@ Override public DescriptorValue calculate ( IAtom atom , IAtomContainer ac ) { IAtomContainer clone ; IAtom localAtom ; try { clone = ( IAtomContainer ) ac . clone ( ) ; localAtom = clone . getAtom ( ac . indexOf ( atom ) ) ; AtomContainerManipulator . percieveAtomTypesAndConfigureAtoms ( clone ) ; } catch ( CDKException e ) { return new DescriptorValue ( getSpecification ( ) , getParameterNames ( ) , getParameters ( ) , new DoubleResult ( Double . NaN ) , NAMES , e ) ; } catch ( CloneNotSupportedException e ) { return new DescriptorValue ( getSpecification ( ) , getParameterNames ( ) , getParameters ( ) , new DoubleResult ( Double . NaN ) , NAMES , e ) ; } if ( maxIterations != - 1 && maxIterations != 0 ) electronegativity . setMaxIterations ( maxIterations ) ; double result = electronegativity . calculateSigmaElectronegativity ( clone , localAtom ) ; return new DescriptorValue ( getSpecification ( ) , getParameterNames ( ) , getParameters ( ) , new DoubleResult ( result ) , NAMES ) ; }
The method calculates the sigma electronegativity of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools . HydrogenAdder .