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

/**
 * get the afp list and residue list for each block
 */

public static void blockInfo(AFPChain afpChain)
{
	int     i, j, k, a, n;

	int blockNum = afpChain.getBlockNum();

	int[] blockSize =afpChain.getBlockSize();
	int[] afpChainList = afpChain.getAfpChainList();
	int[] block2Afp = afpChain.getBlock2Afp();
	int[][][]blockResList = afpChain.getBlockResList();

	List<AFP>afpSet = afpChain.getAfpSet();
	int[] blockResSize = afpChain.getBlockResSize();

	for(i = 0; i < blockNum; i ++)  {
		n = 0;
		for(j = 0; j < blockSize[i]; j ++)      {
			//the index in afpChainList, not in the whole afp set
			a = afpChainList[block2Afp[i] + j];
			for(k = 0; k < afpSet.get(a).getFragLen(); k ++)     {
				blockResList[i][0][n] = afpSet.get(a).getP1() + k;
				blockResList[i][1][n] = afpSet.get(a).getP2() + k;
				n ++;
			}
		}
		blockResSize[i] = n;
	}

	afpChain.setBlockResSize(blockResSize);
	afpChain.setBlockSize(blockSize);
	afpChain.setAfpChainList(afpChainList);
	afpChain.setBlock2Afp(block2Afp);
	afpChain.setBlockResList(blockResList);
}
 

/**
return the rmsd of two blocks
 */
private static double combineRmsd(int b1, int b2, AFPChain afpChain,Atom[] ca1,Atom[] ca2)
{
	int     i;
	int     afpn = 0;

	int[] afpChainList =afpChain.getAfpChainList();

	int[] block2Afp = afpChain.getBlock2Afp();
	int[] blockSize = afpChain.getBlockSize();


	int[]   list = new int[blockSize[b1]+blockSize[b2]];
	for(i = block2Afp[b1]; i < block2Afp[b1] + blockSize[b1]; i ++) {
		list[afpn ++] = afpChainList[i];
	}
	for(i = block2Afp[b2]; i < block2Afp[b2] + blockSize[b2]; i ++) {
		list[afpn ++] = afpChainList[i];
	}
	double  rmsd = AFPChainer.calAfpRmsd(afpn, list,0, afpChain,ca1,ca2);

	afpChain.setBlock2Afp(block2Afp);
	afpChain.setBlockSize(blockSize);
	afpChain.setAfpChainList(afpChainList);

	return rmsd;
}
 

/**
 * to update the chaining score after block delete and merge processed
 * the blockScore value is important for significance evaluation
 */
public static void updateScore(FatCatParameters params, AFPChain afpChain)
{
	int     i, j, bknow, bkold, g1, g2;


	afpChain.setConn(0d);
	afpChain.setDVar(0d);

	int blockNum = afpChain.getBlockNum();
	int alignScoreUpdate = 0;
	double[] blockScore = afpChain.getBlockScore();
	int[] blockGap = afpChain.getBlockGap();
	int[] blockSize =afpChain.getBlockSize();
	int[] afpChainList = afpChain.getAfpChainList();
	List<AFP>afpSet = afpChain.getAfpSet();
	int[] block2Afp = afpChain.getBlock2Afp();

	double torsionPenalty = params.getTorsionPenalty();


	bkold = 0;
	for(i = 0; i < blockNum; i ++)  {
		blockScore[i] = 0;
		blockGap[i] = 0;
		for(j = 0; j < blockSize[i]; j ++)      {
			bknow = afpChainList[block2Afp[i] + j];
			if(j == 0)      {
				blockScore[i] = afpSet.get(bknow).getScore();
			}
			else    {
				AFPChainer.afpPairConn(bkold, bknow, params, afpChain); //note: j, i
				Double conn = afpChain.getConn();
				blockScore[i] += afpSet.get(bknow).getScore() + conn;
				g1 = afpSet.get(bknow).getP1() - afpSet.get(bkold).getP1() - afpSet.get(bkold).getFragLen();
				g2 = afpSet.get(bknow).getP2() - afpSet.get(bkold).getP2() - afpSet.get(bkold).getFragLen();
				blockGap[i] += (g1 > g2)?g1:g2;
			}
			bkold = bknow;
		}
		alignScoreUpdate += blockScore[i];
	}
	if(blockNum >= 2)       {
		alignScoreUpdate += (blockNum - 1) * torsionPenalty;
	}

	afpChain.setBlockGap(blockGap);
	afpChain.setAlignScoreUpdate(alignScoreUpdate);
	afpChain.setBlockScore(blockScore);
	afpChain.setBlockSize(blockSize);
	afpChain.setAfpChainList(afpChainList);
	afpChain.setBlock2Afp(block2Afp);
}
 

