	Ullmann	A structure pattern which utilises the Ullmann algorithm [Ullmann J R. Journal of the Association for Computing Machinery. 1976. 23].
class	VentoFoggia	A structure pattern which utilises the Vento-Foggia (VF) algorithm [Cordella Luigi P et. al.. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE. 2004. 26].

Methods in org.openscience.cdk.isomorphism that return Pattern

Modifier and Type	Method	Description
static Pattern	Pattern.findIdentical(IAtomContainer query)	Create a pattern which can be used to find molecules which are the same as the query structure.
static Pattern	VentoFoggia.findIdentical(IAtomContainer query)	Create a pattern which can be used to find molecules which are the same as the query structure.
static Pattern	VentoFoggia.findIdentical(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher bondMatcher)	Create a pattern which can be used to find molecules which are the same as the query structure.
static Pattern	Pattern.findSubstructure(IAtomContainer query)	Create a pattern which can be used to find molecules which contain the query structure.
static Pattern	Ullmann.findSubstructure(IAtomContainer query)	Create a pattern which can be used to find molecules which contain the query structure.
static Pattern	VentoFoggia.findSubstructure(IAtomContainer query)	Create a pattern which can be used to find molecules which contain the query structure.
static Pattern	VentoFoggia.findSubstructure(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher bondMatcher)	Create a pattern which can be used to find molecules which contain the query structure.

Methods in org.openscience.cdk.isomorphism with parameters of type Pattern

Modifier and Type	Method	Description
void	Transform.init(Pattern pattern, List<TransformOp> ops)	Initialize the transform.
void	Transform.init(Pattern pattern, List<TransformOp> ops, String warning)	Initialize the transform.

Uses of Pattern in org.openscience.cdk.layout

Methods in org.openscience.cdk.layout with parameters of type Pattern

Modifier and Type	Method	Description
static TemplateHandler	TemplateHandler.createFromSubstructure(Pattern ptrn, Iterable<IAtomContainer> mols)	Create a template from a substructure pattern.
static TemplateHandler	TemplateHandler.createFromSubstructure(Pattern ptrn, IAtomContainer mol)	Create a template from a substructure pattern.
void	StructureDiagramGenerator.generateAlignedCoordinates(IAtomContainer mol, IAtomContainer ref, Pattern pattern)	Generate coordinates aligned to a reference based on the provided pattern.
void	StructureDiagramGenerator.generateAlignedCoordinates(IAtomContainer mol, Pattern pattern)	Generate coordinates aligned, the atoms in substructure pattern is used to cache/provide the coordinates.

Uses of Pattern in org.openscience.cdk.smarts

Subclasses of Pattern in org.openscience.cdk.smarts

Modifier and Type	Class	Description
class	SmartsPattern	A Pattern for matching a single SMARTS query against multiple target compounds.

Uses of Pattern in org.openscience.cdk.smiles.smarts

Subclasses of Pattern in org.openscience.cdk.smiles.smarts

Modifier and Type	Class	Description
class	SmartsPattern	Deprecated.