Examples with MolecularAssembly ffx.potential.MolecularAssembly used on opensource projects

Example 11 with MolecularAssembly

use of ffx.potential.MolecularAssembly in project ffx by mjschnie.

the class PDBFilter method writeSIFTFile.

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.");
    }
    if (nSymOp != 0) {
        logger.info(String.format(" Printing atoms with symmetry operator %s", activeMolecularAssembly.getCrystal().spaceGroup.getSymOp(nSymOp).toString()));
    }
    /**
     * 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 && !noVersioning) {
            newFile = version(saveFile);
        }
        activeMolecularAssembly.setFile(newFile);
        activeMolecularAssembly.setName(newFile.getName());
        if (logWrites) {
            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;
}

Example 12 with MolecularAssembly

use of ffx.potential.MolecularAssembly in project ffx by mjschnie.

the class ExtendedVariableTest method setup.

public MolecularAssembly setup(String filename, boolean quietly) {
    if (quietly || resultsOnly) {
        utils.setSilentPotential(true);
    }
    MolecularAssembly mola = openResource(filename, quietly);
    // Turn off checks for overlapping atoms, which is expected for lambda=0.
    mola.getPotentialEnergy().getCrystal().setSpecialPositionCutoff(0.0);
    return mola;
}

Example 13 with MolecularAssembly

use of ffx.potential.MolecularAssembly in project ffx by mjschnie.

the class ExtendedVariableTest method setupWithExtended.

public MolecularAssembly setupWithExtended(String filename, boolean quietly, ExtendedSystemConfig esvConfig) {
    if (quietly || resultsOnly) {
        utils.setSilentPotential(true);
    }
    setProp("pme.qi", true);
    MolecularAssembly mola = openResource(filename, quietly);
    // Turn off checks for overlapping atoms, which is expected for lambda=0.
    mola.getPotentialEnergy().getCrystal().setSpecialPositionCutoff(0.0);
    // Create extended variables; add to system; hook up to assembly.
    ExtendedSystem esvSystem = (esvConfig != null) ? new ExtendedSystem(mola, esvConfig) : new ExtendedSystem(mola);
    esvSystem.setConstantPh(7.4);
    esvSystem.populate(esvResidueIDs);
    mola.getPotentialEnergy().attachExtendedSystem(esvSystem);
    ExtendedSystemConfig.print(esvSystem.config);
    return mola;
}

Example 14 with MolecularAssembly

use of ffx.potential.MolecularAssembly in project ffx by mjschnie.

the class ExtendedVariableTest method testDerivatives.

