1. Initialisation and settings

All scaffold functionalities are accessed via the ScaffoldGenerator class. When it is instantiated, all settings are in default. See the article above for descriptions of the available settings.

//instantiate Scaffold Generator ScaffoldGenerator tmpScaffoldGen = new ScaffoldGenerator();

//print settings; all of them can be configured via the respective set() methods; // all settings can be restored to default values using restoreDefaultSettings() System.out.println("\nSettings:");

//scaffold definition to use, see below for details System.out.println("- Scaffold mode: " + tmpScaffoldGen.getScaffoldModeSetting());

//double bonds can be introduced to retain correct hybridisations in scaffold extraction // and dissection in aromatic systems only or in all cases (if possible) System.out.println("- Retain hybridisations only at aromatic bonds: " + tmpScaffoldGen.areOnlyHybridisationsAtAromaticBondsRetained());

//aromaticity determinations are performed at multiple steps using the set aromaticity model System.out.println("- Determine aromaticity: " + tmpScaffoldGen.isAromaticityDetermined());

//default is aromaticity model constructed from // ElectronDonation.cdk() and Cycles.cdkAromaticSet() System.out.println("- Aromaticity model: " + tmpScaffoldGen.getAromaticityModel());

//the scaffold tree scaffold dissection prioritisation rule nr. 7 can be // turned off individually because it takes long to apply System.out.println("- Apply rule 7 of scaffold tree prioritization: " + tmpScaffoldGen.isRuleSevenApplied());

//SmilesGenerator class instance used to determine molecule identity // when constructing scaffold trees and networks; //default is SmiFlavor.Unique (does *not* encode stereochemistry) in combination // with SmiFlavor.UseAromaticSymbols System.out.println("- SMILES Generator: " + tmpScaffoldGen.getSmilesGenerator());

Output:
Settings:
- Scaffold mode: SCAFFOLD
- Retain hybridisations only at aromatic bonds: false
- Determine aromaticity: true
- Aromaticity model: org.openscience.cdk.aromaticity.Aromaticity@30b7c004
- Apply rule 7 of scaffold tree prioritization: true
- SMILES Generator: org.openscience.cdk.smiles.SmilesGenerator@79efed2d