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

Example 31 with Polymer

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

the class RotamerOptimization method optimize.

/**
 * Execute the rotamer optimization.
 *
 * @return The lowest energy found.
 */
public double optimize() {
    boolean ignoreNA = false;
    String ignoreNAProp = System.getProperty("ignoreNA");
    if (ignoreNAProp != null && ignoreNAProp.equalsIgnoreCase("true")) {
        logger.info("(Key) Ignoring nucleic acids.");
        ignoreNA = true;
    }
    logger.info(format("\n Rotamer Library:     %s", library.getLibrary()));
    logger.info(format(" Algorithm:           %s", algorithm));
    logger.info(format(" Goldstein Criteria:  %b", useGoldstein));
    logger.info(format(" Three-Body Energies: %b\n", threeBodyTerm));
    /*
         * Collect all residues in the MolecularAssembly. Use all Residues with
         * Rotamers and all forced residues if using sliding window and forced
         * residues. Forced residues is meaningless for other algorithms, and
         * will be reverted to false.
         */
    allResiduesList = new ArrayList<>();
    polymers = molecularAssembly.getChains();
    for (Polymer polymer : polymers) {
        ArrayList<Residue> current = polymer.getResidues();
        for (Residue residuej : current) {
            if (useForcedResidues) {
                switch(algorithm) {
                    case WINDOW:
                        if (residuej == null) {
                        // Do nothing.
                        } else if (residuej.getRotamers(library) != null) {
                            allResiduesList.add(residuej);
                        } else {
                            int indexJ = residuej.getResidueNumber();
                            if (checkIfForced(indexJ)) {
                                allResiduesList.add(residuej);
                            }
                        }
                        break;
                    default:
                        // Should only trigger once before resetting useForcedResidues to false.
                        logIfMaster(" Forced residues only applicable to sliding window.", Level.WARNING);
                        useForcedResidues = false;
                        if (residuej != null && (residuej.getRotamers(library) != null)) {
                            if (!(ignoreNA && residuej.getResidueType() == Residue.ResidueType.NA)) {
                                allResiduesList.add(residuej);
                            }
                        }
                        break;
                }
            } else if (residuej != null && (residuej.getRotamers(library) != null)) {
                if (!(ignoreNA && residuej.getResidueType() == Residue.ResidueType.NA)) {
                    allResiduesList.add(residuej);
                }
            }
        }
    }
    sortResidues(allResiduesList);
    sortResidues(residueList);
    // If -DignoreNA=true, then remove nucleic acids from residue list.
    if (ignoreNA) {
        for (int i = 0; i < residueList.size(); i++) {
            Residue res = residueList.get(i);
            if (res.getResidueType() == Residue.ResidueType.NA) {
                residueList.remove(i);
            }
        }
    }
    // for NA only
    RotamerLibrary.initializeDefaultAtomicCoordinates(molecularAssembly.getChains());
    numResidues = allResiduesList.size();
    allResiduesArray = allResiduesList.toArray(new Residue[numResidues]);
    /*
         * Distance matrix is  used to add residues to the sliding window
         * based on distance cutoff, and to automatically set some 3-body terms
         * to 0 at > 10 angstroms.
         *
         * The memory and compute overhead can be a problem for some very large
         * structures.
         */
    if (distance > 0) {
        distanceMatrix();
    }
    double e = 0.0;
    if (residueList != null) {
        done = false;
        terminate = false;
        switch(algorithm) {
            case INDEPENDENT:
                e = independent(residueList);
                break;
            case BRUTE_FORCE:
                e = bruteForce(residueList);
                break;
            case ALL:
                e = globalOptimization(residueList);
                break;
            case WINDOW:
                e = slidingWindowOptimization(residueList, windowSize, increment, revert, distance, direction);
                break;
            case BOX:
                e = boxOptimization(residueList);
                break;
            default:
                break;
        }
        terminate = false;
        done = true;
    }
    return e;
}

Example 32 with Polymer

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

the class PDBFilter method numberAtoms.

