A cutting rule with three SMARTS queries (atom 1, bond, atom2) and options. More...

Collaboration diagram for denoptim.programs.fragmenter.CuttingRule:

Public Member Functions
	CuttingRule (String ruleName, String smartsAtm0, String smartsAtm1, String smartsBnd, int priority, List< String > opts)
	Constructor for a cutting rule. More...

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

int	getPriority ()

APClass	getAPClass0 ()
	Get the AP class with sub class 0. More...

APClass	getAPClass1 ()
	Get the AP class with sub class 1. More...

APClass	getComplementaryAPClass (APClass apc)
	Get complementary class. More...

String	getWholeSMARTSRule ()
	Returns the SMARTS query of the whole rule. More...

String	getSMARTSAtom0 ()
	Get the SMARTS query of the first atom (SubClass 0) More...

String	getSMARTSAtom1 ()
	Get the SMARTS query of the second atom (SubClass 1) More...

String	getSMARTSBnd ()
	Get the SMARTS query of the bond. More...

boolean	hasOptions ()

boolean	isHAPTO ()

boolean	isSymmetric ()

List< String >	getOptions ()
	Returns the list of options. More...

int	getBondOrder ()
	Tries to identify the bond order of the matched bond by searching for the corresponding, non-negated characters. More...

boolean	involvesMetal ()

String	toString ()
	Returns the string representing this rule. More...

boolean	equals (Object o)

Boolean	satisfiesOptions (MatchedBond matchedBond, Logger logger)
	Checks if a given bond satisfies the additional options of this rule beyond the matching of the SMARTS queries. More...

Private Attributes
String	ruleName
	Rule name. More...

APClass	apc0
	First APClass derived from this rule. More...

APClass	apc1
	Second APClass derived from this rule. More...

String	smartsAtm0
	SMARTS query matching the first atom. More...

String	smartsAtm1
	SMARTS query matching the second atom. More...

String	smartsBnd
	SMARTS query matching the bond between first and second atom. More...

int	priority
	Priority index of this rule. More...

List< String >	opts
	Additional Options. More...

Detailed Description

A cutting rule with three SMARTS queries (atom 1, bond, atom2) and options.

A cutting rule is an ordered list of strings that, once put together in the natural order, form the complete SMARTS query for one (or more) bonds between atom pairs. The order in the list of strings defines what 'first' and 'second' (or 0 and 1) mean in the the rest of the documentation, i.e., 'first' refers to anything pertaining atom 1, and 'second' pertains atom 2.

Author: Marco Foscato

Definition at line 31 of file CuttingRule.java.

Constructor & Destructor Documentation

◆ CuttingRule()

denoptim.programs.fragmenter.CuttingRule.CuttingRule	(	String	ruleName,
		String	smartsAtm0,
		String	smartsAtm1,
		String	smartsBnd,
		int	priority,
		List< String >	opts
	)

Constructor for a cutting rule.

Parameters

ruleName	name of the rule
smartsAtm0	the part of the SMARTS query pertaining the first atom.
smartsAtm1	the part of the SMARTS query pertaining the second atom.
smartsBnd	the part of the SMARTS query pertaining the bond.
priority	the priority index
opts	any additional options.

Exceptions

DENOPTIMException

Definition at line 88 of file CuttingRule.java.

Referenced by denoptim.programs.fragmenter.CuttingRule.equals().

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Member Function Documentation

◆ equals()

boolean denoptim.programs.fragmenter.CuttingRule.equals ( Object o )

Definition at line 343 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.CuttingRule(), denoptim.programs.fragmenter.CuttingRule.getName(), denoptim.programs.fragmenter.CuttingRule.getOptions(), denoptim.programs.fragmenter.CuttingRule.getPriority(), denoptim.programs.fragmenter.CuttingRule.getSMARTSAtom0(), denoptim.programs.fragmenter.CuttingRule.getSMARTSAtom1(), and denoptim.programs.fragmenter.CuttingRule.getSMARTSBnd().

