Package org.biojava.bio.structure.align.ce

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

See:
          Description

Interface Summary
ConfigStrucAligParams  
MatrixListener  
UserArgumentProcessor  
 

Class Summary
AbstractUserArgumentProcessor  
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.
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
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
 

Package org.biojava.bio.structure.align.ce Description

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