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

Example 16 with Molecule

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

the class XRayEnergy method setOccupancies.

/**
 * set atom occupancies based on current position
 *
 * @param x current parameters to set occupancies with
 */
public void setOccupancies(double[] x) {
    double occ = 0.0;
    int index = nXYZ + nB;
    for (ArrayList<Residue> list : refinementModel.getAltResidues()) {
        for (Residue r : list) {
            occ = x[index++];
            for (Atom a : r.getAtomList()) {
                if (a.getOccupancy() < 1.0) {
                    a.setOccupancy(occ);
                }
            }
        }
    }
    for (ArrayList<Molecule> list : refinementModel.getAltMolecules()) {
        for (Molecule m : list) {
            occ = x[index++];
            for (Atom a : m.getAtomList()) {
                if (a.getOccupancy() < 1.0) {
                    a.setOccupancy(occ);
                }
            }
        }
    }
}

Example 17 with Molecule

use of ffx.potential.bonded.Molecule 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 18 with Molecule

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

the class PDBFilter method resolvePolymerLinks.

/**
 * Resolves links between polymeric hetero groups; presently only functional
 * for cyclic molecules.
 *
 * @param molecules List of Molecules in the molecular assembly.
 */
private void resolvePolymerLinks(List<Molecule> molecules) {
    CompositeConfiguration ffProps = forceField.getProperties();
    for (String polyLink : ffProps.getStringArray("polymerlink")) {
        logger.info(" Experimental: linking a cyclic hetero group: " + polyLink);
        // Format: polymerlink resname atom1 atom2 [cyclize]
        String[] toks = polyLink.split("\\s+");
        String resName = toks[0];
        String name1 = toks[1];
        String name2 = toks[2];
        int cyclicLen = 0;
        if (toks.length > 3) {
            cyclicLen = Integer.parseInt(toks[3]);
        }
        Molecule[] matches = molecules.stream().filter((Molecule m) -> m.getResidueName().equalsIgnoreCase(resName)).toArray(Molecule[]::new);
        for (int i = 0; i < matches.length; i++) {
            Molecule mi = matches[i];
            int ii = i + 1;
            if (cyclicLen < 1) {
                logger.severe(" No current support for polymeric, non-cyclic hetero groups");
            // Would probably split by chain.
            } else {
                Molecule next;
                if (ii % cyclicLen == 0) {
                    next = matches[ii - cyclicLen];
                    logger.info(String.format(" Cyclizing molecule %s to %s", mi, next));
                } else {
                    next = matches[ii];
                    logger.info(String.format(" Extending chain from %s to %s.", mi, next));
                }
                Atom from = mi.getAtomByName(name1, true);
                Atom to = next.getAtomByName(name2, true);
                buildBond(from, to);
            }
        }
    }
}

Example 19 with Molecule

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

the class BiojavaFilter method writeFile.

