Collaboration diagram for denoptim.graph.FragmentIsomorphismInspector:

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Public Member Functions
	FragmentIsomorphismInspector (Fragment fragA, Fragment fragB)
	Constructs a default inspector with a timeout runtime of 60 seconds. More...

	FragmentIsomorphismInspector (Fragment fragA, Fragment fragB, boolean ignoreAPClasses)
	Constructs a default inspector with a timeout runtime of 60 seconds. More...

	FragmentIsomorphismInspector (Fragment fragA, Fragment fragB, int timeout, boolean ignoreAPClasses)
	Constructs an inspector with a custom timeout limit. More...

boolean	isomorphismExists ()
	Checks if an isomorphism exists between the two fragments. More...

Iterator< GraphMapping< FragIsomorphNode, FragIsomorphEdge > >	getMappings ()

Protected Attributes
boolean	reportTimeoutIncidents = true
	Flag indicating if we print earning in case of timeout or not. More...

Package Attributes
VF2GraphIsomorphismInspector< FragIsomorphNode, FragIsomorphEdge >	vf2
	Implementation of the Vento-Foggia 2 algorithm. More...

Private Attributes
int	timeout
	The maximum time we give the VF2 algorithm (seconds) More...

Fragment	fragA
	One fragment being analyzed. More...

Fragment	fragB
	The other fragment being analyzed. More...

Detailed Description

Inspector for isomorphism on fragments. The graph representation considered is one where both atoms and AttachmentPoints are represented as graph nodes, and edges are either bonds or atom-to-attachment point connections.

Effectively, this class considers the composition and connectivity (including that of AttachmentPoints when comparing the fragments. Geometry and stereochemistry are not considered.

This works with the VF2GraphIsomorphismInspector, see the dedicated documentation for information of pathological cases.

Author: Marco Foscato

Definition at line 34 of file FragmentIsomorphismInspector.java.

Constructor & Destructor Documentation

◆ FragmentIsomorphismInspector() [1/3]

denoptim.graph.FragmentIsomorphismInspector.FragmentIsomorphismInspector	(	Fragment	fragA,
		Fragment	fragB
	)

Constructs a default inspector with a timeout runtime of 60 seconds.

Parameters

fragA
fragB

Definition at line 69 of file FragmentIsomorphismInspector.java.

References denoptim.graph.FragmentIsomorphismInspector.fragA, and denoptim.graph.FragmentIsomorphismInspector.fragB.

◆ FragmentIsomorphismInspector() [2/3]

denoptim.graph.FragmentIsomorphismInspector.FragmentIsomorphismInspector	(	Fragment	fragA,
		Fragment	fragB,
		boolean	ignoreAPClasses
	)

Constructs a default inspector with a timeout runtime of 60 seconds.

Parameters

fragA
fragB
ignoreAPClasses

Definition at line 82 of file FragmentIsomorphismInspector.java.

References denoptim.graph.FragmentIsomorphismInspector.fragA, and denoptim.graph.FragmentIsomorphismInspector.fragB.

◆ FragmentIsomorphismInspector() [3/3]

denoptim.graph.FragmentIsomorphismInspector.FragmentIsomorphismInspector	(	Fragment	fragA,
		Fragment	fragB,
		int	timeout,
		boolean	ignoreAPClasses
	)

Constructs an inspector with a custom timeout limit.

Parameters

fragA	one fragment to compare
fragB	the other fragment to compare
timeout	maximum amount of time (milliseconds) given to the inspector for performing any task. associated with returning from any public method in this class.

Definition at line 99 of file FragmentIsomorphismInspector.java.

References denoptim.graph.FragmentIsomorphismInspector.fragA, denoptim.graph.FragmentIsomorphismInspector.fragB, denoptim.graph.Fragment.getJGraphFragIsomorphism(), denoptim.graph.FragIsomorphNode.isAtm, denoptim.graph.FragIsomorphEdge.label, denoptim.graph.FragIsomorphNode.label, denoptim.graph.FragmentIsomorphismInspector.timeout, and denoptim.graph.FragmentIsomorphismInspector.vf2.

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