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denoptim.programs.fragmenter.MatchedBond Class Reference
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Public Member Functions

 MatchedBond (IAtom atm0, IAtom atm1, CuttingRule rule)
 Creates an instance by defining its components. More...
 
CuttingRule getRule ()
 Returns the name of the cutting rule this bond matches. More...
 
IAtom getAtmSubClass1 ()
 Returns the atom matching subclass '1'. More...
 
IAtom getAtmSubClass0 ()
 Returns the atom matching subclass '0'. More...
 
boolean hasSymmetricSubClass ()
 
boolean satisfiesRuleOptions (Logger logger)
 Checks if this bond satisfies all the option of the cutting rule. More...
 

Private Attributes

IAtom atm0
 Atom matching the first SMARTS query of the CuttingRule. More...
 
IAtom atm1
 Atom matching the second SMARTS query of the CuttingRule. More...
 
boolean isSymm
 Flag signaling the the classes on the two sided of the bond are supposed to be equal (i.e., symmetric match). More...
 
CuttingRule rule
 The cutting rules that matched this bond. More...
 
Boolean satisfiesRuleOptions = null
 Flag indicating that we have checked the additional option from the cutting rule (otherwise this flag is null>) and that those criteria are satisfied (true) or not (false>). More...
 

Detailed Description

Definition at line 7 of file MatchedBond.java.

Constructor & Destructor Documentation

◆ MatchedBond()

denoptim.programs.fragmenter.MatchedBond.MatchedBond ( IAtom  atm0,
IAtom  atm1,
CuttingRule  rule 
)

Creates an instance by defining its components.

Does not check whether the bond between the two atoms satisfies any further critierion beyond SMARTS queries. To test those use satisfiesRuleOptions(Logger).

Parameters
atm0first atom involved in the bond.
atm1second atom involved in the bond
rulethe cutting rules that defines SMARTS queries matching the two atoms and the bond between them.

Definition at line 51 of file MatchedBond.java.

References denoptim.programs.fragmenter.MatchedBond.atm0, denoptim.programs.fragmenter.MatchedBond.atm1, denoptim.programs.fragmenter.CuttingRule.isSymmetric(), and denoptim.programs.fragmenter.MatchedBond.rule.

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Member Function Documentation

◆ getAtmSubClass0()

IAtom denoptim.programs.fragmenter.MatchedBond.getAtmSubClass0 ( )

Returns the atom matching subclass '0'.

Definition at line 84 of file MatchedBond.java.

References denoptim.programs.fragmenter.MatchedBond.atm0.

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

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◆ getAtmSubClass1()

IAtom denoptim.programs.fragmenter.MatchedBond.getAtmSubClass1 ( )

Returns the atom matching subclass '1'.

Definition at line 74 of file MatchedBond.java.

References denoptim.programs.fragmenter.MatchedBond.atm1.

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

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◆ getRule()

CuttingRule denoptim.programs.fragmenter.MatchedBond.getRule ( )

Returns the name of the cutting rule this bond matches.

Definition at line 64 of file MatchedBond.java.

References denoptim.programs.fragmenter.MatchedBond.rule.

◆ hasSymmetricSubClass()

boolean denoptim.programs.fragmenter.MatchedBond.hasSymmetricSubClass ( )
Returns
true if this bond had the same subclass on both atoms

Definition at line 94 of file MatchedBond.java.

References denoptim.programs.fragmenter.MatchedBond.isSymm.

◆ satisfiesRuleOptions()

boolean denoptim.programs.fragmenter.MatchedBond.satisfiesRuleOptions ( Logger  logger)

Checks if this bond satisfies all the option of the cutting rule.

Beyond the matching of SMARTS queries, cutting rules can have further options that restrict the matches. This method asks the cutting rule to verify those options.

Parameters
loggerwhere to direct any log.
Returns
true if all options are satisfied by this bond.

Definition at line 109 of file MatchedBond.java.

References denoptim.programs.fragmenter.MatchedBond.rule, denoptim.programs.fragmenter.CuttingRule.satisfiesOptions(), and denoptim.programs.fragmenter.MatchedBond.satisfiesRuleOptions.

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Member Data Documentation

◆ atm0

IAtom denoptim.programs.fragmenter.MatchedBond.atm0
private

Atom matching the first SMARTS query of the CuttingRule.

Definition at line 12 of file MatchedBond.java.

Referenced by denoptim.programs.fragmenter.MatchedBond.getAtmSubClass0(), and denoptim.programs.fragmenter.MatchedBond.MatchedBond().

◆ atm1

IAtom denoptim.programs.fragmenter.MatchedBond.atm1
private

Atom matching the second SMARTS query of the CuttingRule.

Definition at line 17 of file MatchedBond.java.

Referenced by denoptim.programs.fragmenter.MatchedBond.getAtmSubClass1(), and denoptim.programs.fragmenter.MatchedBond.MatchedBond().

◆ isSymm

boolean denoptim.programs.fragmenter.MatchedBond.isSymm
private

Flag signaling the the classes on the two sided of the bond are supposed to be equal (i.e., symmetric match).

Definition at line 23 of file MatchedBond.java.

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

◆ rule

CuttingRule denoptim.programs.fragmenter.MatchedBond.rule
private

The cutting rules that matched this bond.

Definition at line 28 of file MatchedBond.java.

Referenced by denoptim.programs.fragmenter.MatchedBond.getRule(), denoptim.programs.fragmenter.MatchedBond.MatchedBond(), and denoptim.programs.fragmenter.MatchedBond.satisfiesRuleOptions().

◆ satisfiesRuleOptions

Boolean denoptim.programs.fragmenter.MatchedBond.satisfiesRuleOptions = null
private

Flag indicating that we have checked the additional option from the cutting rule (otherwise this flag is null>) and that those criteria are satisfied (true) or not (false>).

Definition at line 36 of file MatchedBond.java.

Referenced by denoptim.fragmenter.FragmenterTools.getMatchingBondsAllInOne(), and denoptim.programs.fragmenter.MatchedBond.satisfiesRuleOptions().

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