/**
* Builds an {@link AFPChain} from already-matched arrays of atoms and residues.
*
* @param ca1 An array of atoms in the first structure
* @param ca2 An array of atoms in the second structure
* @param residues1 An array of {@link ResidueNumber ResidueNumbers} in the first structure that
* are aligned. Only null ResidueNumbers are considered to be unaligned
* @param residues2 An array of {@link ResidueNumber ResidueNumbers} in the second structure that
* are aligned. Only null ResidueNumbers are considered to be unaligned
* @throws StructureException
*/
private static AFPChain buildAlignment(
Atom[] ca1, Atom[] ca2, ResidueNumber[] residues1, ResidueNumber[] residues2)
throws StructureException {
// remove any gap
// this includes the ones introduced by the nullifying above
List<ResidueNumber> alignedResiduesList1 = new ArrayList<ResidueNumber>();
List<ResidueNumber> alignedResiduesList2 = new ArrayList<ResidueNumber>();
for (int i = 0; i < residues1.length; i++) {
if (residues1[i] != null && residues2[i] != null) {
alignedResiduesList1.add(residues1[i]);
alignedResiduesList2.add(residues2[i]);
}
}
ResidueNumber[] alignedResidues1 =
alignedResiduesList1.toArray(new ResidueNumber[alignedResiduesList1.size()]);
ResidueNumber[] alignedResidues2 =
alignedResiduesList2.toArray(new ResidueNumber[alignedResiduesList2.size()]);
AFPChain afpChain = AlignmentTools.createAFPChain(ca1, ca2, alignedResidues1, alignedResidues2);
afpChain.setAlgorithmName("unknown");
AlignmentTools.updateSuperposition(afpChain, ca1, ca2);
afpChain.setBlockSize(new int[] {afpChain.getNrEQR()});
afpChain.setBlockRmsd(new double[] {afpChain.getTotalRmsdOpt()});
afpChain.setBlockGap(new int[] {afpChain.getGapLen()});
return afpChain;
}
/**
* Guesses the order of symmetry in an alignment
*
* <p>Uses {@link #getSymmetryOrder(Map alignment, Map identity, int, float)} to determine the the
* symmetry order. For the identity alignment, sorts the aligned residues of each protein
* sequentially, then defines the ith residues of each protein to be equivalent.
*/
public static int getSymmetryOrder(AFPChain afpChain, int maxSymmetry, float minimumMetricChange)
throws StructureException {
// alignment comes from the afpChain alignment
Map<Integer, Integer> alignment = AlignmentTools.alignmentAsMap(afpChain);
// Now construct identity to map aligned residues in sequential order
Map<Integer, Integer> identity = guessSequentialAlignment(alignment, true);
return AlignmentTools.getSymmetryOrder(alignment, identity, maxSymmetry, minimumMetricChange);
}
/**
* It replaces an optimal alignment of an AFPChain and calculates all the new alignment scores and
* variables.
*/
public static AFPChain replaceOptAln(int[][][] newAlgn, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
throws StructureException {
// The order is the number of groups in the newAlgn
int order = newAlgn.length;
// Calculate the alignment length from all the subunits lengths
int[] optLens = new int[order];
for (int s = 0; s < order; s++) {
optLens[s] = newAlgn[s][0].length;
}
int optLength = 0;
for (int s = 0; s < order; s++) {
optLength += optLens[s];
}
// Create a copy of the original AFPChain and set everything needed for the structure update
AFPChain copyAFP = (AFPChain) afpChain.clone();
// Set the new parameters of the optimal alignment
copyAFP.setOptLength(optLength);
copyAFP.setOptLen(optLens);
copyAFP.setOptAln(newAlgn);
// Set the block information of the new alignment
copyAFP.setBlockNum(order);
copyAFP.setBlockSize(optLens);
copyAFP.setBlockResList(newAlgn);
copyAFP.setBlockResSize(optLens);
copyAFP.setBlockGap(calculateBlockGap(newAlgn));
// Recalculate properties: superposition, tm-score, etc
Atom[] ca2clone = StructureTools.cloneAtomArray(ca2); // don't modify ca2 positions
AlignmentTools.updateSuperposition(copyAFP, ca1, ca2clone);
// It re-does the sequence alignment strings from the OptAlgn information only
copyAFP.setAlnsymb(null);
AFPAlignmentDisplay.getAlign(copyAFP, ca1, ca2clone);
return copyAFP;
}
/**
* @param afpChain Input afpchain. UNMODIFIED
* @param ca1
* @param ca2
* @param optLens
* @param optAln
* @return A NEW AfpChain based off the input but with the optAln modified
* @throws StructureException if an error occured during superposition
*/
public static AFPChain replaceOptAln(
AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNum, int[] optLens, int[][][] optAln)
throws StructureException {
int optLength = 0;
for (int blk = 0; blk < blockNum; blk++) {
optLength += optLens[blk];
}
// set everything
AFPChain refinedAFP = (AFPChain) afpChain.clone();
refinedAFP.setOptLength(optLength);
refinedAFP.setBlockSize(optLens);
refinedAFP.setOptLen(optLens);
refinedAFP.setOptAln(optAln);
refinedAFP.setBlockNum(blockNum);
// TODO recalculate properties: superposition, tm-score, etc
Atom[] ca2clone = StructureTools.cloneAtomArray(ca2); // don't modify ca2 positions
AlignmentTools.updateSuperposition(refinedAFP, ca1, ca2clone);
AFPAlignmentDisplay.getAlign(refinedAFP, ca1, ca2clone);
return refinedAFP;
}
