Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)

Table 1 Settings and options of Scaffold Generator

Setting name	Options	Default
Scaffold mode	Scaffold	Scaffold
	Murcko framework
	Basic wireframe
	Basic framework
	Elemental wireframe
Determine aromaticity	True/False	True
Aromaticity model	All combinations of CycleFinder and ElectronDonation instances available in CDK	ElectronDonation.cdk and Cycles.cdkAromaticSet
Retain only hybridisations at aromatic bonds	True/False	False
Rule seven applied (“A Fully Aromatic Ring System Must Not Be Dissected in a Way That the Resulting System Is Not Aromatic Any More” [7])	True/False	True
SMILES generator	All SmilesGenerator configurations available in CDK	SmiFlavor.Unique and SmiFlavor.UseAromaticSymbols

The settings listed in this table together with their options and default values are available in Scaffold Generator to adjust its results to specific use cases

ISSN: 1758-2946