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

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Example 1
Source File: AFPCalculator.java    From biojava with GNU Lesser General Public License v2.1 4 votes vote down vote up 
public static final  void extractAFPChains(FatCatParameters params, AFPChain afpChain,Atom[] ca1,Atom[] ca2) throws StructureException {



		List<AFP> afpSet = new ArrayList<AFP>();
		afpChain.setAfpSet(afpSet);

		if ( debug )
			System.err.println("nr of atoms ca1: " + ca1.length + " ca2: " +  ca2.length);



		int     p1, p2;
		@SuppressWarnings("unused")
		int n0, n, n1, n2;
		double  filter1;
		double rmsd = 0;

		Matrix r = new Matrix(3,3);
		Atom   t = new AtomImpl();


		int sparse = params.getSparse();
		int maxTra = params.getMaxTra();
		int fragLen = params.getFragLen();
		double disFilter = params.getDisFilter();
		double rmsdCut = params.getRmsdCut();
		double badRmsd = params.getBadRmsd();
		double fragScore = params.getFragScore();

		int     add = sparse + 1; //if add > 1, use sparse sampling
		n0 = n = n1 = n2 = 0;

		int minLen = 0;

		int prot1Length = ca1.length;
		int prot2Length = ca2.length;

		if(prot1Length < prot2Length)
			minLen = prot1Length;
		else
			minLen = prot2Length;
		afpChain.setMinLen(minLen);

		afpChain.setBlockResList(new int[maxTra+1][2][minLen]);
		afpChain.setFocusRes1(new int[minLen]);
		afpChain.setFocusRes2(new int[minLen]);

		for(p1 = 0; p1 < prot1Length - fragLen; p1 += add )    {
			for(p2 = 0; p2 < prot2Length - fragLen; p2 += add)     {
				n0 ++;
				filter1 = getEnd2EndDistance(ca1, ca2, p1, p1 + fragLen - 1, p2, p2 + fragLen - 1);
				//difference bewteen end-to-end distances
				if(filter1 > disFilter) { n1 ++; continue; }
				boolean filter2 = filterTerminal(ca1,ca2, p1, p1 + fragLen - 1, p2, p2 + fragLen - 1, fragLen, minLen);
				if(filter2)     {
					n2 ++;
					continue;

				} //be cautious to use this filter !!

				// here FATCAT does a a jacobi transformation
				//rmsd = kearsay(fragLen, ca1[p1], ca2[p2], r, t);
				// we use the BioJava SVD instead...

				//
				rmsd = getRmsd(ca1,ca2,fragLen, p1,p2,r,t);

				if(rmsd < rmsdCut)      {
					AFP     afptmp = new AFP();
					afptmp.setP1(p1);
					afptmp.setP2(p2);
					afptmp.setFragLen(fragLen);
					afptmp.setRmsd(rmsd);
					afptmp.setM(r);
					afptmp.setT(t.getCoords());
					afptmp.setScore(scoreAfp(afptmp,badRmsd,fragScore));
					afpSet.add(afptmp);
					n ++;
				}
			}
		}

		int afpNum = afpSet.size();

		if(debug) {
			String msg = String.format("possible AFP-pairs %d, remain %d after filter 1 remove %d; filter 2 remove %d\n",
					n0, afpNum, n1, n2);
			System.err.println(msg);
		}


	}