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

Example 36 with Residue

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

the class RotamerOptimizationTest method testPairEnergyElimination.

@Test
public void testPairEnergyElimination() {
    // Load the test system.
    load();
    // Initialize Parallel Java
    try {
        String[] args = new String[0];
        Comm.init(args);
    } catch (Exception e) {
        String message = String.format(" Exception starting up the Parallel Java communication layer.");
        logger.log(Level.WARNING, message, e.toString());
        message = String.format(" Skipping rotamer optimization test.");
        logger.log(Level.WARNING, message, e.toString());
        return;
    }
    // Run the optimization.
    RotamerLibrary rLib = RotamerLibrary.getDefaultLibrary();
    rLib.setLibrary(RotamerLibrary.ProteinLibrary.Richardson);
    rLib.setUseOrigCoordsRotamer(useOriginalRotamers);
    int counter = 1;
    ArrayList<Residue> residueList = new ArrayList<Residue>();
    Polymer[] polymers = molecularAssembly.getChains();
    int nPolymers = polymers.length;
    for (int p = 0; p < nPolymers; p++) {
        Polymer polymer = polymers[p];
        ArrayList<Residue> residues = polymer.getResidues();
        for (int i = 0; i < endResID; i++) {
            Residue residue = residues.get(i);
            Rotamer[] rotamers = residue.getRotamers(rLib);
            if (rotamers != null) {
                int nrot = rotamers.length;
                if (nrot == 1) {
                    RotamerLibrary.applyRotamer(residue, rotamers[0]);
                }
                if (counter >= startResID) {
                    residueList.add(residue);
                }
            }
            counter++;
        }
    }
    RotamerOptimization rotamerOptimization = new RotamerOptimization(molecularAssembly, forceFieldEnergy, null);
    rotamerOptimization.setThreeBodyEnergy(useThreeBody);
    rotamerOptimization.setUseGoldstein(useGoldstein);
    rotamerOptimization.setPruning(pruningLevel);
    rotamerOptimization.setEnergyRestartFile(restartFile);
    rotamerOptimization.setResidues(residueList);
    double energy;
    int nRes = residueList.size();
    if (doOverallOpt) {
        rotamerOptimization.turnRotamerSingleEliminationOff();
        energy = rotamerOptimization.optimize(RotamerOptimization.Algorithm.ALL);
        // System.out.println("The expected overall energy is: " + energy);
        assertEquals(info + " Total Energy", expectedEnergy, energy, tolerance);
    }
    // ToDo: Test self-energy use for rotamer 2-body eliminations.
    if (doSelfOpt) {
        rotamerOptimization.turnRotamerSingleEliminationOff();
        rotamerOptimization.setTestSelfEnergyEliminations(true);
        energy = rotamerOptimization.optimize(RotamerOptimization.Algorithm.ALL);
        // System.out.println("The expected self energy is: " + energy);
        assertEquals(info + " Self-Energy", expectedSelfEnergy, energy, tolerance);
        // Check that optimized rotamers are equivalent to the lowest self-energy of each residue.
        int[] optimum = rotamerOptimization.getOptimumRotamers();
        // Loop over all residues
        for (int i = 0; i < nRes; i++) {
            Residue res = residueList.get(i);
            Rotamer[] rotI = res.getRotamers(rLib);
            int nRot = rotI.length;
            int rotCounter = 0;
            while (rotCounter < nRot && rotamerOptimization.checkPrunedSingles(i, rotCounter)) {
                rotCounter++;
            }
            double lowEnergy = rotamerOptimization.getSelf(i, rotCounter);
            int bestRot = rotCounter;
            for (int ri = 1; ri < nRot; ri++) {
                if (rotamerOptimization.checkPrunedSingles(i, ri)) {
                    continue;
                } else {
                    double selfEnergy = rotamerOptimization.getSelf(i, ri);
                    if (selfEnergy < lowEnergy) {
                        lowEnergy = selfEnergy;
                        bestRot = ri;
                    }
                }
            }
            assertEquals(String.format(" %s Self-Energy of residue %d", info, i), optimum[i], bestRot);
        }
    }
    // ToDo: Test 2-body energy use for rotamer pair eliminations.
    if (doPairOpt) {
        rotamerOptimization.turnRotamerSingleEliminationOff();
        rotamerOptimization.setTestPairEnergyEliminations(pairResidue);
        energy = rotamerOptimization.optimize(RotamerOptimization.Algorithm.ALL);
        // System.out.println("The expected 2-body energy is: " + energy);
        assertEquals(info + " Pair-Energy", expectedPairEnergy, energy, tolerance);
        // Check that optimized rotamers are equivalent to the lowest 2-body energy sum for the "pairResidue".
        int[] optimum = rotamerOptimization.getOptimumRotamers();
        Residue resI = residueList.get(pairResidue);
        Rotamer[] rotI = resI.getRotamers(rLib);
        int ni = rotI.length;
        double minEnergy = Double.POSITIVE_INFINITY;
        int bestRotI = -1;
        // Loop over the pairResidue rotamers to find its lowest energy rotamer.
        for (int ri = 0; ri < ni; ri++) {
            double energyForRi = 0.0;
            if (rotamerOptimization.checkPrunedSingles(pairResidue, ri)) {
                continue;
            }
            // Loop over residue J
            for (int j = 0; j < nRes; j++) {
                if (j == pairResidue) {
                    continue;
                }
                Residue resJ = residueList.get(j);
                Rotamer[] rotJ = resJ.getRotamers(rLib);
                int nRot = rotJ.length;
                int rj = 0;
                while (rotamerOptimization.checkPrunedSingles(j, rj) || rotamerOptimization.checkPrunedPairs(pairResidue, ri, j, rj)) {
                    if (++rj >= nRot) {
                        logger.warning("RJ is too large.");
                    }
                }
                double lowEnergy = rotamerOptimization.get2Body(pairResidue, ri, j, rj);
                for (rj = 1; rj < nRot; rj++) {
                    if (rotamerOptimization.checkPrunedSingles(j, rj) || rotamerOptimization.checkPrunedPairs(pairResidue, ri, j, rj)) {
                        continue;
                    } else {
                        double pairEnergy = rotamerOptimization.get2Body(pairResidue, ri, j, rj);
                        if (pairEnergy < lowEnergy) {
                            lowEnergy = pairEnergy;
                        }
                    }
                }
                energyForRi += lowEnergy;
            }
            if (energyForRi < minEnergy) {
                minEnergy = energyForRi;
                bestRotI = ri;
            }
        }
        assertEquals(String.format(" %s Best 2-body energy sum for residue %d is with rotamer %d at %10.4f.", info, pairResidue, bestRotI, minEnergy), optimum[pairResidue], bestRotI);
        // Given the minimum energy rotamer for "pairResidue" is "bestRotI", we can check selected rotamers for all other residues.
        for (int j = 0; j < nRes; j++) {
            if (j == pairResidue) {
                continue;
            }
            Residue resJ = residueList.get(j);
            Rotamer[] rotJ = resJ.getRotamers(rLib);
            int nRotJ = rotJ.length;
            int rotCounter = 0;
            while (rotamerOptimization.checkPrunedPairs(pairResidue, bestRotI, j, rotCounter) && rotCounter < nRotJ) {
                rotCounter++;
            }
            double lowEnergy = rotamerOptimization.get2Body(pairResidue, bestRotI, j, rotCounter);
            int bestRotJ = rotCounter;
            for (int rj = 1; rj < nRotJ; rj++) {
                if (rotamerOptimization.checkPrunedSingles(j, rj) || rotamerOptimization.checkPrunedPairs(pairResidue, bestRotI, j, rj)) {
                    continue;
                } else {
                    double pairEnergy = rotamerOptimization.get2Body(pairResidue, bestRotI, j, rj);
                    if (pairEnergy < lowEnergy) {
                        lowEnergy = pairEnergy;
                        bestRotJ = rj;
                    }
                }
            }
            if (bestRotJ != optimum[j]) {
                // Check if 2-body energies are equal.
                if (lowEnergy == rotamerOptimization.get2Body(pairResidue, bestRotI, j, optimum[j])) {
                    logger.warning(String.format(" Identical 2-body energies for %s: resi %d-%d, resj %d, best rotamer J %d, optimum J %d, 2-body energy (both) %10.6f", info, pairResidue, bestRotI, j, bestRotJ, optimum[j], lowEnergy));
                } else {
                    assertEquals(String.format(" %s Pair-Energy of residue (%d,%d) with residue %d", info, pairResidue, bestRotI, j), optimum[j], bestRotJ);
                }
            }
        }
    }
    // ToDo: Test 3-Body use for rotamer pair eliminations.
    if (doTripleOpt) {
        rotamerOptimization.turnRotamerSingleEliminationOff();
        rotamerOptimization.setTestTripleEnergyEliminations(tripleResidue1, tripleResidue2);
        try {
            energy = rotamerOptimization.optimize(RotamerOptimization.Algorithm.ALL);
            assertEquals(info + " Triple-Energy", expectedTripleEnergy, energy, tolerance);
        } catch (Exception e) {
            e.fillInStackTrace();
            e.printStackTrace();
            logger.log(java.util.logging.Level.INFO, "Error in doTripleOpt", e);
        }
        // Check that optimized rotamers are equivalent to the lowest 3-body energy of each residue with the tripleResidue1 and 2.
        int[] optimum = rotamerOptimization.getOptimumRotamers();
        // fix residue 1 and gets its rotamers
        Residue resI = residueList.get(tripleResidue1);