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◆ getAPClass0()

APClass denoptim.programs.fragmenter.CuttingRule.getAPClass0 ( )

Get the AP class with sub class 0.

Definition at line 147 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.apc0.

◆ getAPClass1()

APClass denoptim.programs.fragmenter.CuttingRule.getAPClass1 ( )

Get the AP class with sub class 1.

Definition at line 157 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.apc0, denoptim.programs.fragmenter.CuttingRule.apc1, and denoptim.programs.fragmenter.CuttingRule.isSymmetric().

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◆ getBondOrder()

int denoptim.programs.fragmenter.CuttingRule.getBondOrder ( )

Tries to identify the bond order of the matched bond by searching for the corresponding, non-negated characters.

Definition at line 279 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.smartsBnd.

◆ getComplementaryAPClass()

APClass denoptim.programs.fragmenter.CuttingRule.getComplementaryAPClass ( APClass apc )

Get complementary class.

Definition at line 170 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.apc0, denoptim.programs.fragmenter.CuttingRule.apc1, denoptim.graph.APClass.equals(), and denoptim.programs.fragmenter.CuttingRule.isSymmetric().

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◆ getName()

String denoptim.programs.fragmenter.CuttingRule.getName ( )

Returns the name of the cutting rule.

Definition at line 126 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.ruleName.

Referenced by denoptim.programs.fragmenter.CuttingRule.equals().

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◆ getOptions()

List< String > denoptim.programs.fragmenter.CuttingRule.getOptions ( )

Returns the list of options.

Definition at line 268 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.opts.

Referenced by denoptim.programs.fragmenter.CuttingRule.equals().

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◆ getPriority()

int denoptim.programs.fragmenter.CuttingRule.getPriority ( )

Returns: the priority index of this rule.

Definition at line 137 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.priority.

Referenced by denoptim.programs.fragmenter.CuttingRule.equals(), and denoptim.io.DenoptimIO.readCuttingRules().

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◆ getSMARTSAtom0()

String denoptim.programs.fragmenter.CuttingRule.getSMARTSAtom0 ( )

Get the SMARTS query of the first atom (SubClass 0)

Definition at line 199 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.smartsAtm0.

Referenced by denoptim.programs.fragmenter.CuttingRule.equals(), and denoptim.programs.fragmenter.CuttingRule.satisfiesOptions().

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◆ getSMARTSAtom1()

String denoptim.programs.fragmenter.CuttingRule.getSMARTSAtom1 ( )

Get the SMARTS query of the second atom (SubClass 1)

Definition at line 209 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.smartsAtm1.

Referenced by denoptim.programs.fragmenter.CuttingRule.equals(), and denoptim.programs.fragmenter.CuttingRule.satisfiesOptions().

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◆ getSMARTSBnd()

String denoptim.programs.fragmenter.CuttingRule.getSMARTSBnd ( )

Get the SMARTS query of the bond.

Definition at line 219 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.smartsBnd.

Referenced by denoptim.programs.fragmenter.CuttingRule.equals(), and denoptim.programs.fragmenter.CuttingRule.satisfiesOptions().

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◆ getWholeSMARTSRule()

String denoptim.programs.fragmenter.CuttingRule.getWholeSMARTSRule ( )

Returns the SMARTS query of the whole rule.

Definition at line 189 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.smartsAtm0, denoptim.programs.fragmenter.CuttingRule.smartsAtm1, and denoptim.programs.fragmenter.CuttingRule.smartsBnd.

◆ hasOptions()

boolean denoptim.programs.fragmenter.CuttingRule.hasOptions ( )

Returns: true if this rule has further options.

Definition at line 229 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.opts.

◆ involvesMetal()

boolean denoptim.programs.fragmenter.CuttingRule.involvesMetal ( )

Returns: true if the rule involves metals.

Definition at line 306 of file CuttingRule.java.

References denoptim.constants.DENOPTIMConstants.ALL_METALS, denoptim.programs.fragmenter.CuttingRule.smartsAtm0, and denoptim.programs.fragmenter.CuttingRule.smartsAtm1.