/**
 * <p>
 * numberAtoms</p>
 */
private void numberAtoms() {
    int index = 1;
    for (Atom a : activeMolecularAssembly.getAtomArray()) {
        a.setXyzIndex(index++);
    }
    index--;
    if (logger.isLoggable(Level.INFO)) {
        logger.info(String.format(" Total number of atoms: %d\n", index));
    }
    Polymer[] polymers = activeMolecularAssembly.getChains();
    if (polymers != null) {
        for (Polymer p : polymers) {
            List<Residue> residues = p.getResidues();
            for (Residue r : residues) {
                r.reOrderAtoms();
            }
        }
    }
    List<Molecule> molecules = activeMolecularAssembly.getMolecules();
    for (Molecule n : molecules) {
        n.reOrderAtoms();
    }
    List<MSNode> waters = activeMolecularAssembly.getWaters();
    for (MSNode n : waters) {
        MSGroup m = (MSGroup) n;
        m.reOrderAtoms();
    }
    List<MSNode> ions = activeMolecularAssembly.getIons();
    for (MSNode n : ions) {
        MSGroup m = (MSGroup) n;
        m.reOrderAtoms();
    }
}

Example 33 with Polymer

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

the class PDBFilter method buildMissingResidues.

/**
 * Currently builds missing internal loops based on information in DBREF and
 * SEQRES records.
 *
 * Known limitations include: 1) No building n- and c-terminal loops. 2) No
 * support for DBREF1 or DBREF2 records. 3) Incomplete optimization scheme
 * to position the loops.
 *
 * @param xyzIndex
 *
 * @return xyzIndex updated based on built atoms.
 */
private int buildMissingResidues(int xyzIndex) {
    /**
     * Only build loops if the buildLoops flag is true.
     */
    if (!properties.getBoolean("buildLoops", false)) {
        return xyzIndex;
    }
    Polymer[] polymers = activeMolecularAssembly.getChains();
    for (Polymer polymer : polymers) {
        Character chainID = polymer.getChainID();
        String[] resNames = seqres.get(chainID);
        int[] seqRange = dbref.get(chainID);
        if (resNames == null || seqRange == null) {
            continue;
        }
        int seqBegin = seqRange[0];
        int seqEnd = seqRange[1];
        logger.info(format("\n Checking for missing residues in chain %s between residues %d and %d.", polymer.toString(), seqBegin, seqEnd));
        int firstResID = polymer.getFirstResidue().getResidueNumber();
        for (int i = 0; i < resNames.length; i++) {
            int currentID = seqBegin + i;
            Residue currentResidue = polymer.getResidue(currentID);
            if (currentResidue != null) {
                continue;
            }
            if (currentID <= firstResID) {
                logger.info(format(" Residue %d is missing, but is at the beginning of the chain.", currentID));
                continue;
            }
            Residue previousResidue = polymer.getResidue(currentID - 1);
            if (previousResidue == null) {
                logger.info(format(" Residue %d is missing, but could not be build (previous residue missing).", currentID));
                continue;
            }
            Residue nextResidue = null;
            for (int j = currentID + 1; j <= seqEnd; j++) {
                nextResidue = polymer.getResidue(j);
                if (nextResidue != null) {
                    break;
                }
            }
            /**
             * Residues at the end of the chain are not currently built.
             */
            if (nextResidue == null) {
                logger.info(format(" Residue %d is missing, but is at the end of the chain.", currentID));
                break;
            }
            /**
             * Find the previous carbonyl carbon and next nitrogen.
             */
            Atom C = (Atom) previousResidue.getAtomNode("C");
            Atom N = (Atom) nextResidue.getAtomNode("N");
            if (C == null || N == null) {
                logger.info(format(" Residue %d is missing, but bonding atoms are missing (C or N).", currentID));
                continue;
            }
            /**
             * Build the missing residue.
             */
            currentResidue = polymer.getResidue(resNames[i], currentID, true);
            double[] vector = new double[3];
            int count = 3 * (nextResidue.getResidueNumber() - previousResidue.getResidueNumber());
            VectorMath.diff(N.getXYZ(null), C.getXYZ(null), vector);
            VectorMath.scalar(vector, 1.0 / count, vector);
            double[] nXYZ = new double[3];
            VectorMath.sum(C.getXYZ(null), vector, nXYZ);
            nXYZ[0] += Math.random() - 0.5;
            nXYZ[1] += Math.random() - 0.5;
            nXYZ[2] += Math.random() - 0.5;
            Atom newN = new Atom(xyzIndex++, "N", C.getAltLoc(), nXYZ, resNames[i], currentID, chainID, 1.0, C.getTempFactor(), C.getSegID(), true);
            currentResidue.addMSNode(newN);
            double[] caXYZ = new double[3];
            VectorMath.scalar(vector, 2.0, vector);
            VectorMath.sum(C.getXYZ(null), vector, caXYZ);
            caXYZ[0] += Math.random() - 0.5;
            caXYZ[1] += Math.random() - 0.5;
            caXYZ[2] += Math.random() - 0.5;
            Atom newCA = new Atom(xyzIndex++, "CA", C.getAltLoc(), caXYZ, resNames[i], currentID, chainID, 1.0, C.getTempFactor(), C.getSegID(), true);
            currentResidue.addMSNode(newCA);
            double[] cXYZ = new double[3];
            VectorMath.scalar(vector, 1.5, vector);
            VectorMath.sum(C.getXYZ(null), vector, cXYZ);
            cXYZ[0] += Math.random() - 0.5;
            cXYZ[1] += Math.random() - 0.5;
            cXYZ[2] += Math.random() - 0.5;
            Atom newC = new Atom(xyzIndex++, "C", C.getAltLoc(), cXYZ, resNames[i], currentID, chainID, 1.0, C.getTempFactor(), C.getSegID(), true);
            currentResidue.addMSNode(newC);
            double[] oXYZ = new double[3];
            vector[0] = Math.random() - 0.5;
            vector[1] = Math.random() - 0.5;
            vector[2] = Math.random() - 0.5;
            VectorMath.sum(cXYZ, vector, oXYZ);
            Atom newO = new Atom(xyzIndex++, "O", C.getAltLoc(), oXYZ, resNames[i], currentID, chainID, 1.0, C.getTempFactor(), C.getSegID(), true);
            currentResidue.addMSNode(newO);
            logger.info(String.format(" Building residue %8s.", currentResidue.toString()));
        }
    }
    return xyzIndex;
}

Example 34 with Polymer

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

the class PDBFilter method buildDisulfideBonds.

/**
 * Assign parameters to disulfide bonds.
 *
 * @param ssBondList
 */
private void buildDisulfideBonds(List<Bond> ssBondList) {
    StringBuilder sb = new StringBuilder(" Disulfide Bonds:");
    for (Bond bond : ssBondList) {
        Atom a1 = bond.getAtom(0);
        Atom a2 = bond.getAtom(1);
        int[] c = new int[2];
        c[0] = a1.getAtomType().atomClass;
        c[1] = a2.getAtomType().atomClass;
        String key = BondType.sortKey(c);
        BondType bondType = forceField.getBondType(key);
        if (bondType == null) {
            logger.severe(format("No BondType for key: %s\n %s\n %s", key, a1, a2));
        } else {
            bond.setBondType(bondType);
        }
        double d = VectorMath.dist(a1.getXYZ(null), a2.getXYZ(null));
        Polymer c1 = activeMolecularAssembly.getChain(a1.getSegID());
        Polymer c2 = activeMolecularAssembly.getChain(a2.getSegID());
        Residue r1 = c1.getResidue(a1.getResidueNumber());
        Residue r2 = c2.getResidue(a2.getResidueNumber());
        sb.append(format("\n S-S distance of %6.2f for %s and %s.", d, r1.toString(), r2.toString()));
        bondList.add(bond);
    }
    if (ssBondList.size() > 0) {
        logger.info(sb.toString());
    }
}

Example 35 with Polymer

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

the class PDBFilter method locateDisulfideBonds.

