| Name | Description | Type | Package | Framework |
| AxisAligner | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| C2RotationSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| ChainClusterer | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| ClusterMerger | Merges clusters based on their sequence identity. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| ClusterProteinChains | Clusters the chains of one or two structures by sequence. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| HelicalRepeatUnit | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| Helix | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixAxisAligner | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixExtender | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixLayers | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| PairwiseAlignment | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| PermutationGroup | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| ProteinChainExtractor | Extracts information about all the chains in a structure, including chain Ids, sequences, and atoms. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| ProteinSequenceClusterer | Represents a set of non-identical protein sequences. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| QuatSuperpositionScorer | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| QuatSymmetryDetector | Detects global and local quaternary protein structure symmetry in a structure. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| QuatSymmetryParameters | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| QuatSymmetryResults | Holds the results of quaternary symmetry perception. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| QuatSymmetryScores | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| QuatSymmetrySolver | Interface | org.biojava.nbio.structure.symmetry.core | BioJava | |
| Rotation | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| RotationAxisAligner | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| RotationGroup | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| RotationSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| SequenceAlignmentCluster | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| SubunitGraph | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| Subunits | A bean to represent info about the set of subunits being considered for a QuatSymmetryDetector alignment. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| SystematicSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| UniqueSequenceList | Bean for a single sequence. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |