Java Code Examples for org.biojava.nbio.structure.align.model.AFPChain#getFocusRes2()

/**
 * Set the list of equivalent residues in the two proteins given a list of
 * AFPs
 *
 * WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in
 * afpChain!
 *
 * @param afpChain
 *            the AFPChain to store resuts
 * @param afpn
 *            nr of afp
 * @param afpPositions
 * @param listStart
 * @return nr of eq residues
 */

public static int afp2Res(AFPChain afpChain, int afpn, int[] afpPositions,
		int listStart) {
	int[] res1 = afpChain.getFocusRes1();
	int[] res2 = afpChain.getFocusRes2();
	int minLen = afpChain.getMinLen();

	int n = 0;

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

	for (int i = listStart; i < listStart + afpn; i++) {
		int a = afpPositions[i];
		for (int j = 0; j < afpSet.get(a).getFragLen(); j++) {
			if (n >= minLen) {
				throw new RuntimeException(
						"Error: too many residues in AFPChainer.afp2Res!");
			}
			res1[n] = afpSet.get(a).getP1() + j;
			res2[n] = afpSet.get(a).getP2() + j;
			n++;
		}
	}

	afpChain.setFocusRes1(res1);
	afpChain.setFocusRes2(res2);
	afpChain.setFocusResn(n);

	if (n == 0) {
		logger.warn("n=0!!! + " + afpn + " " + listStart + " "
				+ afpPositions.length);
	}
	return n;
}
 

/**
//return the rmsd of the residues from the segments that form the given AFP list
//this value can be a measurement (1) for the connectivity of the AFPs
 *
 * @param afpn
 * @param afpPositions the positions of AFPs to work on.
 * @param listStart the starting position in the list of AFPs
 * @param afpChain
 * @param ca1
 * @param ca2
 * @return rmsd
 */

protected static double calAfpRmsd(int afpn, int[] afpPositions, int listStart,  AFPChain afpChain,Atom[] ca1, Atom[] ca2)
{


	if (debug)
		System.out.println("XXX calling afp2res "+ afpn + " " + afpPositions.length);

	int focusResn = AFPTwister.afp2Res(afpChain,afpn, afpPositions, listStart);


	int[] focusRes1 = afpChain.getFocusRes1();
	int[] focusRes2 = afpChain.getFocusRes2();

	if (debug)
		System.out.println("XXX calculating calAfpRmsd: " + focusResn + " " + focusRes1.length + " " + focusRes2.length + " " + afpChain.getMinLen() + " " );
	double rmsd = getRmsd(focusResn, focusRes1, focusRes2 , afpChain,ca1,  ca2);

	return rmsd;
}
 

/**
 * superimposing according to the optimized alignment
 *
 * @param afpChain
 * @param ca1
 * @param ca2
 * @return Group array twisted.
 * @throws StructureException
 */
public static Group[] twistOptimized(AFPChain afpChain, Atom[] ca1,
		Atom[] ca2) throws StructureException {

	Atom[] optTwistPdb = new Atom[ca2.length];

	int gPos = -1;
	for (Atom a : ca2) {
		gPos++;
		optTwistPdb[gPos] = a;
	}

	int blockNum = afpChain.getBlockNum();

	int b2 = 0;
	int e2 = 0;
	int focusResn = 0;
	int[] focusRes1 = afpChain.getFocusRes1();
	int[] focusRes2 = afpChain.getFocusRes2();

	if (focusRes1 == null) {
		focusRes1 = new int[afpChain.getCa1Length()];
		afpChain.setFocusRes1(focusRes1);
	}
	if (focusRes2 == null) {
		focusRes2 = new int[afpChain.getCa2Length()];
		afpChain.setFocusRes2(focusRes2);
	}

	int[] optLen = afpChain.getOptLen();
	int[][][] optAln = afpChain.getOptAln();

	for (int bk = 0; bk < blockNum; bk++) {
		// THIS IS TRANSFORMING THE ORIGINAL ca2 COORDINATES, NO CLONING...
		// copies the atoms over to iniTwistPdb later on in modifyCod
		transformOrigPDB(optLen[bk], optAln[bk][0], optAln[bk][1], ca1,
				ca2, afpChain, bk);

		// transform pro2 according to comparison of pro1 and pro2 at give
		// residues
		if (bk > 0) {
			b2 = e2;
		}
		if (bk < blockNum - 1) { // bend at the middle of two consecutive
									// blocks
			e2 = optAln[bk][1][optLen[bk] - 1];
			e2 = (optAln[bk + 1][1][0] - e2) / 2 + e2;
		} else {
			e2 = ca2.length;
		}
		cloneAtomRange(optTwistPdb, ca2, b2, e2);
		for (int i = 0; i < optLen[bk]; i++) {
			focusRes1[focusResn] = optAln[bk][0][i];
			focusRes2[focusResn] = optAln[bk][1][i];
			focusResn++;
		}
	}
	int totalLenOpt = focusResn;
	logger.debug("calrmsdopt for {} residues", focusResn);
	double totalRmsdOpt = calCaRmsd(ca1, optTwistPdb, focusResn, focusRes1,
			focusRes2);
	logger.debug("got opt RMSD: {}", totalRmsdOpt);
	int optLength = afpChain.getOptLength();

	if (totalLenOpt != optLength) {
		logger.warn("Final alignment length is different {} {}",
				totalLenOpt, optLength);
	}
	logger.debug("final alignment length {}, rmsd {}", focusResn,
			totalRmsdOpt);

	afpChain.setTotalLenOpt(totalLenOpt);
	afpChain.setTotalRmsdOpt(totalRmsdOpt);

	return StructureTools.cloneGroups(optTwistPdb);

}