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/* CE Parameters */
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‎wiki/BioJava:CookBook:PDB:CE_Algorithm.md‎

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This CE implementation allows to specify a couple of custom parameters.
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1. int winSize : (default 8) The window size used for the calculation
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of the initial Aligned Fragment Pairs
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2. double rmsdThr; (default 3.0) RMSD threshold used while tracing the
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AFP fragments
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3. double rmsdThrJoin; (default 4.0) RMSD threshold used to decide if
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two AFPs should be joined
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4. String[] alignmentAtoms; (default CA) allows to configure which
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1. private int **maxGapSize**; (default 30) The Max gap size parameter
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G , which has been obtained empirically in the CE paper. The larger
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the max gap size, the longer the compute time, but in same cases
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drastically improved results. (e.g. 1CDG.A vs. 1TIM.A) For no limit
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set this parameter to -1.
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2. boolean **checkCircular**; (default false) A flag that determines if
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CE should check for Circular Permutations (CP). Increases
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calculation time significantly, but can detect CPs.
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3. int **winSize** : (default 8) The window size used for the
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calculation of the initial Aligned Fragment Pairs
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4. double **rmsdThr**; (default 3.0) RMSD threshold used while tracing
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the AFP fragments
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5. double **rmsdThrJoin**; (default 4.0) RMSD threshold used to decide
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if two AFPs should be joined
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6. String[] **alignmentAtoms**; (default CA) allows to configure which
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atoms to use. At the present only supports "CA" and "CA","CB"
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settings
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5. private int maxGapSize; (default 30) The Max gap size parameter G ,
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which was described to have been obtained empirically in the CE
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paper. the larger the max gap size, the longer the compute time, but
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in same cases drastically improved results. (e.g. 1CDG.A vs. 1TIM.A)
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For NO LIMIT set it to -1.
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6. boolean showAFPRanges; (default false) A print flag that allows to
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view the ranges of the inital AFPs, prior to alignment optimization.
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7. boolean checkCircular; (default false) A flag that determines if CE
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should check for Circular Permutations (CP). Increases calculation
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time significantly, but can detect CPs.
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7. boolean **showAFPRanges**; (default false) A print flag that allows
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to view the ranges of the inital AFPs, prior to alignment
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optimization.
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back to <BioJava:CookBook:PDB:align>

‎wiki/BioJava:CookBook:PDB:CE_Algorithm.mediawiki‎

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This CE implementation allows to specify a couple of custom parameters.
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# int winSize : (default 8) The window size used for the calculation of the initial Aligned Fragment Pairs
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# double rmsdThr; (default 3.0) RMSD threshold used while tracing the AFP fragments
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# double rmsdThrJoin; (default 4.0) RMSD threshold used to decide if two AFPs should be joined
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# String[] alignmentAtoms; (default CA) allows to configure which atoms to use. At the present only supports "CA" and "CA","CB" settings
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# private int maxGapSize; (default 30) The Max gap size parameter G , which was described to have been obtained empirically in the CE paper. the larger the max gap size, the longer the compute time, but in same cases drastically improved results. (e.g. 1CDG.A vs. 1TIM.A) For NO LIMIT set it to -1.
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# boolean showAFPRanges; (default false) A print flag that allows to view the ranges of the inital AFPs, prior to alignment optimization.
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# boolean checkCircular; (default false) A flag that determines if CE should check for Circular Permutations (CP). Increases calculation time significantly, but can detect CPs.
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# private int '''maxGapSize'''; (default 30) The Max gap size parameter G , which has been obtained empirically in the CE paper. The larger the max gap size, the longer the compute time, but in same cases drastically improved results. (e.g. 1CDG.A vs. 1TIM.A) For no limit set this parameter to -1.
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# boolean '''checkCircular'''; (default false) A flag that determines if CE should check for Circular Permutations (CP). Increases calculation time significantly, but can detect CPs.
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# int '''winSize''' : (default 8) The window size used for the calculation of the initial Aligned Fragment Pairs
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# double '''rmsdThr'''; (default 3.0) RMSD threshold used while tracing the AFP fragments
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# double '''rmsdThrJoin'''; (default 4.0) RMSD threshold used to decide if two AFPs should be joined
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# String[] '''alignmentAtoms'''; (default CA) allows to configure which atoms to use. At the present only supports "CA" and "CA","CB" settings
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# boolean '''showAFPRanges'''; (default false) A print flag that allows to view the ranges of the inital AFPs, prior to alignment optimization.
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back to [[BioJava:CookBook:PDB:align]]

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