Examples with NucleicAcid3 ffx.potential.bonded.ResidueEnumerations.NucleicAcid3 used on opensource projects

Example 6 with NucleicAcid3

use of ffx.potential.bonded.ResidueEnumerations.NucleicAcid3 in project ffx by mjschnie.

the class RotamerLibrary method measureNARotamer.

/**
 * Measure the current torsions of a nucleic acid Residue, starting from the
 * 5'-most torsion.
 *
 * Chi[0]-chi[6] in order are: delta (i-1), epsilon (i-1), zeta (i-1), alpha
 * (i), beta (i), gamma (i) and delta (i) for residue i.
 *
 * @param residue Residue to be measured.
 * @param chi Array to be filled with torsion values.
 * @param print Verbosity flag.
 */
public static void measureNARotamer(Residue residue, double[] chi, boolean print) {
    NucleicAcid3 name = NucleicAcid3.valueOf(residue.getName());
    Residue prevResidue = residue.getPreviousResidue();
    Torsion torsion;
    Atom C5s = (Atom) residue.getAtomNode("C5\'");
    Atom C4s = (Atom) residue.getAtomNode("C4\'");
    Atom C3s = (Atom) residue.getAtomNode("C3\'");
    Atom O3s = (Atom) residue.getAtomNode("O3\'");
    Atom O5s = (Atom) residue.getAtomNode("O5\'");
    Atom P = (Atom) residue.getAtomNode("P");
    /*
         * Start by measuring delta (i-1) if available, working up to delta.  If
         * there is no prior residue, start measuring from the 5'-most torsion.
         */
    if (prevResidue == null) {
        switch(name) {
            case GUA:
            case ADE:
            case DGU:
            case DAD:
            case CYT:
            case URI:
            case THY:
            case DCY:
            case DTY:
                /*
                     * If there is an H5T, measure alpha based on H5T.  Else,
                     * measure zeta (i-1) based on OP3 and alpha on P.
                     */
                Atom H5T = (Atom) residue.getAtomNode("H5T");
                if (H5T != null) {
                    torsion = H5T.getTorsion(O5s, C5s, C4s);
                    chi[4] = torsion.getValue();
                    if (print) {
                        logger.info(torsion.toString());
                    }
                } else {
                    Atom OP3 = (Atom) residue.getAtomNode("OP3");
                    if (OP3 != null) {
                        torsion = OP3.getTorsion(P, O5s, C5s);
                        chi[3] = torsion.getValue();
                        if (print) {
                            logger.info(torsion.toString());
                        }
                    }
                    torsion = P.getTorsion(O5s, C5s, C4s);
                    chi[4] = torsion.getValue();
                    if (print) {
                        logger.info(torsion.toString());
                    }
                }
                break;
            default:
                break;
        }
    } else {
        switch(name) {
            case GUA:
            case ADE:
            case DGU:
            case DAD:
            case CYT:
            case URI:
            case THY:
            case DCY:
            case DTY:
                Atom O3sPrev = (Atom) prevResidue.getAtomNode("O3\'");
                Atom C3sPrev = (Atom) prevResidue.getAtomNode("C3\'");
                Atom C4sPrev = (Atom) prevResidue.getAtomNode("C4\'");
                Atom C5sPrev = (Atom) prevResidue.getAtomNode("C5\'");
                torsion = C5sPrev.getTorsion(C4sPrev, C3sPrev, O3sPrev);
                chi[0] = torsion.getValue();
                if (print) {
                    logger.info(torsion.toString());
                }
                torsion = C4sPrev.getTorsion(C3sPrev, O3sPrev, P);
                chi[1] = torsion.getValue();
                if (print) {
                    logger.info(torsion.toString());
                }
                torsion = C3sPrev.getTorsion(O3sPrev, P, O5s);
                chi[2] = torsion.getValue();
                if (print) {
                    logger.info(torsion.toString());
                }
                torsion = O3sPrev.getTorsion(P, O5s, C5s);
                chi[3] = torsion.getValue();
                if (print) {
                    logger.info(torsion.toString());
                }
                torsion = P.getTorsion(O5s, C5s, C4s);
                chi[4] = torsion.getValue();
                if (print) {
                    logger.info(torsion.toString());
                }
                break;
            default:
                break;
        }
    }
    /*
         * Measure torsions common to all nucleic acids (gamma, delta).
         */
    torsion = O5s.getTorsion(C5s, C4s, C3s);
    chi[5] = torsion.getValue();
    if (print) {
        logger.info(torsion.toString());
    }
    torsion = C5s.getTorsion(C4s, C3s, O3s);
    chi[6] = torsion.getValue();
    if (print) {
        logger.info(torsion.toString());
    }
}

Example 7 with NucleicAcid3

use of ffx.potential.bonded.ResidueEnumerations.NucleicAcid3 in project ffx by mjschnie.

the class RotamerLibrary method applyNARotamer.