/**
 * <p>
 * writeFile</p>
 *
 * @param saveFile a {@link java.io.File} object.
 * @param append a {@link java.lang.StringBuilder} object.
 * @param printLinear Whether to print atoms linearly or by element
 * @return Success of writing.
 */
public boolean writeFile(File saveFile, boolean append, boolean printLinear) {
    if (saveFile == null) {
        return false;
    }
    if (vdwH) {
        logger.info(" Printing hydrogens to van der Waals centers instead of nuclear locations.");
    }
    /**
     * Create StringBuilders for ATOM, ANISOU and TER records that can be
     * reused.
     */
    StringBuilder sb = new StringBuilder("ATOM  ");
    StringBuilder anisouSB = new StringBuilder("ANISOU");
    StringBuilder terSB = new StringBuilder("TER   ");
    for (int i = 6; i < 80; i++) {
        sb.append(' ');
        anisouSB.append(' ');
        terSB.append(' ');
    }
    FileWriter fw;
    BufferedWriter bw;
    try {
        File newFile = saveFile;
        if (!append) {
            newFile = version(saveFile);
        }
        activeMolecularAssembly.setFile(newFile);
        activeMolecularAssembly.setName(newFile.getName());
        logger.log(Level.INFO, " Saving {0}", newFile.getName());
        fw = new FileWriter(newFile, append);
        bw = new BufferedWriter(fw);
        // =============================================================================
        // The CRYST1 record presents the unit cell parameters, space group, and Z
        // value. If the structure was not determined by crystallographic means, CRYST1
        // simply provides the unitary values, with an appropriate REMARK.
        // 
        // 7 - 15       Real(9.3)     a              a (Angstroms).
        // 16 - 24       Real(9.3)     b              b (Angstroms).
        // 25 - 33       Real(9.3)     c              c (Angstroms).
        // 34 - 40       Real(7.2)     alpha          alpha (degrees).
        // 41 - 47       Real(7.2)     beta           beta (degrees).
        // 48 - 54       Real(7.2)     gamma          gamma (degrees).
        // 56 - 66       LString       sGroup         Space  group.
        // 67 - 70       Integer       z              Z value.
        // =============================================================================
        Crystal crystal = activeMolecularAssembly.getCrystal();
        if (crystal != null && !crystal.aperiodic()) {
            Crystal c = crystal.getUnitCell();
            if (!listMode) {
                bw.write(format("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %10s\n", c.a, c.b, c.c, c.alpha, c.beta, c.gamma, padRight(c.spaceGroup.pdbName, 10)));
            } else {
                listOutput.add(format("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %10s", c.a, c.b, c.c, c.alpha, c.beta, c.gamma, padRight(c.spaceGroup.pdbName, 10)));
            }
        }
        // =============================================================================
        // The SSBOND record identifies each disulfide bond in protein and polypeptide
        // structures by identifying the two residues involved in the bond.
        // The disulfide bond distance is included after the symmetry operations at
        // the end of the SSBOND record.
        // 
        // 8 - 10        Integer         serNum       Serial number.
        // 12 - 14        LString(3)      "CYS"        Residue name.
        // 16             Character       chainID1     Chain identifier.
        // 18 - 21        Integer         seqNum1      Residue sequence number.
        // 22             AChar           icode1       Insertion code.
        // 26 - 28        LString(3)      "CYS"        Residue name.
        // 30             Character       chainID2     Chain identifier.
        // 32 - 35        Integer         seqNum2      Residue sequence number.
        // 36             AChar           icode2       Insertion code.
        // 60 - 65        SymOP           sym1         Symmetry oper for 1st resid
        // 67 - 72        SymOP           sym2         Symmetry oper for 2nd resid
        // 74 – 78        Real(5.2)      Length        Disulfide bond distance
        // 
        // If SG of cysteine is disordered then there are possible alternate linkages.
        // wwPDB practice is to put together all possible SSBOND records. This is
        // problematic because the alternate location identifier is not specified in
        // the SSBOND record.
        // =============================================================================
        int serNum = 1;
        Polymer[] polymers = activeMolecularAssembly.getChains();
        if (polymers != null) {
            for (Polymer polymer : polymers) {
                ArrayList<Residue> residues = polymer.getResidues();
                for (Residue residue : residues) {
                    if (residue.getName().equalsIgnoreCase("CYS")) {
                        List<Atom> cysAtoms = residue.getAtomList();
                        Atom SG1 = null;
                        for (Atom atom : cysAtoms) {
                            if (atom.getName().equalsIgnoreCase("SG")) {
                                SG1 = atom;
                                break;
                            }
                        }
                        List<Bond> bonds = SG1.getBonds();
                        for (Bond bond : bonds) {
                            Atom SG2 = bond.get1_2(SG1);
                            if (SG2.getName().equalsIgnoreCase("SG")) {
                                if (SG1.getIndex() < SG2.getIndex()) {
                                    bond.energy(false);
                                    if (!listMode) {