◆ isHAPTO()

boolean denoptim.programs.fragmenter.CuttingRule.isHAPTO ( )

Returns: true if this rule matches multihapto ligands.

Definition at line 242 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.opts.

◆ isSymmetric()

boolean denoptim.programs.fragmenter.CuttingRule.isSymmetric ( )

Returns: true if this is a symmetric rule (atom SMARTS coincide)

Definition at line 255 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.smartsAtm0, and denoptim.programs.fragmenter.CuttingRule.smartsAtm1.

Referenced by denoptim.programs.fragmenter.CuttingRule.getAPClass1(), denoptim.programs.fragmenter.CuttingRule.getComplementaryAPClass(), and denoptim.programs.fragmenter.MatchedBond.MatchedBond().

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◆ satisfiesOptions()

Boolean denoptim.programs.fragmenter.CuttingRule.satisfiesOptions	(	MatchedBond	matchedBond,
		Logger	logger
	)

Checks if a given bond satisfies the additional options of this rule beyond the matching of the SMARTS queries.

Parameters

matchedBond	the bond to test.
logger	where any log should be directed.

Returns: true if the bond satisfies the condition.

Definition at line 378 of file CuttingRule.java.

References denoptim.constants.DENOPTIMConstants.ALL_METALS, denoptim.programs.fragmenter.MatchedBond.getAtmSubClass0(), denoptim.programs.fragmenter.MatchedBond.getAtmSubClass1(), denoptim.utils.ManySMARTSQuery.getMatchesOfSMARTS(), denoptim.utils.ManySMARTSQuery.getMessage(), denoptim.utils.ManySMARTSQuery.getNumMatchesOfQuery(), denoptim.programs.fragmenter.CuttingRule.getSMARTSAtom0(), denoptim.programs.fragmenter.CuttingRule.getSMARTSAtom1(), denoptim.programs.fragmenter.CuttingRule.getSMARTSBnd(), denoptim.utils.ManySMARTSQuery.hasProblems(), denoptim.utils.MoleculeUtils.isElement(), and denoptim.programs.fragmenter.CuttingRule.opts.

Referenced by denoptim.programs.fragmenter.MatchedBond.satisfiesRuleOptions().

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◆ toString()

String denoptim.programs.fragmenter.CuttingRule.toString ( )

Returns the string representing this rule.

Definition at line 332 of file CuttingRule.java.

References denoptim.programs.fragmenter.CuttingRule.opts, denoptim.programs.fragmenter.CuttingRule.priority, denoptim.programs.fragmenter.CuttingRule.ruleName, denoptim.programs.fragmenter.CuttingRule.smartsAtm0, denoptim.programs.fragmenter.CuttingRule.smartsAtm1, and denoptim.programs.fragmenter.CuttingRule.smartsBnd.

Member Data Documentation

◆ apc0

APClass denoptim.programs.fragmenter.CuttingRule.apc0

private

First APClass derived from this rule.

Definition at line 42 of file CuttingRule.java.

Referenced by denoptim.programs.fragmenter.CuttingRule.CuttingRule(), denoptim.programs.fragmenter.CuttingRule.getAPClass0(), denoptim.programs.fragmenter.CuttingRule.getAPClass1(), and denoptim.programs.fragmenter.CuttingRule.getComplementaryAPClass().

◆ apc1

APClass denoptim.programs.fragmenter.CuttingRule.apc1

private

Second APClass derived from this rule.

Definition at line 47 of file CuttingRule.java.

Referenced by denoptim.programs.fragmenter.CuttingRule.CuttingRule(), denoptim.programs.fragmenter.CuttingRule.getAPClass1(), and denoptim.programs.fragmenter.CuttingRule.getComplementaryAPClass().

◆ opts

List<String> denoptim.programs.fragmenter.CuttingRule.opts

private

Additional Options.

Definition at line 73 of file CuttingRule.java.

