| Name | Description | Type | Package | Framework |
| BadMatrixFormatException | Class | org.openscience.cdk.graph.invariant.exception | CDK | |
| CanonicalLabeler | Canonically labels an atom container implementing the algorithm published in David Weininger et. | Class | org.openscience.cdk.graph.invariant | CDK |
| ConjugatedPiSystemsDetector | Class | org.openscience.cdk.graph.invariant | CDK | |
| EquivalentClassPartitioner | An algorithm for topological symmetry. | Class | org.openscience.cdk.graph.invariant | CDK |
| GIMatrix | This class is intended to provide the user an efficient way of implementing matrix of double number and using normal operations (linear operations, addition, substraction, multiplication, inversion, concatenation) | Class | org.openscience.cdk.graph.invariant | CDK |
| HuLuIndexTool | Class | org.openscience.cdk.graph.invariant | CDK | |
| InChINumbersTools | Tool for calculating atom numbers using the InChI algorithm. | Class | org.openscience.cdk.graph.invariant | CDK |
| IndexOutOfBoundsException | Class | org.openscience.cdk.graph.invariant.exception | CDK | |
| MatrixNotInvertibleException | Class | org.openscience.cdk.graph.invariant.exception | CDK | |
| MorganNumbersTools | Tool for calculating Morgan numbers . | Class | org.openscience.cdk.graph.invariant | CDK |