/**
 * Locate disulfide bonds based on SSBOND records.
 *
 * @param ssbonds
 *
 * @return An ArrayList of Bond instances for SS-Bonds.
 */
private List<Bond> locateDisulfideBonds(List<String> ssbonds) {
    List<Bond> ssBondList = new ArrayList<>();
    for (String ssbond : ssbonds) {
        // =============================================================================
        try {
            char c1ch = ssbond.charAt(15);
            char c2ch = ssbond.charAt(29);
            Polymer c1 = activeMolecularAssembly.getChain(String.format("%c", c1ch));
            Polymer c2 = activeMolecularAssembly.getChain(String.format("%c", c2ch));
            String origResNum1 = ssbond.substring(17, 21).trim();
            char insChar1 = ssbond.charAt(21);
            String origResNum2 = ssbond.substring(31, 35).trim();
            char insChar2 = ssbond.charAt(35);
            String pdbResNum1 = String.format("%c%s%c", c1ch, origResNum1, insChar1);
            String pdbResNum2 = String.format("%c%s%c", c2ch, origResNum2, insChar2);
            String resnum1 = pdbToNewResMap.get(pdbResNum1);
            String resnum2 = pdbToNewResMap.get(pdbResNum2);
            if (resnum1 == null) {
                logger.warning(String.format(" Could not find residue %s for SS-bond %s", pdbResNum1, ssbond));
                continue;
            }
            if (resnum2 == null) {
                logger.warning(String.format(" Could not find residue %s for SS-bond %s", pdbResNum2, ssbond));
                continue;
            }
            Residue r1 = c1.getResidue(Integer.parseInt(resnum1.substring(1)));
            Residue r2 = c2.getResidue(Integer.parseInt(resnum2.substring(1)));
            /*Residue r1 = c1.getResidue(Hybrid36.decode(4, ssbond.substring(17, 21)));
                Residue r2 = c2.getResidue(Hybrid36.decode(4, ssbond.substring(31, 35)));*/
            List<Atom> atoms1 = r1.getAtomList();
            List<Atom> atoms2 = r2.getAtomList();
            Atom SG1 = null;
            Atom SG2 = null;
            for (Atom atom : atoms1) {
                if (atom.getName().equalsIgnoreCase("SG")) {
                    SG1 = atom;
                    break;
                }
            }
            for (Atom atom : atoms2) {
                if (atom.getName().equalsIgnoreCase("SG")) {
                    SG2 = atom;
                    break;
                }
            }
            if (SG1 == null) {
                logger.warning(String.format(" SG atom 1 of SS-bond %s is null", ssbond));
            }
            if (SG2 == null) {
                logger.warning(String.format(" SG atom 2 of SS-bond %s is null", ssbond));
            }
            if (SG1 == null || SG2 == null) {
                continue;
            }
            double d = VectorMath.dist(SG1.getXYZ(null), SG2.getXYZ(null));
            if (d < 3.0) {
                r1.setName("CYX");
                r2.setName("CYX");
                for (Atom atom : atoms1) {
                    atom.setResName("CYX");
                }
                for (Atom atom : atoms2) {
                    atom.setResName("CYX");
                }
                Bond bond = new Bond(SG1, SG2);
                ssBondList.add(bond);
            } else {
                String message = format("Ignoring [%s]\n due to distance %8.3f A.", ssbond, d);
                logger.log(Level.WARNING, message);
            }
        } catch (Exception e) {
            String message = format("Ignoring [%s]", ssbond);
            logger.log(Level.WARNING, message, e);
        }
    }
    return ssBondList;
}