Referenced by denoptim.programs.fragmenter.CuttingRule.CuttingRule(), denoptim.programs.fragmenter.CuttingRule.getOptions(), denoptim.programs.fragmenter.CuttingRule.hasOptions(), denoptim.programs.fragmenter.CuttingRule.isHAPTO(), denoptim.programs.fragmenter.CuttingRule.satisfiesOptions(), and denoptim.programs.fragmenter.CuttingRule.toString().

◆ priority

int denoptim.programs.fragmenter.CuttingRule.priority

private

Priority index of this rule.

The lower the value, the earlier this rule is used and the more dominant it is over other rules.

Definition at line 68 of file CuttingRule.java.

Referenced by denoptim.programs.fragmenter.CuttingRule.CuttingRule(), denoptim.programs.fragmenter.CuttingRule.getPriority(), and denoptim.programs.fragmenter.CuttingRule.toString().

◆ ruleName

String denoptim.programs.fragmenter.CuttingRule.ruleName

private

Rule name.

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

Definition at line 37 of file CuttingRule.java.

Referenced by denoptim.programs.fragmenter.CuttingRule.CuttingRule(), denoptim.programs.fragmenter.CuttingRule.getName(), and denoptim.programs.fragmenter.CuttingRule.toString().

◆ smartsAtm0

String denoptim.programs.fragmenter.CuttingRule.smartsAtm0

private

SMARTS query matching the first atom.

Definition at line 52 of file CuttingRule.java.

Referenced by denoptim.programs.fragmenter.CuttingRule.CuttingRule(), denoptim.programs.fragmenter.CuttingRule.getSMARTSAtom0(), denoptim.programs.fragmenter.CuttingRule.getWholeSMARTSRule(), denoptim.programs.fragmenter.CuttingRule.involvesMetal(), denoptim.programs.fragmenter.CuttingRule.isSymmetric(), and denoptim.programs.fragmenter.CuttingRule.toString().

◆ smartsAtm1

String denoptim.programs.fragmenter.CuttingRule.smartsAtm1

private

SMARTS query matching the second atom.

Definition at line 57 of file CuttingRule.java.

Referenced by denoptim.programs.fragmenter.CuttingRule.CuttingRule(), denoptim.programs.fragmenter.CuttingRule.getSMARTSAtom1(), denoptim.programs.fragmenter.CuttingRule.getWholeSMARTSRule(), denoptim.programs.fragmenter.CuttingRule.involvesMetal(), denoptim.programs.fragmenter.CuttingRule.isSymmetric(), and denoptim.programs.fragmenter.CuttingRule.toString().

◆ smartsBnd

String denoptim.programs.fragmenter.CuttingRule.smartsBnd

private

SMARTS query matching the bond between first and second atom.

Definition at line 62 of file CuttingRule.java.

Referenced by denoptim.programs.fragmenter.CuttingRule.CuttingRule(), denoptim.programs.fragmenter.CuttingRule.getBondOrder(), denoptim.programs.fragmenter.CuttingRule.getSMARTSBnd(), denoptim.programs.fragmenter.CuttingRule.getWholeSMARTSRule(), and denoptim.programs.fragmenter.CuttingRule.toString().

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

/github/workspace/src/main/java/denoptim/programs/fragmenter/CuttingRule.java

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CuttingRule()

Member Function Documentation

◆ equals()

◆ getAPClass0()

◆ getAPClass1()

◆ getBondOrder()

◆ getComplementaryAPClass()

◆ getName()

◆ getOptions()

◆ getPriority()

◆ getSMARTSAtom0()

◆ getSMARTSAtom1()

◆ getSMARTSBnd()

◆ getWholeSMARTSRule()

◆ hasOptions()

◆ involvesMetal()

◆ isHAPTO()

◆ isSymmetric()

◆ satisfiesOptions()

◆ toString()

Member Data Documentation

◆ apc0

◆ apc1

◆ opts

◆ priority

◆ ruleName

◆ smartsAtm0

◆ smartsAtm1

◆ smartsBnd