BioJava:CookBook:PDB:FATCAT Algorithm
FATCAT Algorithm
Biojava 3+ provides a BioJava version of the FATCAT algorithm, originally developed by Yuzhen Ye and A. Godzik. http://www.ncbi.nlm.nih.gov/pubmed/14534198 original publication.
User Interface
Required modules: biojava-structure, biojava-structure-gui, alignment
A user interface for running structure alignments manually is available through the biojava-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
Using BioJava it is possible to align any set of atoms with the FATCAT 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 {`
` // To run FATCAT in the flexible variant say`
` // FatCatFlexible.algorithmName below`
` StructureAlignment algorithm = StructureAlignmentFactory.getAlgorithm(FatCatRigid.algorithmName);`
` `
` structure1 = cache.getStructure(name1);`
` structure2 = cache.getStructure(name2);`
` `
` Atom[] ca1 = StructureTools.getAtomCAArray(structure1);`
` Atom[] ca2 = StructureTools.getAtomCAArray(structure2);`
` `
` // get default parameters`
` FatCatParameters params = new FatCatParameters();`
` `
` `
` AFPChain afpChain = algorithm.align(ca1,ca2,params); `
` afpChain.setName1(name1);`
` afpChain.setName2(name2);`
` // show original FATCAT output:`
` System.out.println(afpChain.toFatcat(ca1,ca2));`
` `
` // 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));`
` `
` StructureAlignmentDisplay.display(afpChain, ca1, ca2);`
` `
` } catch (Exception e) {`
` e.printStackTrace();`
` return;`
` }`
` }`