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: 739-747see 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
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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 forCeMain
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 toCeCPMain
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 CECeSideChainMain CeSideChainUserArgumentProcessor CeUserArgumentProcessor process the arguments from command lineCeUserArgumentProcessor.CeStartupParams GuiWrapper A class to wrap some of the strucutre.gui classes using ReflectionOptimalCECPMain A wrapper forCeMain
which sets default parameters to be appropriate for finding circular permutations.OptimalCECPParameters Contains the parameters that can be sent to CEStartupParameters a simple bean that contains the parameters that can get set at startup -
Enum Summary Enum Description CECPParameters.DuplicationHint CeParameters.ScoringStrategy