| Name | Description | Type | Package | Framework |
| AminoAcids | Tool that provides templates for the (natural) amino acids. | Class | org.openscience.cdk.templates | CDK |
| IsoAlkanes | This class contains methods for generating simple organic alkanes. | Class | org.openscience.cdk.templates.saturatedhydrocarbons | CDK |
| MoleculeFactory | This class contains methods for generating simple organic molecules. | Class | org.openscience.cdk.templates | CDK |