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

Example 6 with Angle

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

the class ForceFieldEnergyOpenMM method addAmoebaMultipoleForce.

private void addAmoebaMultipoleForce() {
    ParticleMeshEwald pme = super.getPmeNode();
    if (pme == null) {
        return;
    }
    int[][] axisAtom = pme.getAxisAtoms();
    double dipoleConversion = OpenMM_NmPerAngstrom;
    double quadrupoleConversion = OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom;
    double polarityConversion = OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom;
    double dampingFactorConversion = sqrt(OpenMM_NmPerAngstrom);
    amoebaMultipoleForce = OpenMM_AmoebaMultipoleForce_create();
    double polarScale = 1.0;
    if (pme.getPolarizationType() != Polarization.MUTUAL) {
        OpenMM_AmoebaMultipoleForce_setPolarizationType(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_Direct);
        if (pme.getPolarizationType() == Polarization.NONE) {
            polarScale = 0.0;
        }
    } else {
        ForceField forceField = molecularAssembly.getForceField();
        String algorithm = forceField.getString(ForceField.ForceFieldString.SCF_ALGORITHM, "CG");
        ParticleMeshEwald.SCFAlgorithm scfAlgorithm;
        try {
            algorithm = algorithm.replaceAll("-", "_").toUpperCase();
            scfAlgorithm = ParticleMeshEwald.SCFAlgorithm.valueOf(algorithm);
        } catch (Exception e) {
            scfAlgorithm = ParticleMeshEwald.SCFAlgorithm.CG;
        }
        switch(scfAlgorithm) {
            case EPT:
                logger.info(" Using extrapolated perturbation theory approximation instead of full SCF calculations. Not supported in FFX reference implementation.");
                OpenMM_AmoebaMultipoleForce_setPolarizationType(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_Extrapolated);
                PointerByReference exptCoefficients = OpenMM_DoubleArray_create(4);
                OpenMM_DoubleArray_set(exptCoefficients, 0, -0.154);
                OpenMM_DoubleArray_set(exptCoefficients, 1, 0.017);
                OpenMM_DoubleArray_set(exptCoefficients, 2, 0.657);
                OpenMM_DoubleArray_set(exptCoefficients, 3, 0.475);
                OpenMM_AmoebaMultipoleForce_setExtrapolationCoefficients(amoebaMultipoleForce, exptCoefficients);
                OpenMM_DoubleArray_destroy(exptCoefficients);
                break;
            case CG:
            case SOR:
            default:
                OpenMM_AmoebaMultipoleForce_setPolarizationType(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_Mutual);
                break;
        }
    }
    PointerByReference dipoles = OpenMM_DoubleArray_create(3);
    PointerByReference quadrupoles = OpenMM_DoubleArray_create(9);
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        MultipoleType multipoleType = atom.getMultipoleType();
        PolarizeType polarType = atom.getPolarizeType();
        /**
         * Define the frame definition.
         */
        int axisType = OpenMM_AmoebaMultipoleForce_NoAxisType;
        switch(multipoleType.frameDefinition) {
            case ZONLY:
                axisType = OpenMM_AmoebaMultipoleForce_ZOnly;
                break;
            case ZTHENX:
                axisType = OpenMM_AmoebaMultipoleForce_ZThenX;
                break;
            case BISECTOR:
                axisType = OpenMM_AmoebaMultipoleForce_Bisector;
                break;
            case ZTHENBISECTOR:
                axisType = OpenMM_AmoebaMultipoleForce_ZBisect;
                break;
            case TRISECTOR:
                axisType = OpenMM_AmoebaMultipoleForce_ThreeFold;
                break;
            default:
                break;
        }
        double useFactor = 1.0;
        if (!atoms[i].getUse() || !atoms[i].getElectrostatics()) {
            // if (!atoms[i].getUse()) {
            useFactor = 0.0;
        }
        // Should be 1.0 at this point.
        double lambdaScale = lambda;
        if (!atom.applyLambda()) {
            lambdaScale = 1.0;
        }
        useFactor *= lambdaScale;
        /**
         * Load local multipole coefficients.
         */
        for (int j = 0; j < 3; j++) {
            OpenMM_DoubleArray_set(dipoles, j, multipoleType.dipole[j] * dipoleConversion * useFactor);
        }
        int l = 0;
        for (int j = 0; j < 3; j++) {
            for (int k = 0; k < 3; k++) {
                OpenMM_DoubleArray_set(quadrupoles, l++, multipoleType.quadrupole[j][k] * quadrupoleConversion * useFactor / 3.0);
            }
        }
        // int zaxis = 0;
        int zaxis = 1;
        // int xaxis = 0;
        int xaxis = 1;
        // int yaxis = 0;
        int yaxis = 1;
        int[] refAtoms = axisAtom[i];
        if (refAtoms != null) {
            zaxis = refAtoms[0];
            if (refAtoms.length > 1) {
                xaxis = refAtoms[1];
                if (refAtoms.length > 2) {
                    yaxis = refAtoms[2];
                }
            }
        } else {
            axisType = OpenMM_AmoebaMultipoleForce_NoAxisType;
            logger.info(String.format(" Atom type %s", atom.getAtomType().toString()));
        }
        double charge = multipoleType.charge * useFactor;
        /**
         * Add the multipole.
         */
        OpenMM_AmoebaMultipoleForce_addMultipole(amoebaMultipoleForce, charge, dipoles, quadrupoles, axisType, zaxis, xaxis, yaxis, polarType.thole, polarType.pdamp * dampingFactorConversion, polarType.polarizability * polarityConversion * polarScale);
    }
    OpenMM_DoubleArray_destroy(dipoles);
    OpenMM_DoubleArray_destroy(quadrupoles);
    Crystal crystal = super.getCrystal();
    if (!crystal.aperiodic()) {
        OpenMM_AmoebaMultipoleForce_setNonbondedMethod(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_PME);
        OpenMM_AmoebaMultipoleForce_setCutoffDistance(amoebaMultipoleForce, pme.getEwaldCutoff() * OpenMM_NmPerAngstrom);
        OpenMM_AmoebaMultipoleForce_setAEwald(amoebaMultipoleForce, pme.getEwaldCoefficient() / OpenMM_NmPerAngstrom);
        double ewaldTolerance = 1.0e-04;
        OpenMM_AmoebaMultipoleForce_setEwaldErrorTolerance(amoebaMultipoleForce, ewaldTolerance);
        PointerByReference gridDimensions = OpenMM_IntArray_create(3);
        ReciprocalSpace recip = pme.getReciprocalSpace();
        OpenMM_IntArray_set(gridDimensions, 0, recip.getXDim());
        OpenMM_IntArray_set(gridDimensions, 1, recip.getYDim());
        OpenMM_IntArray_set(gridDimensions, 2, recip.getZDim());
        OpenMM_AmoebaMultipoleForce_setPmeGridDimensions(amoebaMultipoleForce, gridDimensions);
        OpenMM_IntArray_destroy(gridDimensions);
    } else {
        OpenMM_AmoebaMultipoleForce_setNonbondedMethod(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_NoCutoff);
    }
    OpenMM_AmoebaMultipoleForce_setMutualInducedMaxIterations(amoebaMultipoleForce, 500);
    OpenMM_AmoebaMultipoleForce_setMutualInducedTargetEpsilon(amoebaMultipoleForce, pme.getPolarEps());
    int[][] ip11 = pme.getPolarization11();
    int[][] ip12 = pme.getPolarization12();
    int[][] ip13 = pme.getPolarization13();
    ArrayList<Integer> list12 = new ArrayList<>();
    ArrayList<Integer> list13 = new ArrayList<>();
    ArrayList<Integer> list14 = new ArrayList<>();
    PointerByReference covalentMap = OpenMM_IntArray_create(0);
    for (int i = 0; i < nAtoms; i++) {
        Atom ai = atoms[i];
        list12.clear();
        list13.clear();
        list14.clear();
        for (Bond bond : ai.getBonds()) {
            int index = bond.get1_2(ai).getIndex() - 1;
            OpenMM_IntArray_append(covalentMap, index);
            list12.add(index);
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent12, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (Angle angle : ai.getAngles()) {
            Atom ak = angle.get1_3(ai);
            if (ak != null) {
                int index = ak.getIndex() - 1;
                if (!list12.contains(index)) {
                    list13.add(index);
                    OpenMM_IntArray_append(covalentMap, index);
                }
            }
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent13, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (Torsion torsion : ai.getTorsions()) {
            Atom ak = torsion.get1_4(ai);
            if (ak != null) {
                int index = ak.getIndex() - 1;
                if (!list12.contains(index) && !list13.contains(index)) {
                    list14.add(index);
                    OpenMM_IntArray_append(covalentMap, index);
                }
            }
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent14, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (Atom ak : ai.get1_5s()) {
            int index = ak.getIndex() - 1;
            if (!list12.contains(index) && !list13.contains(index) && !list14.contains(index)) {
                OpenMM_IntArray_append(covalentMap, index);
            }
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent15, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (int j = 0; j < ip11[i].length; j++) {
            OpenMM_IntArray_append(covalentMap, ip11[i][j]);
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_PolarizationCovalent11, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
    // for (int j = 0; j < ip12[i].length; j++) {
    // OpenMM_IntArray_append(covalentMap, ip12[i][j]);
    // }
    // OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i,
    // OpenMM_AmoebaMultipoleForce_PolarizationCovalent12, covalentMap);
    // OpenMM_IntArray_resize(covalentMap, 0);
    // 
    // for (int j = 0; j < ip13[i].length; j++) {
    // OpenMM_IntArray_append(covalentMap, ip13[i][j]);
    // }
    // OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i,
    // OpenMM_AmoebaMultipoleForce_PolarizationCovalent13, covalentMap);
    // OpenMM_IntArray_resize(covalentMap, 0);
    // 
    // OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i,
    // OpenMM_AmoebaMultipoleForce_PolarizationCovalent14, covalentMap);
    }
    OpenMM_IntArray_destroy(covalentMap);
    OpenMM_System_addForce(system, amoebaMultipoleForce);
    OpenMM_Force_setForceGroup(amoebaMultipoleForce, 1);
    logger.log(Level.INFO, " Added polarizable multipole force.");
    GeneralizedKirkwood gk = super.getGK();
    if (gk != null) {
        addGKForce();
    }
}

Example 7 with Angle

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

the class ForceFieldEnergyOpenMM method addInPlaneAngleForce.

private void addInPlaneAngleForce() {
    Angle[] angles = super.getAngles();
    if (angles == null || angles.length < 1) {
        return;
    }
    int nAngles = angles.length;
    List<Angle> inPlaneAngles = new ArrayList<>();
    // Sort all in-plane angles from normal angles
    for (int i = 0; i < nAngles; i++) {
        if (angles[i].getAngleMode() == Angle.AngleMode.IN_PLANE) {
            inPlaneAngles.add(angles[i]);
        }
    }
    nAngles = inPlaneAngles.size();
    if (nAngles < 1) {
        return;
    }
    amoebaInPlaneAngleForce = OpenMM_AmoebaInPlaneAngleForce_create();
    for (int i = 0; i < nAngles; i++) {
        Angle angle = inPlaneAngles.get(i);
        int i1 = angle.getAtom(0).getXyzIndex() - 1;
        int i2 = angle.getAtom(1).getXyzIndex() - 1;
        int i3 = angle.getAtom(2).getXyzIndex() - 1;
        int i4 = angle.getAtom4().getXyzIndex() - 1;
        int nh = angle.nh;
        OpenMM_AmoebaInPlaneAngleForce_addAngle(amoebaInPlaneAngleForce, i1, i2, i3, i4, angle.angleType.angle[nh], OpenMM_KJPerKcal * AngleType.units * angle.angleType.forceConstant);
    }
    OpenMM_AmoebaInPlaneAngleForce_setAmoebaGlobalInPlaneAngleCubic(amoebaInPlaneAngleForce, AngleType.cubic);
    OpenMM_AmoebaInPlaneAngleForce_setAmoebaGlobalInPlaneAngleQuartic(amoebaInPlaneAngleForce, AngleType.quartic);
    OpenMM_AmoebaInPlaneAngleForce_setAmoebaGlobalInPlaneAnglePentic(amoebaInPlaneAngleForce, AngleType.quintic);
    OpenMM_AmoebaInPlaneAngleForce_setAmoebaGlobalInPlaneAngleSextic(amoebaInPlaneAngleForce, AngleType.sextic);
    OpenMM_System_addForce(system, amoebaInPlaneAngleForce);
    logger.log(Level.INFO, " Added in-plane angles ({0})", nAngles);
}

Example 8 with Angle

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

the class PhMD method meltdown.

private void meltdown() {
    writeSnapshot(".meltdown-");
    ffe.energy(false, true);
    if (ffe.getBondEnergy() > 1000) {
        for (ROLS rols : previousTarget.getBondList()) {
            ((Bond) rols).log();
        }
    }
    if (ffe.getAngleEnergy() > 1000) {
        for (ROLS rols : previousTarget.getAngleList()) {
            ((Angle) rols).log();
        }
    }
    if (ffe.getVanDerWaalsEnergy() > 1000) {
        for (Atom a1 : previousTarget.getAtomList()) {
            for (Atom a2 : mola.getAtomArray()) {
                if (a1 == a2 || a1.getBond(a2) != null) {
                    continue;
                }
                double dist = sqrt(pow((a1.getX() - a2.getX()), 2) + pow((a1.getY() - a2.getY()), 2) + pow((a1.getZ() - a2.getZ()), 2));
                if (dist < 0.8 * (a1.getVDWR() + a2.getVDWR())) {
                    logger.warning(String.format("Close vdW contact for atoms: \n   %s\n   %s", a1, a2));
                }
            }
        }
    }
    logger.severe(String.format("Temperature above critical threshold: %f", thermostat.getCurrentTemperature()));
}

Example 9 with Angle

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

the class RosenbluthChiAllMove method createBackBondedMap.

/**
 * Maps the back-bonded terms affected by key atoms in an amino acid. Here,
 * 'key atom' refers to each new rotamer-torsion-completing atom. e.g. VAL
 * has 1 key atom (CG1), ARG has 4 key atoms (CG,CD,NE,CZ). 'Back-bonded'
 * means we only map terms that lead toward the backbone.
 */
private HashMap<Integer, BackBondedList> createBackBondedMap(AminoAcid3 name) {
    HashMap<Integer, BackBondedList> map = new HashMap<>();
    List<Atom> chain = new ArrayList<>();
    Atom N = (Atom) target.getAtomNode("N");
    Atom CA = (Atom) target.getAtomNode("CA");
    Atom CB = (Atom) target.getAtomNode("CB");
    List<Atom> keyAtoms = new ArrayList<>();
    switch(name) {
        case VAL:
            {
                Atom CG1 = (Atom) target.getAtomNode("CG1");
                keyAtoms.add(CG1);
                keyAtoms.add(CB);
                break;
            }
        case LEU:
            {
                Atom CG = (Atom) target.getAtomNode("CG");
                Atom CD1 = (Atom) target.getAtomNode("CD1");
                keyAtoms.add(CG);
                keyAtoms.add(CD1);
                break;
            }
        case ILE:
            {
                Atom CD1 = (Atom) target.getAtomNode("CD1");
                Atom CG1 = (Atom) target.getAtomNode("CG1");
                keyAtoms.add(CD1);
                keyAtoms.add(CG1);
                break;
            }
        case SER:
            {
                Atom OG = (Atom) target.getAtomNode("OG");
                Atom HG = (Atom) target.getAtomNode("HG");
                keyAtoms.add(OG);
                keyAtoms.add(HG);
                break;
            }
        case THR:
            {
                Atom OG1 = (Atom) target.getAtomNode("OG1");
                Atom HG1 = (Atom) target.getAtomNode("HG1");
                keyAtoms.add(OG1);
                keyAtoms.add(HG1);
                break;
            }
        case CYX:
        case CYD:
            {
                Atom SG = (Atom) target.getAtomNode("SG");
                keyAtoms.add(SG);
                break;
            }
        case PHE:
            {
                Atom CD1 = (Atom) target.getAtomNode("CD1");
                Atom CG = (Atom) target.getAtomNode("CG");
                keyAtoms.add(CG);
                break;
            }
        case PRO:
            {
                // Not allowed yet.
                Atom CD = (Atom) target.getAtomNode("CD");
                Atom CG = (Atom) target.getAtomNode("CG");
                keyAtoms.add(CG);
                keyAtoms.add(CD);
                break;
            }
        case TYR:
            {
                Atom CD1 = (Atom) target.getAtomNode("CD1");
                Atom CE2 = (Atom) target.getAtomNode("CE2");
                Atom CG = (Atom) target.getAtomNode("CG");
                Atom CZ = (Atom) target.getAtomNode("CZ");
                Atom OH = (Atom) target.getAtomNode("OH");
                Atom HH = (Atom) target.getAtomNode("HH");
                // SPECIAL CASE: have to create map manualy.
                Bond b1 = CG.getBond(CB);
                Angle a1 = CG.getAngle(CB, CA);
                Torsion t1 = CG.getTorsion(CB, CA, N);
                Bond b2 = CD1.getBond(CG);
                Angle a2 = CD1.getAngle(CG, CB);
                Torsion t2 = CD1.getTorsion(CG, CB, CA);
                Bond b3 = HH.getBond(OH);
                Angle a3 = HH.getAngle(OH, CZ);
                Torsion t3 = HH.getTorsion(OH, CZ, CE2);
                BackBondedList bbl1 = new BackBondedList(b1, a1, t1);
                BackBondedList bbl2 = new BackBondedList(b2, a2, t2);
                BackBondedList bbl3 = new BackBondedList(b3, a3, t3);
                map.put(0, bbl1);
                map.put(1, bbl2);
                map.put(2, bbl3);
                // Note the return here.
                return map;
            }
        case TYD:
            {
                Atom CD1 = (Atom) target.getAtomNode("CD1");
                Atom CG = (Atom) target.getAtomNode("CG");
                keyAtoms.add(CG);
                keyAtoms.add(CD1);
                break;
            }
        case TRP:
            {
                Atom CD1 = (Atom) target.getAtomNode("CD1");
                Atom CG = (Atom) target.getAtomNode("CG");
                keyAtoms.add(CG);
                keyAtoms.add(CD1);
                break;
            }
        case HIS:
        case HID:
        case HIE:
            {
                Atom CG = (Atom) target.getAtomNode("CG");
                Atom ND1 = (Atom) target.getAtomNode("ND1");
                keyAtoms.add(CG);
                keyAtoms.add(ND1);
                break;
            }
        case ASP:
            {
                Atom CG = (Atom) target.getAtomNode("CG");
                keyAtoms.add(CG);
                break;
            }
        case ASH:
            {
                Atom CG = (Atom) target.getAtomNode("CG");
                Atom OD1 = (Atom) target.getAtomNode("OD1");
                keyAtoms.add(CG);
                keyAtoms.add(OD1);
                break;
            }
        case ASN:
            {
                Atom CG = (Atom) target.getAtomNode("CG");
                Atom OD1 = (Atom) target.getAtomNode("OD1");
                keyAtoms.add(CG);
                keyAtoms.add(OD1);
                break;
            }
        case GLU:
        case GLH:
            {
                Atom CG = (Atom) target.getAtomNode("CG");
                Atom CD = (Atom) target.getAtomNode("CD");
                Atom OE1 = (Atom) target.getAtomNode("OE1");
                keyAtoms.add(CG);
                keyAtoms.add(CD);
                keyAtoms.add(OE1);
                break;
            }
        case GLN:
            {
                Atom CG = (Atom) target.getAtomNode("CG");
                Atom CD = (Atom) target.getAtomNode("CD");
                Atom OE1 = (Atom) target.getAtomNode("OE1");
                keyAtoms.add(CG);
                keyAtoms.add(CD);
                keyAtoms.add(OE1);
                break;
            }
        case MET:
            {
                Atom CG = (Atom) target.getAtomNode("CG");
                Atom CE = (Atom) target.getAtomNode("CE");
                Atom SD = (Atom) target.getAtomNode("SD");
                keyAtoms.add(CG);
                keyAtoms.add(SD);
                keyAtoms.add(CE);
                break;
            }
        case LYS:
        case LYD:
            {
                Atom CD = (Atom) target.getAtomNode("CD");
                Atom CE = (Atom) target.getAtomNode("CE");
                Atom CG = (Atom) target.getAtomNode("CG");
                Atom NZ = (Atom) target.getAtomNode("NZ");
                keyAtoms.add(CG);
                keyAtoms.add(CD);
                keyAtoms.add(CE);
                keyAtoms.add(NZ);
                break;
            }
        case ARG:
            {
                Atom CD = (Atom) target.getAtomNode("CD");
                Atom CG = (Atom) target.getAtomNode("CG");
                Atom CZ = (Atom) target.getAtomNode("CZ");
                Atom NE = (Atom) target.getAtomNode("NE");
                keyAtoms.add(CG);
                keyAtoms.add(CD);
                keyAtoms.add(NE);
                keyAtoms.add(CZ);
                break;
            }
        default:
            logger.severe(String.format("CBMC called on unsupported residue: %s", name.toString()));
    }
    // Build the chain and assign back-bonded terms.
    chain.add(N);
    chain.add(CA);
    chain.add(CB);
    chain.addAll(keyAtoms);
    for (int i = 3; i < chain.size(); i++) {
        Atom key = chain.get(i);
        Bond bond = key.getBond(chain.get(i - 1));
        Angle angle = key.getAngle(chain.get(i - 1), chain.get(i - 2));
        Torsion torsion = key.getTorsion(chain.get(i - 1), chain.get(i - 2), chain.get(i - 3));
        BackBondedList bbl = new BackBondedList(bond, angle, torsion);
        map.put(i - 3, bbl);
    // report.append(String.format("    BackBondedMap: %s\t\t%s\n", key, torsion));
    }
    return map;
}

