Examples with NACorrectionException ffx.potential.bonded.NACorrectionException used on opensource projects

Example 1 with NACorrectionException

use of ffx.potential.bonded.NACorrectionException in project ffx by mjschnie.

the class RotamerOptimization method eliminateNABackboneRotamers.

/**
 * Eliminates NA backbone rotamers with corrections greater than threshold.
 * The int[] parameter allows the method to know how many Rotamers for each
 * residue have previously been pruned; currently, this means any Rotamer
 * pruned by reconcileNARotamersWithPriorResidues.
 * <p>
 * A nucleic correction threshold of 0 skips the entire method; this check
 * is presently being performed inside the method in case it is called again
 * at some point.
 *
 * @param residues Residues to eliminate bad backbone rotamers over.
 * @param numEliminatedRotamers Number of previously eliminated rotamers per
 * residue.
 */
private void eliminateNABackboneRotamers(Residue[] residues, int[] numEliminatedRotamers) {
    /* Atom atoms[] = molecularAssembly.getAtomArray();
         int nAtoms = atoms.length;
         String begin[] = new String[nAtoms];
         for (int i = 0; i < nAtoms; i++) {
         begin[i] = atoms[i].toString();
         } */
    if (nucleicCorrectionThreshold != 0) {
        logIfMaster(format(" Eliminating nucleic acid rotamers with correction vectors larger than %5.3f A", nucleicCorrectionThreshold));
        logIfMaster(format(" A minimum of %d rotamers per NA residue will carry through to energy calculations.", minNumberAcceptedNARotamers));
        ArrayList<Residue> resList = new ArrayList<>();
        resList.addAll(Arrays.asList(residues));
        ResidueState[] origCoordinates = ResidueState.storeAllCoordinates(resList);
        for (int j = 0; j < residues.length; j++) {
            Residue nucleicResidue = residues[j];
            Rotamer[] rotamers = nucleicResidue.getRotamers(library);
            if (nucleicResidue.getResidueType() == NA && rotamers != null) {
                int nrotamers = rotamers.length;
                // Default to all rotamers that have not previously been
                // eliminated; subtract as rotamers are rejected.
                int numAcceptedRotamers = nrotamers - numEliminatedRotamers[j];
                if (minNumberAcceptedNARotamers >= numAcceptedRotamers) {
                    continue;
                }
                ArrayList<DoubleIndexPair> rejectedRotamers = new ArrayList<>();
                for (int i = 0; i < nrotamers; i++) {
                    if (!check(j, i)) {
                        try {
                            RotamerLibrary.applyRotamer(nucleicResidue, rotamers[i], nucleicCorrectionThreshold);
                        } catch (NACorrectionException error) {
                            double rejectedCorrection = error.getCorrection();
                            numAcceptedRotamers--;
                            DoubleIndexPair rejected = new DoubleIndexPair(i, rejectedCorrection);
                            rejectedRotamers.add(rejected);
                        }
                    }
                }
                int numAdditionalRotamersToAccept = minNumberAcceptedNARotamers - numAcceptedRotamers;
                if (numAdditionalRotamersToAccept > 0) {
                    DoubleIndexPair[] rejectedArray = new DoubleIndexPair[rejectedRotamers.size()];
                    for (int i = 0; i < rejectedArray.length; i++) {
                        rejectedArray[i] = rejectedRotamers.get(i);
                    }
                    Arrays.sort(rejectedArray);
                    rejectedRotamers = new ArrayList<>();
                    rejectedRotamers.addAll(Arrays.asList(rejectedArray));
                    for (int i = 0; i < numAdditionalRotamersToAccept; i++) {
                        rejectedRotamers.remove(0);
                    }
                }
                for (DoubleIndexPair rotToReject : rejectedRotamers) {
                    eliminateRotamer(residues, j, rotToReject.getIndex(), print);
                    logIfMaster(format(" Correction magnitude was %6.4f A > %5.3f A", rotToReject.getDoubleValue(), nucleicCorrectionThreshold));
                }
            }
            nucleicResidue.revertState(origCoordinates[j]);
        // revertSingleResidueCoordinates(nucleicResidue, originalCoordinates[j]);
        }
    }
}