        Rotamer[] rotI = resI.getRotamers(rLib);
        int ni = rotI.length;
        // fix residue 2 and get its rotamers
        Residue resJ = residueList.get(tripleResidue2);
        Rotamer[] rotJ = resJ.getRotamers(rLib);
        int nj = rotJ.length;
        double minEnergyIJ = Double.POSITIVE_INFINITY;
        int bestRotI = -1;
        int bestRotJ = -1;
        for (int ri = 0; ri < ni; ri++) {
            // loop through rot I
            if (rotamerOptimization.check(tripleResidue1, ri)) {
                continue;
            }
            for (int rj = 0; rj < nj; rj++) {
                // loop through rot J
                if (rotamerOptimization.checkPrunedSingles(tripleResidue2, rj) || rotamerOptimization.checkPrunedPairs(tripleResidue1, ri, tripleResidue2, rj)) {
                    continue;
                }
                double currentEnergy = 0.0;
                for (int k = 0; k < nRes; k++) {
                    // loop through all other residues
                    if (k == tripleResidue1 || k == tripleResidue2) {
                        continue;
                    }
                    Residue resK = residueList.get(k);
                    Rotamer[] rotK = resK.getRotamers(rLib);
                    int nk = rotK.length;
                    int rkStart = 0;
                    while (rotamerOptimization.checkPrunedSingles(k, rkStart) || rotamerOptimization.checkPrunedPairs(tripleResidue1, ri, k, rkStart) || rotamerOptimization.checkPrunedPairs(tripleResidue2, rj, k, rkStart)) {
                        if (++rkStart >= nk) {
                            logger.warning("RJ is too large.");
                        }
                    }
                    double lowEnergy = rotamerOptimization.get3Body(tripleResidue1, ri, tripleResidue2, rj, k, rkStart);
                    for (int rk = rkStart; rk < nk; rk++) {
                        if (rotamerOptimization.checkPrunedSingles(k, rk) || rotamerOptimization.checkPrunedPairs(tripleResidue1, ri, k, rk) || rotamerOptimization.checkPrunedPairs(tripleResidue2, rj, k, rk)) {
                            continue;
                        } else {
                            double tripleEnergy = rotamerOptimization.get3Body(tripleResidue1, ri, tripleResidue2, rj, k, rk);
                            if (tripleEnergy < lowEnergy) {
                                lowEnergy = tripleEnergy;
                            }
                        }
                    }
                    // adds lowest energy conformation of residue k to that of the rotamer I
                    currentEnergy += lowEnergy;
                }
                if (currentEnergy < minEnergyIJ) {
                    minEnergyIJ = currentEnergy;
                    bestRotI = ri;
                    bestRotJ = rj;
                }
            }
        }
        assertEquals(String.format(" %s Best three-body energy sum for residue %d is with rotamer %d at %10.4f.", info, tripleResidue1, bestRotI, minEnergyIJ), optimum[tripleResidue1], bestRotI);
        assertEquals(String.format(" %s Best three-body energy sum for residue %d is with rotamer %d at %10.4f.", info, tripleResidue2, bestRotJ, minEnergyIJ), optimum[tripleResidue2], bestRotJ);
        // loop over the residues to find the best rotamer per residue given bestRotI and bestRotJ
        for (int k = 0; k < nRes; k++) {
            if (k == tripleResidue1 || k == tripleResidue2) {
                continue;
            }
            Residue resK = residueList.get(k);
            Rotamer[] rotK = resK.getRotamers(rLib);
            int nk = rotK.length;
            int rotCounter = 0;
            while (rotamerOptimization.checkPrunedPairs(tripleResidue1, bestRotI, k, rotCounter) && rotamerOptimization.checkPrunedPairs(tripleResidue2, bestRotJ, k, rotCounter) && rotCounter < nk) {
                rotCounter++;
            }
            double lowEnergy = rotamerOptimization.get3Body(tripleResidue1, bestRotI, tripleResidue2, bestRotJ, k, rotCounter);
            int bestRotK = rotCounter;
            for (int rk = 1; rk < nk; rk++) {
                if (rotamerOptimization.checkPrunedSingles(k, rk) || rotamerOptimization.checkPrunedPairs(tripleResidue1, bestRotI, k, rk) || rotamerOptimization.checkPrunedPairs(tripleResidue2, bestRotJ, k, rk)) {
                    continue;
                } else {
                    double tripleEnergy = rotamerOptimization.get3Body(tripleResidue1, bestRotI, tripleResidue2, bestRotJ, k, rk);
                    if (tripleEnergy < lowEnergy) {
                        lowEnergy = tripleEnergy;
                        bestRotK = rk;
                    }
                }
            }
            assertEquals(String.format(" %s Triple-Energy of residue (%d,%d) and residue (%d,%d) with residue %d", info, tripleResidue1, bestRotI, tripleResidue2, bestRotJ, k), optimum[k], bestRotK);
        }
    }
}

Example 37 with Residue

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

the class ExtendedSystem method populate.

public void populate(List<String> residueIDs) {
    // Locate the Residue identified by the given resid.
    Polymer[] polymers = mola.getChains();
    for (String token : residueIDs) {
        char chainID = token.charAt(0);
        int resNum = Integer.parseInt(token.substring(1));
        Residue target = null;
        for (Polymer p : polymers) {
            char pid = p.getChainID().charValue();
            if (pid == chainID) {
                for (Residue res : p.getResidues()) {
                    if (res.getResidueNumber() == resNum) {
                        target = res;
                        break;
                    }
                }
                if (target != null) {
                    break;
                }
            }
        }
        if (target == null) {
            logger.severe("Couldn't find target residue " + token);
        }
        MultiResidue titrating = TitrationUtils.titratingMultiresidueFactory(mola, target);
        TitrationESV esv = new TitrationESV(this, titrating);
        this.addVariable(esv);
    }
}

Example 38 with Residue

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

the class TitrationUtils method chooseTitratables.

/**
 * Identify titratable residues and choose them all.
 */
public static List<Residue> chooseTitratables(MolecularAssembly searchMe) {
    List<Residue> chosen = new ArrayList<>();
    Polymer[] polymers = searchMe.getChains();
    for (int i = 0; i < polymers.length; i++) {
        ArrayList<Residue> residues = polymers[i].getResidues();
        for (int j = 0; j < residues.size(); j++) {
            Residue res = residues.get(j);
            Titration[] avail = Titration.multiLookup(res);
            if (avail != null) {
                chosen.add(residues.get(j));
            }
        }
    }
    return chosen;
}

Example 39 with Residue

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

the class TitrationUtils method propagateInactiveResidues.