/**
 * in some special cases, there is no maginificent twists in the
final chaining result; however, their rmsd (original and after
optimizing) are very large. Therefore, a post-process is taken
to split the blocks further at the ralative bad connections (
with relative high distance variation)
to be tested:
  split or not according to optimized or initial chaining???
 */

private static void splitBlock(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
{
	if ( debug)
		System.err.println("AFPPostProcessor: splitBlock");
	int     i, a, bk, cut;
	double  maxs, maxt;
	int blockNum = afpChain.getBlockNum();
	int maxTra = params.getMaxTra();
	double badRmsd = params.getBadRmsd();

	int     blockNum0 = blockNum;

	double[] blockRmsd = afpChain.getBlockRmsd();
	int[] blockSize = afpChain.getBlockSize();
	int[] block2Afp = afpChain.getBlock2Afp();
	double[] afpChainTwiList = afpChain.getAfpChainTwiList();

	bk = 0;
	while(blockNum < maxTra + 1)    {
		maxs = 0;
		for(i = 0; i < blockNum; i ++)   {
			if(blockRmsd[i] > maxs && blockSize[i] > 2) { //according to the optimized alignment
				maxs = blockRmsd[i];
				bk = i;
			} //!(Note: optRmsd, not blockRmsd, according to the optimized alignment
		}
		if(maxs < badRmsd)      break;
		maxt = 0;
		cut = 0;
		for(i = 1; i < blockSize[bk]; i ++)     {
			a = i + block2Afp[bk];
			if(afpChainTwiList[a] > maxt)   {
				maxt = afpChainTwiList[a];
				cut = i;

			}
		}
		if(debug)
			System.out.println(String.format("block %d original size %d rmsd %.3f maxt %.2f cut at %d\n", bk, blockSize[bk], maxs, maxt, cut));
		for(i = blockNum - 1; i > bk; i --)     {
			block2Afp[i + 1] = block2Afp[i];
			blockSize[i + 1] = blockSize[i];
			blockRmsd[i + 1] = blockRmsd[i];
		} //update block information
		block2Afp[bk + 1] = cut + block2Afp[bk];
		blockSize[bk + 1] = blockSize[bk] - cut;
		blockSize[bk] = cut;

		if(debug)
			System.out.println(String.format("  split into %d and %d sizes\n", blockSize[bk], blockSize[bk + 1]));


		int[] afpChainList = afpChain.getAfpChainList();
		//int[] subrange1    = getSubrange(afpChainList, block2Afp[bk + 1] );
		blockRmsd[bk + 1]  = AFPChainer.calAfpRmsd(blockSize[bk + 1],  afpChainList, block2Afp[bk + 1] , afpChain, ca1, ca2);

		//int[] subrange2    = getSubrange(afpChainList, block2Afp[bk] );
		blockRmsd[bk]      = AFPChainer.calAfpRmsd(blockSize[bk],      afpChainList, block2Afp[bk], afpChain, ca1, ca2);

		//split a block at the biggest position
		blockNum ++;
		afpChain.setAfpChainList(afpChainList);
	}
	if(blockNum - blockNum0 > 0)    {
		if(debug)
			System.out.println(String.format("Split %d times:\n", blockNum - blockNum0));
		for(i = 0; i < blockNum; i ++)  {
			if(debug)
				System.out.println(String.format("  block %d size %d from %d rmsd %.3f\n", i, blockSize[i], block2Afp[i], blockRmsd[i]));
		}
	}


	afpChain.setBlockNum(blockNum);
	afpChain.setBlockSize(blockSize);
	afpChain.setBlockRmsd(blockRmsd);
	afpChain.setBlock2Afp(block2Afp);


}
 

/**
 * remove the artifical small rigid-body superimpose in the middle
 clust the similar superimpositions (caused by the small flexible
 region, which is detected as a seperate rigid superimposing region by adding
 two twists before and after it(artifically!)
 one possible solution: allowing long enough loops in the chaining process,
 which however increase the calculation complexity
 */
private static void deleteBlock(FatCatParameters params, AFPChain afpChain,Atom[] ca1, Atom[] ca2)
{
	int blockNum = afpChain.getBlockNum();
	List<AFP> afpSet = afpChain.getAfpSet();

	int[] afpChainList =afpChain.getAfpChainList();



	int[] block2Afp = afpChain.getBlock2Afp();
	int[] blockSize = afpChain.getBlockSize();

	double[] blockRmsd = afpChain.getBlockRmsd();

	int fragLen = params.getFragLen();

	//remove those blocks (both in terminals and in the middle) with only a AFP
	//but still keep those small blocks spaning large regions
	if(blockNum <= 1)       return;
	int     blockNumOld = blockNum;
	int     i, j, b1, b2, e1, e2, len;
	e1 = e2 = 0;
	for(i = 0; i < blockNum; i ++) {
		b1 = e1;
		b2 = e2;
		if(i < blockNum - 1)    {
			e1 = afpSet.get(afpChainList[block2Afp[i + 1]]).getP1();
			e2 = afpSet.get(afpChainList[block2Afp[i + 1]]).getP2();
		}
		else    {
			e1 = ca1.length;
			e2 = ca2.length;
		}
		if(blockSize[i] > 1)    continue;
		len = (e1 - b1) < (e2 - b2)?(e1 - b1):(e2 - b2);
		//if(i == blockNum - 1) blockNum --;
		if(len < 2 * fragLen)   {
			for(j = i; j < blockNum - 1; j ++)      {
				blockRmsd[j] = blockRmsd[j + 1];
				blockSize[j] = blockSize[j + 1];
				block2Afp[j] = block2Afp[j + 1];
			}
			blockNum --;
			i --;
		} //delete a block
	}
	if(blockNumOld > blockNum)
		if(debug)
			System.out.println(
					String.format("Delete %d small blocks\n", blockNumOld - blockNum)
			);


	if (debug)
		System.err.println("deleteBlock: end blockNum:"+ blockNum);
	afpChain.setBlock2Afp(block2Afp);
	afpChain.setBlockSize(blockSize);
	afpChain.setAfpChainList(afpChainList);
	afpChain.setBlockNum(blockNum);
	afpChain.setBlockRmsd(blockRmsd);
}