Java Code Examples for org.biojava.nbio.structure.align.model.AFPChain#setProbability()

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Example 1
Source File: FatCatAligner.java    From biojava with GNU Lesser General Public License v2.1 2 votes vote down vote up 
/**
 * run AFP chaining allowing up to maxTra flexible regions.
 * Input is original coordinates.
 *
 */
private static Group[] chainAfp(FatCatParameters params,AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException{

	// we don;t want to rotate input atoms, do we?
	Atom[] ca2clone = StructureTools.cloneAtomArray(ca2);

	List<AFP> afpSet = afpChain.getAfpSet();

	if (debug)
		System.out.println("entering chainAfp");
	int afpNum = afpSet.size();

	if ( afpNum < 1)
		return new Group[0];

	long bgtime = System.currentTimeMillis();
	if(debug)    {
		System.out.println(String.format("total AFP %d\n", afpNum));
	}

	//run AFP chaining

	AFPChainer.doChainAfp(params,afpChain ,ca1,ca2);

	int afpChainLen = afpChain.getAfpChainLen();

	if(afpChainLen < 1)     {

		afpChain.setShortAlign(true);
		return new Group[0];
	} //very short alignment

	long chaintime = System.currentTimeMillis();
	if(debug)    {

		System.out.println("Afp chaining: time " + (chaintime-bgtime));
	}

	// do post processing

	AFPPostProcessor.postProcess(params, afpChain,ca1,ca2);

	// Optimize the final alignment

	AFPOptimizer.optimizeAln(params, afpChain,ca1,ca2);

	AFPOptimizer.blockInfo( afpChain);

	AFPOptimizer.updateScore(params,afpChain);

	AFPAlignmentDisplay.getAlign(afpChain,ca1,ca2);

	Group[] twistedPDB = AFPTwister.twistPDB(afpChain, ca1, ca2clone);

	SigEva sig =  new SigEva();
	double probability = sig.calSigAll(params, afpChain);
	afpChain.setProbability(probability);
	double normAlignScore = sig.calNS(params,afpChain);
	afpChain.setNormAlignScore(normAlignScore);
	double tmScore = AFPChainScorer.getTMScore(afpChain, ca1, ca2,false);
	afpChain.setTMScore(tmScore);

	/*

	SIGEVA  sig;
	probability = sig.calSigAll(maxTra, sparse, pro1Len, pro2Len, alignScore, totalRmsdOpt, optLength, blockNum - 1);
	normAlignScore = sig.calNS(pro1Len, pro2Len, alignScore, totalRmsdOpt, optLength, blockNum - 1);

	 */

	//if(maxTra == 0)       probability = sig.calSigRigid(pro1Len, pro2Len, alignScore, totalRmsdOpt, optLength);
	//else  probability = sig.calSigFlexi(pro1Len, pro2Len, alignScore, totalRmsdOpt, optLength, blockNum - 1);

	if(debug)    {

		long nowtime = System.currentTimeMillis();
		long diff = nowtime - chaintime;
		System.out.println("Alignment optimization: time "+ diff);

		System.out.println("score:      " + afpChain.getAlignScore());
		System.out.println("opt length: " + afpChain.getOptLength());
		System.out.println("opt rmsd:   "+ afpChain.getTotalRmsdOpt());

	}
	return twistedPDB;

}