| Name | Description | Type | Package | Framework |
| AbstractAlignmentJmol | An Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol. | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| AtomInfo | This class uniquely describes an atomAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| AtomInfoParser | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| JmolPanel | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| JmolTools | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| MultipleAlignmentJmol | A class that provides a 3D visualization Frame in Jmol for MultipleAlignments. | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| MyJmolStatusListener | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| RasmolCommandListener | a utility class that listens to Ramsol script commands in the @link BiojavaJmol classAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| StructureAlignmentJmol | A class that provides a simple GUI for JmolSince:1. | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |