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

Example 11 with Atom

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

the class BiojavaFilter method renameNonstandardHydrogens.

/**
 * Ensures proper naming of hydrogens according to latest PDB format.
 * Presently mostly guesses at which hydrogens to re-assign, which may cause
 * chirality errors for prochiral hydrogens. If necessary, we will implement
 * more specific mapping.
 *
 * @param residue
 */
private void renameNonstandardHydrogens(Residue residue) {
    switch(fileStandard) {
        case VERSION3_3:
            return;
        case VERSION3_2:
        default:
            break;
    }
    // May have to get position.
    String residueType = residue.getName().toUpperCase();
    ArrayList<Atom> resAtoms = residue.getAtomList();
    for (Atom atom : resAtoms) {
        if (atom == null) {
            continue;
        }
        String atomName = atom.getName().toUpperCase();
        // Handles situations such as 1H where it should be NA_H1, etc.
        if (atomName.contains("H")) {
            try {
                String firstChar = atomName.substring(0, 1);
                Integer.parseInt(firstChar);
                atomName = atomName.substring(1);
                atomName = atomName.concat(firstChar);
                atom.setName(atomName);
            } catch (NumberFormatException e) {
            // Do nothing.
            }
        }
    }
    // Ensures proper hydrogen assignment; for example, Gln should have HB2,
    // HB3 instead of HB1, HB2.
    ArrayList<Atom> betas;
    ArrayList<Atom> gammas;
    ArrayList<Atom> deltas;
    ArrayList<Atom> epsilons;
    ArrayList<Atom> zetas;
    String atomName;
    Atom OH;
    Atom HH;
    Atom HG;
    Atom HD2;
    switch(getAminoAcid(residueType)) {
        case GLY:
            ArrayList<Atom> alphas = new ArrayList<>();
            for (Atom atom : resAtoms) {
                if (atom.getName().toUpperCase().contains("HA")) {
                    alphas.add(atom);
                }
            }
            renameGlycineAlphaHydrogens(residue, alphas);
            break;
        case ALA:
            // No known errors with alanine
            break;
        case VAL:
            // No known errors with valine
            break;
        case LEU:
            betas = new ArrayList<>();
            for (Atom atom : resAtoms) {
                if (atom.getName().toUpperCase().contains("HB")) {
                    betas.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            break;
        case ILE:
            ArrayList<Atom> ileAtoms = new ArrayList<>();
            for (Atom atom : resAtoms) {
                if (atom.getName().toUpperCase().contains("HG1")) {
                    ileAtoms.add(atom);
                }
            }
            renameIsoleucineHydrogens(residue, ileAtoms);
            break;
        case SER:
            betas = new ArrayList<>();
            for (Atom atom : resAtoms) {
                if (atom.getName().toUpperCase().contains("HB")) {
                    betas.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            break;
        case THR:
            Atom HG1 = (Atom) residue.getAtomNode("HG1");
            if (HG1 == null) {
                for (Atom atom : resAtoms) {
                    atomName = atom.getName().toUpperCase();
                    // Length < 4 avoids bringing in HG21, HG22, or HG23.
                    if (atomName.length() < 4 && atomName.contains("HG")) {
                        atom.setName("HG1");
                        break;
                    }
                }
            }
            break;
        case CYS:
            betas = new ArrayList<>();
            HG = (Atom) residue.getAtomNode("HG");
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (HG == null && atomName.contains("HG")) {
                    HG = atom;
                    HG.setName("HG");
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            break;
        case CYX:
            // I pray this is never important, because I don't have an example CYX to work from.
            break;
        case CYD:
            betas = new ArrayList<>();
            for (Atom atom : resAtoms) {
                if (atom.getName().toUpperCase().contains("HB")) {
                    betas.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            break;
        case PRO:
            betas = new ArrayList<>();
            gammas = new ArrayList<>();
            deltas = new ArrayList<>();
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HG")) {
                    gammas.add(atom);
                } else if (atomName.contains("HD")) {
                    deltas.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameGammaHydrogens(residue, gammas, 23);
            renameDeltaHydrogens(residue, deltas, 23);
            break;
        case PHE:
            betas = new ArrayList<>();
            deltas = new ArrayList<>();
            epsilons = new ArrayList<>();
            Atom HZ = (Atom) residue.getAtomNode("HZ");
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HD")) {
                    deltas.add(atom);
                } else if (atomName.contains("HE")) {
                    epsilons.add(atom);
                } else if (HZ == null && atomName.contains("HZ")) {
                    HZ = atom;
                    HZ.setName("HZ");
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameDeltaHydrogens(residue, deltas, 12);
            renameEpsilonHydrogens(residue, epsilons, 12);
            break;
        case TYR:
            betas = new ArrayList<>();
            deltas = new ArrayList<>();
            epsilons = new ArrayList<>();
            HH = (Atom) residue.getAtomNode("HH");
            OH = (Atom) residue.getAtomNode("OH");
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HD")) {
                    deltas.add(atom);
                } else if (atomName.contains("HE")) {
                    epsilons.add(atom);
                } else if (HH == null && atomName.contains("HH")) {
                    HH = atom;
                    HH.setName("HH");
                } else if (OH == null && atomName.contains("O") && atomName.contains("H")) {
                    OH = atom;
                    OH.setName("OH");
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameDeltaHydrogens(residue, deltas, 12);
            renameEpsilonHydrogens(residue, epsilons, 12);
            break;
        case TYD:
            betas = new ArrayList<>();
            deltas = new ArrayList<>();
            epsilons = new ArrayList<>();
            OH = (Atom) residue.getAtomNode("OH");
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HD")) {
                    deltas.add(atom);
                } else if (atomName.contains("HE")) {
                    epsilons.add(atom);
                } else if (OH == null && atomName.contains("O") && atomName.contains("H")) {
                    OH = atom;
                    OH.setName("OH");
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameDeltaHydrogens(residue, deltas, 12);
            renameEpsilonHydrogens(residue, epsilons, 12);
            break;
        case TRP:
            betas = new ArrayList<>();
            epsilons = new ArrayList<>();
            zetas = new ArrayList<>();
            Atom HD1 = (Atom) residue.getAtomNode("HD1");
            Atom HH2 = (Atom) residue.getAtomNode("HH2");
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HE")) {
                    epsilons.add(atom);
                } else if (atomName.contains("HZ")) {
                    zetas.add(atom);
                } else if (HD1 == null && atomName.contains("HD")) {
                    HD1 = atom;
                    HD1.setName("HD1");
                } else if (HH2 == null && atomName.contains("HH")) {
                    HH2 = atom;
                    HH2.setName("HH2");
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameEpsilonHydrogens(residue, epsilons, 13);
            renameZetaHydrogens(residue, zetas, 23);
            break;
        case HIS:
            betas = new ArrayList<>();
            deltas = new ArrayList<>();
            epsilons = new ArrayList<>();
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HD")) {
                    deltas.add(atom);
                } else if (atomName.contains("HE")) {
                    epsilons.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameDeltaHydrogens(residue, deltas, 12);
            renameEpsilonHydrogens(residue, epsilons, 12);
            break;
        case HID:
            betas = new ArrayList<>();
            deltas = new ArrayList<>();
            Atom HE1 = (Atom) residue.getAtomNode("HE1");
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HD")) {
                    deltas.add(atom);
                } else if (HE1 == null && atomName.contains("HE")) {
                    HE1 = atom;
                    HE1.setName("HE1");
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameDeltaHydrogens(residue, deltas, 12);
            break;
        case HIE:
            betas = new ArrayList<>();
            epsilons = new ArrayList<>();
            HD2 = (Atom) residue.getAtomNode("HD2");
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HE")) {
                    epsilons.add(atom);
                } else if (HD2 == null && atomName.contains("HD")) {
                    HD2 = atom;
                    HD2.setName("HD2");
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameEpsilonHydrogens(residue, epsilons, 12);
            break;
        case ASP:
            betas = new ArrayList<>();
            for (Atom atom : resAtoms) {
                if (atom.getName().toUpperCase().contains("HB")) {
                    betas.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            break;
        case ASH:
            betas = new ArrayList<>();
            HD2 = (Atom) residue.getAtomNode("HD2");
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (HD2 == null && atomName.contains("HD")) {
                    HD2 = atom;
                    HD2.setName("HD2");
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            break;
        case ASN:
            betas = new ArrayList<>();
            ArrayList<Atom> HD2s = new ArrayList<>();
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HD")) {
                    HD2s.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameAsparagineHydrogens(residue, HD2s);
            break;
        case GLU:
            betas = new ArrayList<>();
            gammas = new ArrayList<>();
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HG")) {
                    gammas.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameGammaHydrogens(residue, gammas, 23);
            break;
        case GLH:
            betas = new ArrayList<>();
            gammas = new ArrayList<>();
            Atom HE2 = (Atom) residue.getAtomNode("HE2");
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HG")) {
                    gammas.add(atom);
                } else if (HE2 == null && atomName.contains("HE")) {
                    HE2 = atom;
                    HE2.setName("HE2");
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameGammaHydrogens(residue, gammas, 23);
            break;
        case GLN:
            betas = new ArrayList<>();
            gammas = new ArrayList<>();
            epsilons = new ArrayList<>();
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HG")) {
                    gammas.add(atom);
                } else if (atomName.contains("HE")) {
                    epsilons.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameGammaHydrogens(residue, gammas, 23);
            renameGlutamineHydrogens(residue, epsilons);
            break;
        case MET:
            betas = new ArrayList<>();
            gammas = new ArrayList<>();
            // Epsilons should not break, as they are 1-3.
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HG")) {
                    gammas.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameGammaHydrogens(residue, gammas, 23);
            break;
        case LYS:
            betas = new ArrayList<>();
            gammas = new ArrayList<>();
            deltas = new ArrayList<>();
            epsilons = new ArrayList<>();
            // Zetas are 1-3, should not break.
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HG")) {
                    gammas.add(atom);
                } else if (atomName.contains("HD")) {
                    deltas.add(atom);
                } else if (atomName.contains("HE")) {
                    epsilons.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameGammaHydrogens(residue, gammas, 23);
            renameDeltaHydrogens(residue, deltas, 23);
            renameEpsilonHydrogens(residue, epsilons, 23);
            break;
        case LYD:
            betas = new ArrayList<>();
            gammas = new ArrayList<>();
            deltas = new ArrayList<>();
            epsilons = new ArrayList<>();
            zetas = new ArrayList<>();
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HG")) {
                    gammas.add(atom);
                } else if (atomName.contains("HD")) {
                    deltas.add(atom);
                } else if (atomName.contains("HE")) {
                    epsilons.add(atom);
                } else if (atomName.contains("HZ")) {
                    zetas.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameGammaHydrogens(residue, gammas, 23);
            renameDeltaHydrogens(residue, deltas, 23);
            renameEpsilonHydrogens(residue, epsilons, 23);
            renameZetaHydrogens(residue, zetas, 12);
            break;
        case ARG:
            betas = new ArrayList<>();
            gammas = new ArrayList<>();
            deltas = new ArrayList<>();
            Atom HE = (Atom) residue.getAtomNode("HE");
            ArrayList<Atom> HHn = new ArrayList<>();
            for (Atom atom : resAtoms) {
                atomName = atom.getName().toUpperCase();
                if (atomName.contains("HB")) {
                    betas.add(atom);
                } else if (atomName.contains("HG")) {
                    gammas.add(atom);
                } else if (atomName.contains("HD")) {
                    deltas.add(atom);
                } else if (HE == null && atomName.contains("HE")) {
                    HE = atom;
                    HE.setName("HE");
                } else if (atomName.contains("HH")) {
                    HHn.add(atom);
                }
            }
            renameBetaHydrogens(residue, betas, 23);
            renameGammaHydrogens(residue, gammas, 23);
            renameDeltaHydrogens(residue, deltas, 23);
            renameArginineHydrogens(residue, HHn);
            break;
        case ORN:
        case AIB:
        case PCA:
        case UNK:
        default:
            // Pray, for I have no examples to work from.
            break;
    }
}

Example 12 with Atom

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

the class CrystalEnergyTest method testSoftCore.

public void testSoftCore() {
    logger.info(String.format(" Testing crystal softcore unity of %s with %s.", filename, pmeName));
    boolean gradient = false;
    boolean print = true;
    double e = forceFieldEnergy.energy(gradient, print);
    Atom[] atoms = molecularAssembly.getAtomArray();
    int n = atoms.length;
    // Make the 3 atoms soft
    for (int i = n; i > n - 3; i--) {
        Atom ai = atoms[i - 1];
        ai.setApplyLambda(true);
    }
    // Compute the energy with Lambda = 1.0;
    double lambda = 1.0;
    forceFieldEnergy.setLambda(lambda);
    double e2 = forceFieldEnergy.energy(gradient, print);
    assertEquals(e, e2, tolerance);
}

Example 13 with Atom

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

the class OPLSCrystalEnergyTest method testSoftCore.

public void testSoftCore() {
    boolean gradient = false;
    boolean print = true;
    double e = forceFieldEnergy.energy(gradient, print);
    Atom[] atoms = molecularAssembly.getAtomArray();
    int n = atoms.length;
    // Make the 3 atoms soft
    for (int i = n; i > n - 3; i--) {
        Atom ai = atoms[i - 1];
        ai.setApplyLambda(true);
    }
    // Compute the energy with Lambda = 1.0;
    double lambda = 1.0;
    forceFieldEnergy.setLambda(lambda);
    double e2 = forceFieldEnergy.energy(gradient, print);
    assertEquals(e, e2, tolerance);
}

Example 14 with Atom

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

the class SimulationFilter method readFile.

/**
 * {@inheritDoc}
 */
@Override
public boolean readFile() {
    // information
    for (int i = 0; i < system.numatoms; i++) {
        AtomType atomType = atomTypes.get(system.types[i]);
        if (atomType == null) {
            atomType = new AtomType(system.types[i], -1, system.name[i], system.story[i], system.atomic[i], system.mass[i], 0);
            atomTypes.put(system.types[i], atomType);
        }
    }
    atomList = new ArrayList<Atom>();
    Vector<Integer> bonds1 = new Vector<Integer>();
    Vector<Integer> bonds2 = new Vector<Integer>();
    double[] d = new double[3];
    int[] b = new int[4];
    for (int i = 0; i < system.numatoms; i++) {
        d[0] = system.coordinates[0][i];
        d[1] = system.coordinates[1][i];
        d[2] = system.coordinates[2][i];
        String s = new String("" + system.types[i]);
        AtomType atomType = atomTypes.get(s);
        Atom a = new Atom(i + 1, new String("" + atomType.type), atomType, d);
        atomList.add(a);
        int b1 = i + 1;
        b[0] = system.connectivity[0][i];
        b[1] = system.connectivity[1][i];
        b[2] = system.connectivity[2][i];
        b[3] = system.connectivity[3][i];
        int j = 0;
        while (j < 4 && b[j] != 0) {
            int b2 = b[j];
            bonds1.add(b1);
            bonds2.add(b2);
            j++;
        }
    }
    bondList = new ArrayList<Bond>();
    for (int i = 0; i < bonds1.size(); i++) {
        int a1 = bonds1.get(i);
        int a2 = bonds2.get(i);
        if (a1 < a2) {
            Atom atom1 = atomList.get(a1 - 1);
            Atom atom2 = atomList.get(a2 - 1);
            bondList.add(new Bond(atom1, atom2));
        }
    }
    setFileRead(true);
    return true;
}

Example 15 with Atom

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

the class CrystalReciprocalSpaceTest method test1N7SPermanent.

/**
 * Test of permanent method, of class CrystalReciprocalSpace.
 */
@Test
public void test1N7SPermanent() {
    String filename = "ffx/xray/structures/1N7S.pdb";
    int index = filename.lastIndexOf(".");
    String name = filename.substring(0, index);
    // load the structure
    ClassLoader cl = this.getClass().getClassLoader();
    File structure = new File(cl.getResource(filename).getPath());
    PotentialsUtils potutil = new PotentialsUtils();
    MolecularAssembly mola = potutil.open(structure);
    CompositeConfiguration properties = mola.getProperties();
    Crystal crystal = new Crystal(39.767, 51.750, 132.938, 90.00, 90.00, 90.00, "P212121");
    Resolution resolution = new Resolution(1.45);
    ReflectionList reflectionList = new ReflectionList(crystal, resolution);
    DiffractionRefinementData refinementData = new DiffractionRefinementData(properties, reflectionList);
    mola.finalize(true, mola.getForceField());
    ForceFieldEnergy energy = mola.getPotentialEnergy();
    List<Atom> atomList = mola.getAtomList();
    Atom[] atomArray = atomList.toArray(new Atom[atomList.size()]);
    // set up FFT and run it
    ParallelTeam parallelTeam = new ParallelTeam();
    CrystalReciprocalSpace crs = new CrystalReciprocalSpace(reflectionList, atomArray, parallelTeam, parallelTeam);
    crs.computeAtomicDensity(refinementData.fc);
    // tests
    ComplexNumber b = new ComplexNumber(-828.584, -922.704);
    HKL hkl = reflectionList.getHKL(1, 1, 4);
    ComplexNumber a = refinementData.getFc(hkl.index());
    System.out.println("1 1 4: " + a.toString() + " | " + b.toString() + " | " + a.divides(b).toString());
    assertEquals("1 1 4 reflection should be correct", -753.4722104328416, a.re(), 0.0001);
    assertEquals("1 1 4 reflection should be correct", -1012.1341308707799, a.im(), 0.0001);
    b.re(-70.4582);
    b.im(-486.142);
    hkl = reflectionList.getHKL(2, 1, 10);
    a = refinementData.getFc(hkl.index());
    System.out.println("2 1 10: " + a.toString() + " | " + b.toString() + " | " + a.divides(b).toString());
    assertEquals("2 1 10 reflection should be correct", -69.39660884054359, a.re(), 0.0001);
    assertEquals("2 1 10 reflection should be correct", -412.0147625765328, a.im(), 0.0001);
}