Example 10 with Angle

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

the class ParticleMeshEwaldQI method applyMaskingRules.

/**
 * This enables PermanentRealSpaceFieldLoop and RealSpaceEnergyLoop to share
 * a code path for masking rule treatment. Defaults: d11scale = 0.0;
 * (scaleD) p12scale = p13scale = 0.0;	(scaleP) m12scale = m13scale = 0.0;
 * (scale) m14scale = 0.4 amoeba, 1/1.2 amber, 0.5 else; m15scale = 0.8
 * amoeba, 1 else.
 */
private void applyMaskingRules(boolean set, int i, double[] maskPerm, double[] maskPolD, double[] maskPolP) {
    final Atom ai = atoms[i];
    for (Atom ak : ai.get1_5s()) {
        if (maskPerm != null) {
            maskPerm[ak.getArrayIndex()] = (set) ? m15scale : 1.0;
        }
    }
    for (Torsion torsion : ai.getTorsions()) {
        Atom ak = torsion.get1_4(ai);
        if (ak != null) {
            final int index = ak.getArrayIndex();
            if (maskPerm != null) {
                maskPerm[index] = (set) ? m14scale : 1.0;
            }
            for (int member : ip11[i]) {
                if (member == index) {
                    maskPolP[index] = (set) ? intra14Scale : 1.0;
                }
            }
        }
    }
    for (Angle angle : ai.getAngles()) {
        Atom ak = angle.get1_3(ai);
        if (ak != null) {
            final int index = ak.getArrayIndex();
            if (maskPerm != null) {
                maskPerm[index] = (set) ? m13scale : 1.0;
            }
            maskPolP[index] = (set) ? p13scale : 1.0;
        }
    }
    for (Bond bond : ai.getBonds()) {
        Atom ak = bond.get1_2(ai);
        final int index = ak.getArrayIndex();
        if (maskPerm != null) {
            maskPerm[index] = (set) ? m12scale : 1.0;
        }
        maskPolP[index] = (set) ? p12scale : 1.0;
    }
    for (int index : ip11[i]) {
        maskPolD[index] = (set) ? d11scale : 1.0;
    }
}