SMARTS-based rules to identify potential bridge head atoms for ring fusion operations. More...

Public Member Functions
	BridgeHeadFindingRule (String name, String smarts, int[] bridgeHeadPositions, int[] allowedBridgeLength, int lengthInAtoms)
	Constructs a new rule defined by the given arguments. More...

String	getName ()
	Returns the name of this rule. More...

String	getSMARTS ()

int[]	getBridgeHeadPositions ()

int[]	getAllowedBridgeLength ()

int[]	getAllowedBridgeLength (int maxRingSize)

int	getExistingBridgeLength ()

Private Attributes
String	ruleName
	Rule name. More...

String	smarts
	SMARTS query matching the substructure of interest. More...

int[]	bridgeHeadPositions
	The indexes of the atoms that can be bridge head in the matches substructure. More...

int[]	allowedBridgeLength
	Allowed bridge length in number of atoms. More...

int	lengthInAtoms
	Number of atoms in the existing bridge connecting the bridge-head atoms, including the bridge-head atoms. More...

Detailed Description

SMARTS-based rules to identify potential bridge head atoms for ring fusion operations.

Author: Marco Foscato

Definition at line 25 of file BridgeHeadFindingRule.java.

Constructor & Destructor Documentation

◆ BridgeHeadFindingRule()

denoptim.fragmenter.BridgeHeadFindingRule.BridgeHeadFindingRule	(	String	name,
		String	smarts,
		int[]	bridgeHeadPositions,
		int[]	allowedBridgeLength,
		int	lengthInAtoms
	)

Constructs a new rule defined by the given arguments.

Parameters

name	the string identifying the name of this rule.
smarts	the SMARTS string meant to match substructures that pertain this rule.
bridgeHeadPositions	the identification of potential bridge-head atoms in the substructure matched by the SMARTS query.
lengthInAtoms	the number of atoms in the existing bridge connecting the bridge-head atoms including the bridge-head atoms.

Definition at line 70 of file BridgeHeadFindingRule.java.

References denoptim.fragmenter.BridgeHeadFindingRule.allowedBridgeLength, denoptim.fragmenter.BridgeHeadFindingRule.bridgeHeadPositions, denoptim.fragmenter.BridgeHeadFindingRule.lengthInAtoms, and denoptim.fragmenter.BridgeHeadFindingRule.smarts.

Member Function Documentation

◆ getAllowedBridgeLength() [1/2]

int[] denoptim.fragmenter.BridgeHeadFindingRule.getAllowedBridgeLength ( )

Returns: the allowed length of the new bridge this rule allows to define between the bridge-head atoms. This can be null.

Definition at line 119 of file BridgeHeadFindingRule.java.

References denoptim.fragmenter.BridgeHeadFindingRule.allowedBridgeLength.

Referenced by denoptim.ga.GraphOperations.addFusedRing().

Here is the caller graph for this function:

◆ getAllowedBridgeLength() [2/2]

int[] denoptim.fragmenter.BridgeHeadFindingRule.getAllowedBridgeLength ( int maxRingSize )

Returns: the allowed length of the new bridge this rule allows to define between the bridge-head atoms. This cannot be null because if this rule does not specify any allowed bridge length, then this method generated a return value that corresponds to saying "any bridge length is allowed as long as it leads to a ring with size smaller than the given maximum size".

Definition at line 134 of file BridgeHeadFindingRule.java.

References denoptim.fragmenter.BridgeHeadFindingRule.allowedBridgeLength, and denoptim.fragmenter.BridgeHeadFindingRule.lengthInAtoms.

◆ getBridgeHeadPositions()

int[] denoptim.fragmenter.BridgeHeadFindingRule.getBridgeHeadPositions ( )

Returns: the positions of the potential bridge head atoms in the substructure.

Definition at line 107 of file BridgeHeadFindingRule.java.

References denoptim.fragmenter.BridgeHeadFindingRule.bridgeHeadPositions.

