| Name | Description | Type | Package | Framework |
| AdjacencyMatrix | Calculator for a adjacency matrix representation of this AtomContainer. | Class | org.openscience.cdk.graph.matrix | CDK |
| ConnectionMatrix | Calculator for a connection matrix representation of this AtomContainer. | Class | org.openscience.cdk.graph.matrix | CDK |
| IGraphMatrix | Interface | org.openscience.cdk.graph.matrix | CDK | |
| TopologicalMatrix | Calculator for a topological matrix representation of this AtomContainer. | Class | org.openscience.cdk.graph.matrix | CDK |