                                        bw.write(format("SSBOND %3d CYS %1s %4s    CYS %1s %4s %36s %5.2f\n", serNum++, SG1.getChainID().toString(), Hybrid36.encode(4, SG1.getResidueNumber()), SG2.getChainID().toString(), Hybrid36.encode(4, SG2.getResidueNumber()), "", bond.getValue()));
                                    } else {
                                        listOutput.add(format("SSBOND %3d CYS %1s %4s    CYS %1s %4s %36s %5.2f\n", serNum++, SG1.getChainID().toString(), Hybrid36.encode(4, SG1.getResidueNumber()), SG2.getChainID().toString(), Hybrid36.encode(4, SG2.getResidueNumber()), "", bond.getValue()));
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
        // =============================================================================
        // 
        // 7 - 11        Integer       serial       Atom serial number.
        // 13 - 16        Atom          name         Atom name.
        // 17             Character     altLoc       Alternate location indicator.
        // 18 - 20        Residue name  resName      Residue name.
        // 22             Character     chainID      Chain identifier.
        // 23 - 26        Integer       resSeq       Residue sequence number.
        // 27             AChar         iCode        Code for insertion of residues.
        // 31 - 38        Real(8.3)     x            Orthogonal coordinates for X in Angstroms.
        // 39 - 46        Real(8.3)     y            Orthogonal coordinates for Y in Angstroms.
        // 47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
        // 55 - 60        Real(6.2)     occupancy    Occupancy.
        // 61 - 66        Real(6.2)     tempFactor   Temperature factor.
        // 77 - 78        LString(2)    element      Element symbol, right-justified.
        // 79 - 80        LString(2)    charge       Charge  on the atom.
        // =============================================================================
        // 1         2         3         4         5         6         7
        // 123456789012345678901234567890123456789012345678901234567890123456789012345678
        // ATOM      1  N   ILE A  16      60.614  71.140 -10.592  1.00  7.38           N
        // ATOM      2  CA  ILE A  16      60.793  72.149  -9.511  1.00  6.91           C
        MolecularAssembly[] molecularAssemblies = this.getMolecularAssemblys();
        int serial = 1;
        // Loop over biomolecular chains
        if (polymers != null) {
            for (Polymer polymer : polymers) {
                currentSegID = polymer.getName();
                currentChainID = polymer.getChainID();
                sb.setCharAt(21, currentChainID);
                // Loop over residues
                ArrayList<Residue> residues = polymer.getResidues();
                for (Residue residue : residues) {
                    String resName = residue.getName();
                    if (resName.length() > 3) {
                        resName = resName.substring(0, 3);
                    }
                    int resID = residue.getResidueNumber();
                    sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
                    sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
                    // Loop over atoms
                    ArrayList<Atom> residueAtoms = residue.getAtomList();
                    ArrayList<Atom> backboneAtoms = residue.getBackboneAtoms();
                    boolean altLocFound = false;
                    for (Atom atom : backboneAtoms) {
                        writeAtom(atom, serial++, sb, anisouSB, bw);
                        Character altLoc = atom.getAltLoc();
                        if (altLoc != null && !altLoc.equals(' ')) {
                            altLocFound = true;
                        }
                        residueAtoms.remove(atom);
                    }
                    for (Atom atom : residueAtoms) {
                        writeAtom(atom, serial++, sb, anisouSB, bw);
                        Character altLoc = atom.getAltLoc();
                        if (altLoc != null && !altLoc.equals(' ')) {
                            altLocFound = true;
                        }
                    }
                    // Write out alternate conformers
                    if (altLocFound) {
                        for (int ma = 1; ma < molecularAssemblies.length; ma++) {
                            MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
                            Polymer altPolymer = altMolecularAssembly.getPolymer(currentChainID, currentSegID, false);
                            Residue altResidue = altPolymer.getResidue(resName, resID, false);
                            backboneAtoms = altResidue.getBackboneAtoms();
                            residueAtoms = altResidue.getAtomList();
                            for (Atom atom : backboneAtoms) {
                                if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
                                    writeAtom(atom, serial++, sb, anisouSB, bw);
                                }
                                residueAtoms.remove(atom);
                            }
                            for (Atom atom : residueAtoms) {
                                if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
                                    writeAtom(atom, serial++, sb, anisouSB, bw);
                                }
                            }
                        }
                    }
                }
                terSB.replace(6, 11, String.format("%5s", Hybrid36.encode(5, serial++)));
                terSB.replace(12, 16, "    ");
                terSB.replace(16, 26, sb.substring(16, 26));
                if (!listMode) {
                    bw.write(terSB.toString());
                    bw.newLine();
                } else {
                    listOutput.add(terSB.toString());
                }
            }