/**
 * Analytic Derivative vs Finite Difference: VdW,PermReal,PermRecip,Total
 */
public void testDerivatives(ExtendedSystemConfig esvConfig) {
    if (esvConfig == null) {
        esvConfig = setDebugParameters();
    }
    MolecularAssembly mola = setupWithExtended(esvFilename, false, esvConfig);
    ForceFieldEnergy ffe = mola.getPotentialEnergy();
    ExtendedSystem esvSystem = ffe.getExtendedSystem();
    if (resultsOnly) {
        utils.setSilentPotential(true);
    }
    final double step = 1e-6;
    for (int i = 0; i < esvSystem.size(); i++) {
        final String esvName = esvSystem.getEsv(i).getName();
        if (!mola.getCrystal().aperiodic()) {
            sb.append(format(" Finite Diff: %5.5s (Crystal)\n", esvName));
        } else {
            sb.append(format(" Finite Diff: %5.5s (Aprodc.)\n", esvName));
        }
        // Reset lambdas.
        for (int k = 0; k < esvSystem.size(); k++) {
            esvSystem.setLambda(k, initialLambda[k]);
        }
        for (double lambda : lambdaValuesToTest) {
            final double center, low, high;
            if (oneSidedFiniteAtExtremes) {
                center = lambda;
                low = (center - step >= 0.0) ? center - step : center;
                high = (center + step <= 1.0) ? center + step : center;
            } else {
                center = (lambda - step < 0.0) ? lambda + step : (lambda + step > 1.0) ? lambda - step : lambda;
                low = center - step;
                high = center + step;
            }
            final double width = high - low;
            // Collect numeric derivative components.
            esvSystem.setLambda(i, low);
            ffe.energy(true, false);
            final double vdwLow = ffe.getEnergyComponent(PotentialComponent.VanDerWaals);
            final double bondedLow = ffe.getEnergyComponent(PotentialComponent.Bonded);
            final double biasLow = ffe.getEnergyComponent(PotentialComponent.pHMD);
            final double permRealLow = ffe.getEnergyComponent(PotentialComponent.PermanentRealSpace);
            final double permSelfLow = ffe.getEnergyComponent(PotentialComponent.PermanentSelf);
            final double permRecipLow = ffe.getEnergyComponent(PotentialComponent.PermanentReciprocal);
            final double indRealLow = ffe.getEnergyComponent(PotentialComponent.InducedRealSpace);
            final double indSelfLow = ffe.getEnergyComponent(PotentialComponent.InducedSelf);
            final double indRecipLow = ffe.getEnergyComponent(PotentialComponent.InducedReciprocal);
            final double totalLow = ffe.getEnergyComponent(PotentialComponent.ForceFieldEnergy);
            esvSystem.setLambda(i, high);
            ffe.energy(true, false);
            final double vdwHigh = ffe.getEnergyComponent(PotentialComponent.VanDerWaals);
            final double bondedHigh = ffe.getEnergyComponent(PotentialComponent.Bonded);
            final double biasHigh = ffe.getEnergyComponent(PotentialComponent.pHMD);
            final double permRealHigh = ffe.getEnergyComponent(PotentialComponent.PermanentRealSpace);
            final double permSelfHigh = ffe.getEnergyComponent(PotentialComponent.PermanentSelf);
            final double permRecipHigh = ffe.getEnergyComponent(PotentialComponent.PermanentReciprocal);
            final double indRealHigh = ffe.getEnergyComponent(PotentialComponent.InducedRealSpace);
            final double indSelfHigh = ffe.getEnergyComponent(PotentialComponent.InducedSelf);
            final double indRecipHigh = ffe.getEnergyComponent(PotentialComponent.InducedReciprocal);
            final double totalHigh = ffe.getEnergyComponent(PotentialComponent.ForceFieldEnergy);
            // Get analytic derivatives from the center.
            esvSystem.setLambda(i, center);
            ffe.energy(true, false);
            final double vdwAna = esvSystem.getDerivativeComponent(PotentialComponent.VanDerWaals, i);
            final double bondedAna = esvSystem.getDerivativeComponent(PotentialComponent.Bonded, i);
            final double biasAna = esvSystem.getDerivativeComponent(PotentialComponent.pHMD, i);
            final double permRealAna = esvSystem.getDerivativeComponent(PotentialComponent.PermanentRealSpace, i);
            final double permSelfAna = esvSystem.getDerivativeComponent(PotentialComponent.PermanentSelf, i);
            final double permRecipAna = esvSystem.getDerivativeComponent(PotentialComponent.PermanentReciprocal, i);
            final double indRealAna = esvSystem.getDerivativeComponent(PotentialComponent.InducedRealSpace, i);
            final double indSelfAna = esvSystem.getDerivativeComponent(PotentialComponent.InducedSelf, i);
