Package org.biojava.nbio.structure.align.ce

Classes related to the implementation of the CE alignment algorithm, here called jCE. CE reference:

 Shindyalov IN, Bourne PE (1998)
 Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
 Protein Eng 11: 739-747
 

see also:

 Andreas Prlic; Spencer Bliven; Peter W. Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne (2010)
 Pre-calculated protein structure alignments at the RCSB PDB website
 Bioinformatics 26: 2983-2985
 

Interface Summary

Interface	Description
ConfigStrucAligParams
MatrixListener
UserArgumentProcessor

Class Summary

Class	Description
AbstractUserArgumentProcessor	Base class for a new structure alignment CLI.
CECalculator	This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CeCalculatorEnhanced	This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CeCPMain	A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.
CeCPMain.CPRange	Tiny wrapper for the disallowed regions of an alignment.
CECPParameters	Provides parameters to CeCPMain
CeCPUserArgumentProcessor
CeMain	The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.
CeParameters	Contains the parameters that can be sent to CE
CeSideChainMain
CeSideChainUserArgumentProcessor
CeUserArgumentProcessor	process the arguments from command line
CeUserArgumentProcessor.CeStartupParams
GuiWrapper	A class to wrap some of the strucutre.gui classes using Reflection
OptimalCECPMain	A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.
OptimalCECPParameters	Contains the parameters that can be sent to CE
StartupParameters	A simple bean that contains the parameters that can get set at startup

Enum Summary

Enum	Description
CECPParameters.DuplicationHint
CeParameters.ScoringStrategy