        }
        sb.replace(0, 6, "HETATM");
        sb.setCharAt(21, 'A');
        int resID = 1;
        Polymer polymer = activeMolecularAssembly.getPolymer('A', "A", false);
        if (polymer != null) {
            ArrayList<Residue> residues = polymer.getResidues();
            for (Residue residue : residues) {
                int resID2 = residue.getResidueNumber();
                if (resID2 >= resID) {
                    resID = resID2 + 1;
                }
            }
        }
        /**
         * Loop over molecules, ions and then water.
         */
        ArrayList<Molecule> molecules = activeMolecularAssembly.getMolecules();
        for (int i = 0; i < molecules.size(); i++) {
            Molecule molecule = (Molecule) molecules.get(i);
            Character chainID = molecule.getChainID();
            sb.setCharAt(21, chainID);
            String resName = molecule.getResidueName();
            if (resName.length() > 3) {
                resName = resName.substring(0, 3);
            }
            sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
            sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
            ArrayList<Atom> moleculeAtoms = molecule.getAtomList();
            boolean altLocFound = false;
            for (Atom atom : moleculeAtoms) {
                writeAtom(atom, serial++, sb, anisouSB, bw);
                Character altLoc = atom.getAltLoc();
                if (altLoc != null && !altLoc.equals(' ')) {
                    altLocFound = true;
                }
            }
            // Write out alternate conformers
            if (altLocFound) {
                for (int ma = 1; ma < molecularAssemblies.length; ma++) {
                    MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
                    MSNode altmolecule = altMolecularAssembly.getMolecules().get(i);
                    moleculeAtoms = altmolecule.getAtomList();
                    for (Atom atom : moleculeAtoms) {
                        if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
                            writeAtom(atom, serial++, sb, anisouSB, bw);
                        }
                    }
                }
            }
            resID++;
        }
        ArrayList<MSNode> ions = activeMolecularAssembly.getIons();
        for (int i = 0; i < ions.size(); i++) {
            Molecule ion = (Molecule) ions.get(i);
            Character chainID = ion.getChainID();
            sb.setCharAt(21, chainID);
            String resName = ion.getResidueName();
            if (resName.length() > 3) {
                resName = resName.substring(0, 3);
            }
            sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
            sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
            ArrayList<Atom> ionAtoms = ion.getAtomList();
            boolean altLocFound = false;
            for (Atom atom : ionAtoms) {
                writeAtom(atom, serial++, sb, anisouSB, bw);
                Character altLoc = atom.getAltLoc();
                if (altLoc != null && !altLoc.equals(' ')) {
                    altLocFound = true;
                }
            }
            // Write out alternate conformers
            if (altLocFound) {
                for (int ma = 1; ma < molecularAssemblies.length; ma++) {
                    MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
                    MSNode altion = altMolecularAssembly.getIons().get(i);
                    ionAtoms = altion.getAtomList();
                    for (Atom atom : ionAtoms) {
                        if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
                            writeAtom(atom, serial++, sb, anisouSB, bw);
                        }
                    }
                }
            }
            resID++;
        }
        ArrayList<MSNode> waters = activeMolecularAssembly.getWaters();
        for (int i = 0; i < waters.size(); i++) {
            Molecule water = (Molecule) waters.get(i);
            Character chainID = water.getChainID();
            sb.setCharAt(21, chainID);
            String resName = water.getResidueName();
            if (resName.length() > 3) {
                resName = resName.substring(0, 3);
            }
            sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
            sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
            ArrayList<Atom> waterAtoms = water.getAtomList();
            boolean altLocFound = false;
            for (Atom atom : waterAtoms) {
                writeAtom(atom, serial++, sb, anisouSB, bw);
                Character altLoc = atom.getAltLoc();
                if (altLoc != null && !altLoc.equals(' ')) {
                    altLocFound = true;
                }
            }
            // Write out alternate conformers
            if (altLocFound) {
                for (int ma = 1; ma < molecularAssemblies.length; ma++) {
                    MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
                    MSNode altwater = altMolecularAssembly.getWaters().get(i);
                    waterAtoms = altwater.getAtomList();
                    for (Atom atom : waterAtoms) {
                        if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
                            writeAtom(atom, serial++, sb, anisouSB, bw);
                        }
                    }
                }
            }
            resID++;
        }
        if (!listMode) {
            bw.write("END");
            bw.newLine();
        } else {
            listOutput.add("END");
        }
        bw.close();
    } catch (Exception e) {
        String message = "Exception writing to file: " + saveFile.toString();
        logger.log(Level.WARNING, message, e);
        return false;
    }
    return true;
}