            final double indRecipAna = esvSystem.getDerivativeComponent(PotentialComponent.InducedReciprocal, i);
            final double totalAna = esvSystem.getDerivativeComponent(PotentialComponent.ForceFieldEnergy, i);
            // Calculate numeric derivatives and error.
            final double vdwNum = (vdwHigh - vdwLow) / (width);
            final double vdwErr = (vdwAna - vdwNum);
            final double bondedNum = (bondedHigh - bondedLow) / (width);
            final double bondedErr = (bondedAna - bondedNum);
            final double biasNum = (biasHigh - biasLow) / (width);
            final double biasErr = (biasAna - biasNum);
            final double permRealNum = (permRealHigh - permRealLow) / (width);
            final double permRealErr = (permRealAna - permRealNum);
            final double permSelfNum = (permSelfHigh - permSelfLow) / (width);
            final double permSelfErr = (permSelfAna - permSelfNum);
            final double permRecipNum = (permRecipHigh - permRecipLow) / (width);
            final double permRecipErr = (permRecipAna - permRecipNum);
            final double indRealNum = (indRealHigh - indRealLow) / (width);
            final double indRealErr = (indRealAna - indRealNum);
            final double indSelfNum = (indSelfHigh - indSelfLow) / (width);
            final double indSelfErr = (indSelfAna - indSelfNum);
            final double indRecipNum = (indRecipHigh - indRecipLow) / (width);
            final double indRecipErr = (indRecipAna - indRecipNum);
            final double totalNum = (totalHigh - totalLow) / (width);
            final double totalErr = (totalAna - totalNum);
            sb.append(format(" %-28s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s\n", StringUtils.repeat("*", 28), "vdw ", "bonded", "bias", "permReal", "permSelf", "permRecip", "indReal", "indSelf", "indRecip", "total"));
            sb.append(format(" %-28s %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g\n", format("Numeric  @L=%s", esvSystem.getLambdaList()), vdwNum, bondedNum, biasNum, permRealNum, permSelfNum, permRecipNum, indRealNum, indSelfNum, indRecipNum, totalNum));
            sb.append(format(" %-28s %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g %+12.6g\n", format("Analytic @L=%s", esvSystem.getLambdaList()), vdwAna, bondedAna, biasAna, permRealAna, permSelfAna, permRecipAna, indRealAna, indSelfAna, indRecipAna, totalAna));
            sb.append(format(" %-28s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s\n", "Error:", err(vdwAna, vdwNum), err(bondedAna, bondedNum), err(biasAna, biasNum), err(permRealAna, permRealNum), err(permSelfAna, permSelfNum), err(permRecipAna, permRecipNum), err(indRealAna, indRealNum), err(indSelfAna, indSelfNum), err(indRecipAna, indRecipNum), err(totalAna, totalNum)));
            utils.setSilentPotential(false);
            logger.info(sb.toString());
            if (assertions) {
                assertEquals("VanDerWaals Deriv Error", 0.0, vdwErr, tolerance);
                assertEquals("Bonded Deriv Error", 0.0, bondedErr, tolerance);
                assertEquals("Bias Deriv Error", 0.0, biasErr, tolerance);
                assertEquals("PermReal Deriv Error", 0.0, permRealErr, tolerance);
                assertEquals("PermSelf Deriv Error", 0.0, permSelfErr, tolerance);
                assertEquals("PermRecip Deriv Error", 0.0, permRecipErr, tolerance);
                assertEquals("IndReal Deriv Error", 0.0, indRealErr, tolerance);
                assertEquals("IndSelf Deriv Error", 0.0, indSelfErr, tolerance);
                assertEquals("IndRecip Deriv Error", 0.0, indRecipErr, tolerance);
                assertEquals("Total Deriv Error", 0.0, totalErr, tolerance);
            }
        }
    // lambda loop
    }
// ESV loop
}

Example 15 with MolecularAssembly

use of ffx.potential.MolecularAssembly in project ffx by mjschnie.

the class ModelingShell method returnEnergy.

/**
 * <p>
 * returnEnergy</p>
 *
 * @return Current system energy (a double).
 */
public double returnEnergy() {
    if (interrupted) {
        logger.info(" Algorithm interrupted - skipping energy.");
        return 0.0;
    }
    if (terminatableAlgorithm != null) {
        logger.info(" Algorithm already running - skipping energy.");
        return 0.0;
    }
    MolecularAssembly active = mainPanel.getHierarchy().getActive();
    if (active != null) {
        ForceFieldEnergy energy = active.getPotentialEnergy();
        if (energy == null) {
            energy = ForceFieldEnergy.energyFactory(active);
            active.setPotential(energy);
        }
        return energy.energy(false, true);
    }
    logger.warning(" Energy could not be calculated");
    return 0.0;
}