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See:
Description
Interface Summary | |
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ConfigStrucAligParams | |
MatrixListener | |
UserArgumentProcessor |
Class Summary | |
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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 |
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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