Package org.biojava.nbio.structure.align.ce
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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ClassDescriptionBase class for a new structure alignment CLI.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.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.A wrapper for
CeMainwhich sets default parameters to be appropriate for finding circular permutations.Tiny wrapper for the disallowed regions of an alignment.Provides parameters toCeCPMainThe main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.Contains the parameters that can be sent to CEprocess the arguments from command lineA class to wrap some of the strucutre.gui classes using ReflectionA wrapper forCeMainwhich sets default parameters to be appropriate for finding circular permutations.Contains the parameters that can be sent to CEa simple bean that contains the parameters that can get set at startup