| Package | Description |
|---|---|
| org.biojava.nbio.structure.align |
Classes for the alignment of structures.
|
| org.biojava.nbio.structure.align.gui | |
| org.biojava.nbio.structure.align.gui.aligpanel | |
| org.biojava.nbio.structure.align.gui.jmol |
Utility methods for better interaction with Jmol.
|
| org.biojava.nbio.structure.align.multiple | |
| org.biojava.nbio.structure.align.multiple.mc | |
| org.biojava.nbio.structure.align.multiple.util | |
| org.biojava.nbio.structure.align.quaternary | |
| org.biojava.nbio.structure.align.xml |
Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
|
| org.biojava.nbio.structure.cluster | |
| org.biojava.nbio.structure.symmetry.internal | |
| org.biojava.nbio.structure.symmetry.utils |
| Class and Description |
|---|
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| Class and Description |
|---|
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| Class and Description |
|---|
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| Class and Description |
|---|
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| Class and Description |
|---|
| AbstractScoresCache
Abstact implementation of the
ScoresCache with the shared code used
in all objects with a variables cache. |
| Block
A Block is a Data Structure that stores aligned positions of a
MultipleAlignment with the condition that residues are in a
sequential order. |
| BlockImpl
General implementation of a
Block that supports any type of
sequential alignment with gaps. |
| BlockSet
A BlockSet is a Data Structure to store a flexible alignment part of a
multiple alignment.
|
| BlockSetImpl
A general implementation of a BlockSet to store a flexible part of a multiple
alignment.
|
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| MultipleAlignmentEnsemble
A MultipleAlignmentEnsemble is a collection of
MultipleAlignments
that share the same structures (Atoms) and creation properties (algorithm,
version, creation time, etc.). |
| MultipleAlignmentEnsembleImpl
A general implementation of a
MultipleAlignmentEnsemble. |
| MultipleAlignmentImpl
A general implementation of a
MultipleAlignment. |
| ScoresCache
Interface for classes which implement a temporary cache for various numeric
scores, e.g.
|
| Class and Description |
|---|
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| Class and Description |
|---|
| Block
A Block is a Data Structure that stores aligned positions of a
MultipleAlignment with the condition that residues are in a
sequential order. |
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| MultipleAlignmentEnsemble
A MultipleAlignmentEnsemble is a collection of
MultipleAlignments
that share the same structures (Atoms) and creation properties (algorithm,
version, creation time, etc.). |
| Class and Description |
|---|
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| Class and Description |
|---|
| Block
A Block is a Data Structure that stores aligned positions of a
MultipleAlignment with the condition that residues are in a
sequential order. |
| BlockSet
A BlockSet is a Data Structure to store a flexible alignment part of a
multiple alignment.
|
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| MultipleAlignmentEnsemble
A MultipleAlignmentEnsemble is a collection of
MultipleAlignments
that share the same structures (Atoms) and creation properties (algorithm,
version, creation time, etc.). |
| ScoresCache
Interface for classes which implement a temporary cache for various numeric
scores, e.g.
|
| Class and Description |
|---|
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| Class and Description |
|---|
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| Class and Description |
|---|
| MultipleAlignment
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
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