Example 20 with Molecule

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

the class BiojavaFilter method writeSIFTFile.

/*public Structure writeToStructure(String header) {
     return writeToStructure(activeMolecularAssembly, header);
     }

     public static Structure writeToStructure(MolecularAssembly assembly, String header) {
     Structure structure = new StructureImpl();
     for (Polymer polymer : assembly.getChains()) {
     Chain chain = new ChainImpl();
     for (Residue residue : polymer.getResidues()) {
     Group group;
     switch (residue.getResidueType()) {
     case AA:
     group = new AminoAcidImpl();
     break;
     case NA:
     group = new NucleotideImpl();
     break;
     default:
     group = new HetatomImpl();
     break;
     }
     for (Atom atom : residue.getAtomList()) {
     org.biojava.bio.structure.Atom bjAtom = new AtomImpl();
     group.addAtom(bjAtom);
     }
     chain.addGroup(group);
     }
     structure.addChain(chain);
     }

     for (Molecule molecule : assembly.getMolecules()) {
     for (Atom atom : molecule.getAtomList()) {

     }
     }
     }*/
public boolean writeSIFTFile(File saveFile, boolean append, String[] resAndScore) {
    if (saveFile == null) {
        return false;
    }
    if (vdwH) {
        logger.info(" Printing hydrogens to van der Waals centers instead of nuclear locations.");
    }
    /**
     * Create StringBuilders for ATOM, ANISOU and TER records that can be
     * reused.
     */
    StringBuilder sb = new StringBuilder("ATOM  ");
    StringBuilder anisouSB = new StringBuilder("ANISOU");
    StringBuilder terSB = new StringBuilder("TER   ");
    for (int i = 6; i < 80; i++) {
        sb.append(' ');
        anisouSB.append(' ');
        terSB.append(' ');
    }
    FileWriter fw;
    BufferedWriter bw;
    try {
        File newFile = saveFile;
        if (!append) {
            newFile = version(saveFile);
        }
        activeMolecularAssembly.setFile(newFile);
        activeMolecularAssembly.setName(newFile.getName());
        logger.log(Level.INFO, " Saving {0}", newFile.getName());
        fw = new FileWriter(newFile, append);
        bw = new BufferedWriter(fw);
        // =============================================================================
        // The CRYST1 record presents the unit cell parameters, space group, and Z
        // value. If the structure was not determined by crystallographic means, CRYST1
        // simply provides the unitary values, with an appropriate REMARK.
        // 
        // 7 - 15       Real(9.3)     a              a (Angstroms).
        // 16 - 24       Real(9.3)     b              b (Angstroms).
        // 25 - 33       Real(9.3)     c              c (Angstroms).
        // 34 - 40       Real(7.2)     alpha          alpha (degrees).
        // 41 - 47       Real(7.2)     beta           beta (degrees).
        // 48 - 54       Real(7.2)     gamma          gamma (degrees).
        // 56 - 66       LString       sGroup         Space  group.
        // 67 - 70       Integer       z              Z value.
        // =============================================================================
        Crystal crystal = activeMolecularAssembly.getCrystal();
        if (crystal != null && !crystal.aperiodic()) {
            Crystal c = crystal.getUnitCell();
            if (!listMode) {
                bw.write(format("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %10s\n", c.a, c.b, c.c, c.alpha, c.beta, c.gamma, padRight(c.spaceGroup.pdbName, 10)));
            } else {
                listOutput.add(format("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %10s", c.a, c.b, c.c, c.alpha, c.beta, c.gamma, padRight(c.spaceGroup.pdbName, 10)));
            }
        }
        // =============================================================================
        // The SSBOND record identifies each disulfide bond in protein and polypeptide
        // structures by identifying the two residues involved in the bond.
        // The disulfide bond distance is included after the symmetry operations at
        // the end of the SSBOND record.
        // 
        // 8 - 10        Integer         serNum       Serial number.
        // 12 - 14        LString(3)      "CYS"        Residue name.
        // 16             Character       chainID1     Chain identifier.
        // 18 - 21        Integer         seqNum1      Residue sequence number.
        // 22             AChar           icode1       Insertion code.
        // 26 - 28        LString(3)      "CYS"        Residue name.
        // 30             Character       chainID2     Chain identifier.
