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Package Summary
Package
Description
Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
Set of classes that enable the conversion protein sequences into various attributes.
Set of classes that handles the reading and writing of xml files.
Set of classes that responsible for data handling.
Tools for loading and saving ontologies.
BioJava provide a module biojava-protein-disorder for prediction disordered regions
from a protein sequence.
FASTQ and variants sequence format I/O.
Interfaces and classes for protein structure (PDB).
Classes for the alignment of structures.
Classes related to the implementation of the CE alignment algorithm, here called jCE.
This package deals with the server communication for auto-downloading pre-calculated alignments.
Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
Utility methods for better interaction with Jmol.
Helper classes for structural alignment.
Classes for the pairwise alignment of structures.
Classes related to Java Web Start
Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
A few convenience classes to view protein structures with Jmol (if it is on the classpath),
to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
Some event classes for the protein structure GUIs.
Some utility classes for the protein structure GUIs.
Input and Output of Structures
Input and Output of mmcif files.
Datamodel objects used for processing mmcif files.
Matrix package for from JAMA
Parsers and API for SCOP, Structural Classification of Proteins.
This package contains the interfaces that need to be implemented by discrete alignment services.