BioJava:CookBook:PDB:CE Algorithm

CE Algorithm

The BioJava 3 release provides a version of the Combinatorial Extension Algorithm (CE), originally developed by Shindyalov and Bourne. http://peds.oxfordjournals.org/cgi/content/short/11/9/739 original manuscript.

User Interface

Required modules: biojava-structure, biojava-structure-gui, alignment

A user interface for running structure alignments manually is available through the biojava3-structure-gui modules. ```java public static void main(String[] args) {

       System.setProperty("PDB_DIR","/tmp/");
   
       AlignmentGui.getInstance();

} ```

The PDB_DIR property allows to specify the path, where in the local file system PDB files are stored.

Local Execution

Required modules: biojava-structure, alignment

Optional module : biojava-structure-gui for the 3D visualisation

Using BioJava3 it is possible to align any set of atoms with the CE algorithm. This example demonstrates how to align two protein chains and edit some of the parameters.


`  public static void main(String[] args){`  
`      `  
`      String pdbFilePath="/tmp/";`  
`      `  
`      boolean isSplit = true;`  
`           `  
`      String name1 = "1cdg.A";`  
`      String name2 = "1tim.B";`  
`      `  
`      AtomCache cache = new AtomCache(pdbFilePath, isSplit);`  
`              `  
`      Structure structure1 = null;`  
`      Structure structure2 = null;`

`      try {`

`         StructureAlignment algorithm  = StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);`  
`         `  
`          structure1 = cache.getStructure(name1);`  
`          structure2 = cache.getStructure(name2);`  
`          `  
`          Atom[] ca1 = StructureTools.getAtomCAArray(structure1);`  
`          Atom[] ca2 = StructureTools.getAtomCAArray(structure2);`  
`          `  
`          // get default parameters`  
`          CeParameters params = new CeParameters();`  
`          `  
`          // add more print`  
`          params.setShowAFPRanges(true);`  
`          `  
`          // set the maximum gap size to unlimited `  
`          params.setMaxGapSize(-1);`  
`          `  
`          // The results are stored in an AFPChain object           `  
`          AFPChain afpChain = algorithm.align(ca1,ca2,params);            `

`          afpChain.setName1(name1);`  
`          afpChain.setName2(name2);`

`           // show a nice summary print`  
`          System.out.println(AfpChainWriter.toWebSiteDisplay(afpChain, ca1, ca2));`  
`          `  
`          // print rotation matrices`  
`          System.out.println(afpChain.toRotMat());`  
`          //System.out.println(afpChain.toCE(ca1, ca2));`  
`          `  
`          // print XML representation`  
`          //System.out.println(AFPChainXMLConverter.toXML(afpChain,ca1,ca2));`  
`                       `  
`          // This line requires the biojava3-structure-gui module   `  
`          StructureAlignmentDisplay.display(afpChain, ca1, ca2);`  
`          `  
`      } catch (Exception e) {`  
`          e.printStackTrace();`  
`          return;`  
`      }`  
`  }`

CE Parameters

This CE implementation allows to specify a couple of custom parameters.

  1. 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.
  2. boolean checkCircular; (default false) A flag that determines if CE should check for Circular Permutations (CP). Increases calculation time significantly, but can detect CPs.
  3. int winSize : (default 8) The window size used for the calculation of the initial Aligned Fragment Pairs
  4. double rmsdThr; (default 3.0) RMSD threshold used while tracing the AFP fragments
  5. double rmsdThrJoin; (default 4.0) RMSD threshold used to decide if two AFPs should be joined
  6. String[] alignmentAtoms; (default CA) allows to configure which atoms to use. At the present only supports “CA” and “CA”,”CB” settings
  7. 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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See also