        // 32 - 35        Integer         seqNum2      Residue sequence number.
        // 36             AChar           icode2       Insertion code.
        // 60 - 65        SymOP           sym1         Symmetry oper for 1st resid
        // 67 - 72        SymOP           sym2         Symmetry oper for 2nd resid
        // 74 – 78        Real(5.2)      Length        Disulfide bond distance
        // 
        // If SG of cysteine is disordered then there are possible alternate linkages.
        // wwPDB practice is to put together all possible SSBOND records. This is
        // problematic because the alternate location identifier is not specified in
        // the SSBOND record.
        // =============================================================================
        int serNum = 1;
        Polymer[] polymers = activeMolecularAssembly.getChains();
        if (polymers != null) {
            for (Polymer polymer : polymers) {
                ArrayList<Residue> residues = polymer.getResidues();
                for (Residue residue : residues) {
                    if (residue.getName().equalsIgnoreCase("CYS")) {
                        List<Atom> cysAtoms = residue.getAtomList();
                        Atom SG1 = null;
                        for (Atom atom : cysAtoms) {
                            if (atom.getName().equalsIgnoreCase("SG")) {
                                SG1 = atom;
                                break;
                            }
                        }
                        List<Bond> bonds = SG1.getBonds();
                        for (Bond bond : bonds) {
                            Atom SG2 = bond.get1_2(SG1);
                            if (SG2.getName().equalsIgnoreCase("SG")) {
                                if (SG1.getIndex() < SG2.getIndex()) {
                                    bond.energy(false);
                                    if (!listMode) {
                                        bw.write(format("SSBOND %3d CYS %1s %4s    CYS %1s %4s %36s %5.2f\n", serNum++, SG1.getChainID().toString(), Hybrid36.encode(4, SG1.getResidueNumber()), SG2.getChainID().toString(), Hybrid36.encode(4, SG2.getResidueNumber()), "", bond.getValue()));
                                    } else {
                                        listOutput.add(format("SSBOND %3d CYS %1s %4s    CYS %1s %4s %36s %5.2f\n", serNum++, SG1.getChainID().toString(), Hybrid36.encode(4, SG1.getResidueNumber()), SG2.getChainID().toString(), Hybrid36.encode(4, SG2.getResidueNumber()), "", bond.getValue()));
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
        // =============================================================================
        // 
        // 7 - 11        Integer       serial       Atom serial number.
        // 13 - 16        Atom          name         Atom name.
        // 17             Character     altLoc       Alternate location indicator.
        // 18 - 20        Residue name  resName      Residue name.
        // 22             Character     chainID      Chain identifier.
        // 23 - 26        Integer       resSeq       Residue sequence number.
        // 27             AChar         iCode        Code for insertion of residues.
        // 31 - 38        Real(8.3)     x            Orthogonal coordinates for X in Angstroms.
        // 39 - 46        Real(8.3)     y            Orthogonal coordinates for Y in Angstroms.
        // 47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
        // 55 - 60        Real(6.2)     occupancy    Occupancy.
        // 61 - 66        Real(6.2)     tempFactor   Temperature factor.
        // 77 - 78        LString(2)    element      Element symbol, right-justified.
        // 79 - 80        LString(2)    charge       Charge  on the atom.
        // =============================================================================
        // 1         2         3         4         5         6         7
        // 123456789012345678901234567890123456789012345678901234567890123456789012345678
        // ATOM      1  N   ILE A  16      60.614  71.140 -10.592  1.00  7.38           N
        // ATOM      2  CA  ILE A  16      60.793  72.149  -9.511  1.00  6.91           C
        MolecularAssembly[] molecularAssemblies = this.getMolecularAssemblys();
        int serial = 1;
        // Loop over biomolecular chains
        if (polymers != null) {
            for (Polymer polymer : polymers) {
                currentSegID = polymer.getName();
                currentChainID = polymer.getChainID();
                sb.setCharAt(21, currentChainID);
                // Loop over residues
                ArrayList<Residue> residues = polymer.getResidues();