◆ getExistingBridgeLength()

int denoptim.fragmenter.BridgeHeadFindingRule.getExistingBridgeLength ( )

Returns: the number of atoms in the existing bridge, i.e., the number of atoms between the bridge-head atoms plus 2 (we count also the bridge-head atoms.

Definition at line 154 of file BridgeHeadFindingRule.java.

References denoptim.fragmenter.BridgeHeadFindingRule.lengthInAtoms.

Referenced by denoptim.ga.GraphOperations.addFusedRing().

Here is the caller graph for this function:

◆ getName()

String denoptim.fragmenter.BridgeHeadFindingRule.getName ( )

Returns the name of this rule.

Definition at line 86 of file BridgeHeadFindingRule.java.

References denoptim.fragmenter.BridgeHeadFindingRule.ruleName.

◆ getSMARTS()

String denoptim.fragmenter.BridgeHeadFindingRule.getSMARTS ( )

Returns: the SMARTS for matching substructures.

Definition at line 96 of file BridgeHeadFindingRule.java.

References denoptim.fragmenter.BridgeHeadFindingRule.smarts.

Member Data Documentation

◆ allowedBridgeLength

int [] denoptim.fragmenter.BridgeHeadFindingRule.allowedBridgeLength

private

Allowed bridge length in number of atoms.

This is the allowed length of the new bridge this rule allows to define between the bridge-head atoms. The length is given in number of actual atoms (no RCA included).

Definition at line 49 of file BridgeHeadFindingRule.java.

Referenced by denoptim.fragmenter.BridgeHeadFindingRule.BridgeHeadFindingRule(), and denoptim.fragmenter.BridgeHeadFindingRule.getAllowedBridgeLength().

◆ bridgeHeadPositions

int [] denoptim.fragmenter.BridgeHeadFindingRule.bridgeHeadPositions

private

The indexes of the atoms that can be bridge head in the matches substructure.

Definition at line 42 of file BridgeHeadFindingRule.java.

Referenced by denoptim.fragmenter.BridgeHeadFindingRule.BridgeHeadFindingRule(), and denoptim.fragmenter.BridgeHeadFindingRule.getBridgeHeadPositions().

◆ lengthInAtoms

int denoptim.fragmenter.BridgeHeadFindingRule.lengthInAtoms

private

Number of atoms in the existing bridge connecting the bridge-head atoms, including the bridge-head atoms.

Definition at line 55 of file BridgeHeadFindingRule.java.

Referenced by denoptim.fragmenter.BridgeHeadFindingRule.BridgeHeadFindingRule(), denoptim.fragmenter.BridgeHeadFindingRule.getAllowedBridgeLength(), and denoptim.fragmenter.BridgeHeadFindingRule.getExistingBridgeLength().

◆ ruleName

String denoptim.fragmenter.BridgeHeadFindingRule.ruleName

private

Rule name.

Usually a human-readable string giving a hint on what this rule is supposed to identify or represent.

Definition at line 31 of file BridgeHeadFindingRule.java.

Referenced by denoptim.fragmenter.BridgeHeadFindingRule.getName().

◆ smarts

String denoptim.fragmenter.BridgeHeadFindingRule.smarts

private

SMARTS query matching the substructure of interest.

Definition at line 36 of file BridgeHeadFindingRule.java.

Referenced by denoptim.fragmenter.BridgeHeadFindingRule.BridgeHeadFindingRule(), and denoptim.fragmenter.BridgeHeadFindingRule.getSMARTS().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/fragmenter/BridgeHeadFindingRule.java

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BridgeHeadFindingRule()

Member Function Documentation

◆ getAllowedBridgeLength() [1/2]

◆ getAllowedBridgeLength() [2/2]

◆ getBridgeHeadPositions()

◆ getExistingBridgeLength()

◆ getName()

◆ getSMARTS()

Member Data Documentation

◆ allowedBridgeLength

◆ bridgeHeadPositions

◆ lengthInAtoms

◆ ruleName

◆ smarts