/**
 * Applies a nucleic acid Rotamer, and throws NACorrectionException
 * if the Rotamer must be corrected too far to correctly join to Residue
 * i-1. correctionThreshold and independent are both special-case variables;
 * a non-zero correctionThreshold is used to prune Rotamers with excessively
 * large corrections, and independent disables the NA correction, presently
 * only performed by saveRotamers.
 *
 * Note that the independent flag is separate from DEE independence: DEE
 * independence is preserved by applying corrections based on a non-variable
 * set of coordinates, and is wholly independent of what is happening to
 * residue i-1.
 *
 * Cannot presently handle 3' phosphate caps: I do not know what they would
 * be labeled as in PDB files. A template for how to handle 3' phosphate
 * caps is written but commented out.
 *
 * @param residue Residue.
 * @param rotamer Rotamer to be applied to Residue.
 * @param correctionThreshold Maximum acceptable backbone correction.
 * @param independent Whether to draw NA rotamer independent of chain
 * context.
 * @throws NACorrectionException If correction .GT.
 * correctionThreshold.
 */
private static void applyNARotamer(Residue residue, Rotamer rotamer, double correctionThreshold, boolean independent) throws NACorrectionException {
    NucleicAcid3 na = NucleicAcid3.valueOf(residue.getName());
    Residue prevResidue = residue.getPreviousResidue();
    // 3' terminal
    boolean is3sTerminal = false;
    int sugarPucker;
    int prevSugarPucker;
    if (residue.getNextResidue() == null) {
        is3sTerminal = true;
    }
    // Check if this is a 3' phosphate being listed as its own residue.
    /* if (residue.getAtomList().size() == 1) {
         return;
         } */
    // Could be specified by appplySugarPucker, but that
    boolean isDeoxy;
    // would be confusing.
    switch(na) {
        case DTY:
        case DGU:
        case DAD:
        case DCY:
            isDeoxy = true;
            break;
        case GUA:
        case CYT:
        case URI:
        case ADE:
        case THY:
        default:
            isDeoxy = false;
            break;
    }
    // Note: chi values will generally be applied from chi7 to chi1.
    // Will have to add an else-if to handle DNA C3'-exo configurations.
    // Sugar pucker = 1: North pucker.  2: South pucker.  3: C3'-exo pucker.
    sugarPucker = checkPucker(rotamer.chi7);
    prevSugarPucker = checkPucker(rotamer.chi1);
    // Revert C1', O4', and C4' coordinates to PDB defaults.
    Atom C1s = (Atom) residue.getAtomNode("C1\'");
    C1s.moveTo(residue.getC1sCoords());
    Atom O4s = (Atom) residue.getAtomNode("O4\'");
    O4s.moveTo(residue.getO4sCoords());
    Atom C4s = (Atom) residue.getAtomNode("C4\'");
    C4s.moveTo(residue.getC4sCoords());
    // Presently, the exterior method loadPriorAtomicCoordinates() directly
    // calls applySugarPucker instead of going through applyRotamer().
    applySugarPucker(residue, sugarPucker, isDeoxy, true);
    applyNABackbone(residue, rotamer, prevResidue);
    if (prevResidue != null && !independent) {
        applyNACorrections(residue, prevResidue, rotamer, prevSugarPucker, correctionThreshold, isDeoxy, is3sTerminal);
    }
    /* else if (!independent) {
         startingResidueConsistencyCheck(residue, rotamer, correctionThreshold);
         } */
    applyNASideAtoms(residue, rotamer, prevResidue, isDeoxy, is3sTerminal, prevSugarPucker);
}

Example 8 with NucleicAcid3

use of ffx.potential.bonded.ResidueEnumerations.NucleicAcid3 in project ffx by mjschnie.

the class MultiResidue method getRotamers.

@Override
public Rotamer[] getRotamers(RotamerLibrary library) {
    if (rotamers != null) {
        return rotamers;
    }
    List<Rotamer[]> usual = new ArrayList<>();
    int nRots = 0;
    for (Residue residue : consideredResidues) {
        Rotamer[] rotamers = library.getRotamers(residue);
        if (rotamers != null && rotamers.length > 0) {
            usual.add(rotamers);
            nRots += rotamers.length;
        }
    }
    if (library.getUsingOrigCoordsRotamer()) {
        if (originalRotamer == null && (residueType == ResidueType.AA || residueType == ResidueType.NA)) {
            ResidueState origState = storeState();
            double[] chi = RotamerLibrary.measureRotamer(activeResidue, false);
            if (residueType == ResidueType.AA) {
                AminoAcid3 aa3 = this.getAminoAcid3();
                originalRotamer = new Rotamer(aa3, origState, chi);
            } else if (residueType == ResidueType.NA) {
                NucleicAcid3 na3 = this.getNucleicAcid3();
                originalRotamer = new Rotamer(na3, origState, chi);
            }
        }
        Rotamer[] allRotamers;
        if (originalRotamer != null) {
            allRotamers = new Rotamer[nRots + 1];
            int index;
            if (origAtEnd) {
                index = 0;
                allRotamers[allRotamers.length - 1] = originalRotamer;
            } else {
                index = 1;
                allRotamers[0] = originalRotamer;
            }
            for (Rotamer[] rotamersI : usual) {
                int nrotamers = rotamersI.length;
                System.arraycopy(rotamersI, 0, allRotamers, index, nrotamers);
                index += nrotamers;
            }
        } else {
            allRotamers = addAllDefaultRotamers(usual, nRots);
        }
        return allRotamers;
    } else {
        return addAllDefaultRotamers(usual, nRots);
    }
}