                for (Residue residue : residues) {
                    String resName = residue.getName();
                    if (resName.length() > 3) {
                        resName = resName.substring(0, 3);
                    }
                    int resID = residue.getResidueNumber();
                    int i = 0;
                    String[] entries = null;
                    for (; i < resAndScore.length; i++) {
                        entries = resAndScore[i].split("\\t");
                        if (!entries[0].equals(entries[0].replaceAll("\\D+", ""))) {
                            String[] subEntries = entries[0].split("[^0-9]");
                            entries[0] = subEntries[0];
                        }
                        if (entries[0].equals(String.valueOf(resID)) && !".".equals(entries[1])) {
                            break;
                        }
                    }
                    sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
                    sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
                    // Loop over atoms
                    ArrayList<Atom> residueAtoms = residue.getAtomList();
                    boolean altLocFound = false;
                    for (Atom atom : residueAtoms) {
                        if (i != resAndScore.length) {
                            writeSIFTAtom(atom, serial++, sb, anisouSB, bw, entries[1]);
                        } else {
                            writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
                        }
                        Character altLoc = atom.getAltLoc();
                        if (altLoc != null && !altLoc.equals(' ')) {
                            altLocFound = true;
                        }
                    }
                    // Write out alternate conformers
                    if (altLocFound) {
                        for (int ma = 1; ma < molecularAssemblies.length; ma++) {
                            MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
                            Polymer altPolymer = altMolecularAssembly.getPolymer(currentChainID, currentSegID, false);
                            Residue altResidue = altPolymer.getResidue(resName, resID, false);
                            residueAtoms = altResidue.getAtomList();
                            for (Atom atom : residueAtoms) {
                                if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
                                    if (i != resAndScore.length) {
                                        writeSIFTAtom(atom, serial++, sb, anisouSB, bw, entries[1]);
                                    } else {
                                        writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
                                    }
                                }
                            }
                        }
                    }
                }
                terSB.replace(6, 11, String.format("%5s", Hybrid36.encode(5, serial++)));
                terSB.replace(12, 16, "    ");
                terSB.replace(16, 26, sb.substring(16, 26));
                if (!listMode) {
                    bw.write(terSB.toString());
                    bw.newLine();
                } else {
                    listOutput.add(terSB.toString());
                }
            }
        }
        sb.replace(0, 6, "HETATM");
        sb.setCharAt(21, 'A');
        int resID = 1;
        Polymer polymer = activeMolecularAssembly.getPolymer('A', "A", false);
        if (polymer != null) {
            ArrayList<Residue> residues = polymer.getResidues();
            for (Residue residue : residues) {
                int resID2 = residue.getResidueNumber();
                if (resID2 >= resID) {
                    resID = resID2 + 1;
                }
            }
        }
        /**
         * Loop over molecules, ions and then water.
         */
        ArrayList<Molecule> molecules = activeMolecularAssembly.getMolecules();
        for (int i = 0; i < molecules.size(); i++) {
            Molecule molecule = (Molecule) molecules.get(i);
            Character chainID = molecule.getChainID();
            sb.setCharAt(21, chainID);
            String resName = molecule.getResidueName();
            if (resName.length() > 3) {
                resName = resName.substring(0, 3);
            }
            sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
            sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
            ArrayList<Atom> moleculeAtoms = molecule.getAtomList();
            boolean altLocFound = false;
            for (Atom atom : moleculeAtoms) {
                writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
                Character altLoc = atom.getAltLoc();
                if (altLoc != null && !altLoc.equals(' ')) {
                    altLocFound = true;
                }
            }
            // Write out alternate conformers
            if (altLocFound) {
                for (int ma = 1; ma < molecularAssemblies.length; ma++) {
                    MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
                    MSNode altmolecule = altMolecularAssembly.getMolecules().get(i);
                    moleculeAtoms = altmolecule.getAtomList();
                    for (Atom atom : moleculeAtoms) {
                        if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
                            writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
                        }
                    }
                }
            }
            resID++;
        }
        ArrayList<MSNode> ions = activeMolecularAssembly.getIons();
        for (int i = 0; i < ions.size(); i++) {
            Molecule ion = (Molecule) ions.get(i);
            Character chainID = ion.getChainID();
            sb.setCharAt(21, chainID);
            String resName = ion.getResidueName();
            if (resName.length() > 3) {
                resName = resName.substring(0, 3);
            }
            sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
            sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
            ArrayList<Atom> ionAtoms = ion.getAtomList();
            boolean altLocFound = false;
            for (Atom atom : ionAtoms) {
                writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
                Character altLoc = atom.getAltLoc();
                if (altLoc != null && !altLoc.equals(' ')) {
                    altLocFound = true;
                }
            }
            // Write out alternate conformers
            if (altLocFound) {
                for (int ma = 1; ma < molecularAssemblies.length; ma++) {
                    MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
                    MSNode altion = altMolecularAssembly.getIons().get(i);
                    ionAtoms = altion.getAtomList();
                    for (Atom atom : ionAtoms) {
                        if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
                            writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
                        }
                    }
                }
            }
            resID++;
        }
        ArrayList<MSNode> waters = activeMolecularAssembly.getWaters();
        for (int i = 0; i < waters.size(); i++) {
            Molecule water = (Molecule) waters.get(i);
            Character chainID = water.getChainID();
            sb.setCharAt(21, chainID);
            String resName = water.getResidueName();
            if (resName.length() > 3) {
                resName = resName.substring(0, 3);
            }
            sb.replace(17, 20, padLeft(resName.toUpperCase(), 3));
            sb.replace(22, 26, String.format("%4s", Hybrid36.encode(4, resID)));
            ArrayList<Atom> waterAtoms = water.getAtomList();
            boolean altLocFound = false;
            for (Atom atom : waterAtoms) {
                writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
                Character altLoc = atom.getAltLoc();
                if (altLoc != null && !altLoc.equals(' ')) {
                    altLocFound = true;
                }
            }
            // Write out alternate conformers
            if (altLocFound) {
                for (int ma = 1; ma < molecularAssemblies.length; ma++) {
                    MolecularAssembly altMolecularAssembly = molecularAssemblies[ma];
                    MSNode altwater = altMolecularAssembly.getWaters().get(i);
                    waterAtoms = altwater.getAtomList();
                    for (Atom atom : waterAtoms) {
                        if (atom.getAltLoc() != null && !atom.getAltLoc().equals(' ') && !atom.getAltLoc().equals('A')) {
                            writeSIFTAtom(atom, serial++, sb, anisouSB, bw, null);
                        }
                    }
                }
            }
            resID++;
        }
        if (!listMode) {
            bw.write("END");
            bw.newLine();
        } else {
            listOutput.add("END");
        }
        bw.close();
    } catch (Exception e) {
        String message = "Exception writing to file: " + saveFile.toString();
        logger.log(Level.WARNING, message, e);
        return false;
    }
    return true;
}