/**
 * Copies atomic coordinates from each active residue to its inactive
 * counterparts. Inactive hydrogen coordinates are updated by geometry with
 * the propagated heavies.
 */
public static void propagateInactiveResidues(MultiResidue multiRes, boolean propagateDynamics) {
    // Propagate all atom coordinates from active residues to their inactive counterparts.
    Residue active = multiRes.getActive();
    String activeResName = active.getName();
    List<Residue> inactives = multiRes.getInactive();
    for (Atom activeAtom : active.getAtomList()) {
        String activeName = activeAtom.getName();
        for (Residue inactive : inactives) {
            Atom inactiveAtom = (Atom) inactive.getAtomNode(activeName);
            if (inactiveAtom != null) {
                // Propagate position and gradient.
                double[] activeXYZ = activeAtom.getXYZ(null);
                inactiveAtom.setXYZ(activeXYZ);
                double[] grad = new double[3];
                activeAtom.getXYZGradient(grad);
                inactiveAtom.setXYZGradient(grad[0], grad[1], grad[2]);
                if (propagateDynamics) {
                    // Propagate velocity, acceleration, and previous acceleration.
                    double[] activeVelocity = new double[3];
                    activeAtom.getVelocity(activeVelocity);
                    inactiveAtom.setVelocity(activeVelocity);
                    double[] activeAccel = new double[3];
                    activeAtom.getAcceleration(activeAccel);
                    inactiveAtom.setAcceleration(activeAccel);
                    double[] activePrevAcc = new double[3];
                    activeAtom.getPreviousAcceleration(activePrevAcc);
                    inactiveAtom.setPreviousAcceleration(activePrevAcc);
                }
            } else {
                if (activeName.equals("C") || activeName.equals("O") || activeName.equals("N") || activeName.equals("CA") || activeName.equals("H") || activeName.equals("HA")) {
                // Backbone atoms aren't supposed to exist in inactive multiResidue components; so no problem.
                } else if (isTitratableHydrogen(activeAtom)) {
                /**
                 * i.e. ((activeResName.equals("LYS") &&
                 * activeName.equals("HZ3")) ||
                 * (activeResName.equals("TYR") &&
                 * activeName.equals("HH")) ||
                 * (activeResName.equals("CYS") &&
                 * activeName.equals("HG")) ||
                 * (activeResName.equals("HIS") &&
                 * (activeName.equals("HD1") ||
                 * activeName.equals("HE2"))) ||
                 * (activeResName.equals("HID") &&
                 * activeName.equals("HD1")) ||
                 * (activeResName.equals("HIE") &&
                 * activeName.equals("HE2")) ||
                 * (activeResName.equals("ASH") &&
                 * activeName.equals("HD2")) ||
                 * (activeResName.equals("GLH") &&
                 * activeName.equals("HE2")))
                 */
                // These titratable protons are handled below; so no problem.
                } else {
                    // Now we have a problem.
                    logger.warning(format("Couldn't propagate inactive MultiResidue atom: %s: %s, %s", multiRes, activeName, activeAtom));
                }
            }
        }
    }
    rebuildStrandedProtons(multiRes);
}

Example 40 with Residue

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

the class TitrationUtils method chooseTitratables.

public static List<Residue> chooseTitratables(List<String> crIDs, MolecularAssembly searchMe) {
    List<Residue> chosen = new ArrayList<>();
    for (String crID : crIDs) {
        char chain = crID.charAt(0);
        int num = Integer.parseInt(crID.substring(1));
        boolean found = false;
        List<Residue> allRes = searchMe.getResidueList();
        for (Residue res : allRes) {
            if (res.getChainID() == chain && res.getResidueNumber() == num) {
                chosen.add(res);
                found = true;
                break;
            }
        }
        if (!found) {
            logger.severe(format("Couldn't find residue for crID %c,%d.", chain, num));
        }
    }
    return chosen;
}