Examples with HKL ffx.crystal.HKL used on opensource projects

Example 16 with HKL

use of ffx.crystal.HKL in project ffx by mjschnie.

the class SplineEnergy method target.

/**
 * <p>
 * target</p>
 *
 * @param x an array of double.
 * @param g an array of double.
 * @param gradient a boolean.
 * @param print a boolean.
 * @return a double.
 */
public double target(double[] x, double[] g, boolean gradient, boolean print) {
    double r = 0.0;
    double rf = 0.0;
    double rfree = 0.0;
    double rfreef = 0.0;
    double sum = 0.0;
    double sumfo = 0.0;
    // Zero out the gradient.
    if (gradient) {
        fill(g, 0.0);
    }
    for (HKL ih : reflectionlist.hkllist) {
        int i = ih.index();
        if (Double.isNaN(fc[i][0]) || Double.isNaN(fo[i][0]) || fo[i][1] <= 0.0) {
            continue;
        }
        if (type == Type.FOTOESQ && fo[i][0] <= 0.0) {
            continue;
        }
        double eps = ih.epsilon();
        double s = Crystal.invressq(crystal, ih);
        // spline setup
        double fh = spline.f(s, x);
        refinementdata.getFcTotIP(i, fct);
        double d2 = 0.0;
        double dr = 0.0;
        double w = 0.0;
        switch(type) {
            case Type.FOFC:
                w = 1.0;
                double f1 = refinementdata.getF(i);
                double f2 = fct.abs();
                double d = f1 - fh * f2;
                d2 = d * d;
                dr = -2.0 * f2 * d;
                sumfo += f1 * f1;
                break;
            case Type.F1F2:
                w = 2.0 / ih.epsilonc();
                double ieps = 1.0 / eps;
                f1 = pow(fct.abs(), 2.0) * ieps;
                f2 = pow(refinementdata.getF(i), 2) * ieps;
                d = fh * f1 - f2;
                d2 = d * d / f1;
                dr = 2.0 * d;
                sumfo = 1.0;
                break;
            case Type.FCTOESQ:
                w = 2.0 / ih.epsilonc();
                f1 = pow(fct.abs() / sqrt(eps), 2);
                d = f1 * fh - 1.0;
                d2 = d * d / f1;
                dr = 2.0 * d;
                sumfo = 1.0;
                break;
            case Type.FOTOESQ:
                w = 2.0 / ih.epsilonc();
                f1 = pow(refinementdata.getF(i) / sqrt(eps), 2);
                d = f1 * fh - 1.0;
                d2 = d * d / f1;
                dr = 2.0 * d;
                sumfo = 1.0;
                break;
        }
        sum += w * d2;
        double afo = abs(fo[i][0]);
        double afh = abs(fh * fct.abs());
        if (refinementdata.isFreeR(i)) {
            rfree += abs(afo - afh);
            rfreef += afo;
        } else {
            r += abs(afo - afh);
            rf += afo;
        }
        if (gradient) {
            int i0 = spline.i0();
            int i1 = spline.i1();
            int i2 = spline.i2();
            double g0 = spline.dfi0();
            double g1 = spline.dfi1();
            double g2 = spline.dfi2();
            g[i0] += w * dr * g0;
            g[i1] += w * dr * g1;
            g[i2] += w * dr * g2;
        }
    }
    /**
     * Tim - should this only be done for Type.FOFC??
     */
    if (gradient) {
        double isumfo = 1.0 / sumfo;
        for (int i = 0; i < g.length; i++) {
            g[i] *= isumfo;
        }
    }
    if (print) {
        StringBuilder sb = new StringBuilder("\n");
        sb.append(" Computed Potential Energy\n");
        sb.append(String.format("   residual:  %8.3f\n", sum / sumfo));
        if (type == Type.FOFC || type == Type.F1F2) {
            sb.append(String.format("   R:  %8.3f  Rfree:  %8.3f\n", (r / rf) * 100.0, (rfree / rfreef) * 100.0));
        }
        sb.append("x: ");
        for (int i = 0; i < x.length; i++) {
            sb.append(String.format("%8g ", x[i]));
        }
        sb.append("\ng: ");
        for (int i = 0; i < g.length; i++) {
            sb.append(String.format("%8g ", g[i]));
        }
        sb.append("\n");
        logger.info(sb.toString());
    }
    totalEnergy = sum / sumfo;
    return sum / sumfo;
}

Example 17 with HKL

use of ffx.crystal.HKL in project ffx by mjschnie.

the class CrystalReciprocalSpace method computeAtomicGradients.

/**
 * compute inverse FFT to determine atomic gradients
 *
 * @param hklData structure factors to apply inverse FFT
 * @param freer array of free r flags corresponding to hkldata
 * @param flag Rfree flag value
 * @param refinementMode
 * {@link RefinementMinimize.RefinementMode refinement mode}
 * @param print if true, print information on timings during the calculation
 * @see RefinementMinimize.RefinementMode
 * @see DiffractionRefinementData
 */
public void computeAtomicGradients(double[][] hklData, int[] freer, int flag, RefinementMode refinementMode, boolean print) {
    if (solvent && solventModel == SolventModel.NONE) {
        return;
    }
    // zero out the density
    for (int i = 0; i < complexFFT3DSpace; i++) {
        densityGrid[i] = 0.0;
    }
    int nfree = 0;
    StringBuilder sb = new StringBuilder();
    long symtime = -System.nanoTime();
    int nsym = crystal.spaceGroup.symOps.size();
    // int nsym = 1;
    List<SymOp> symops = crystal.spaceGroup.symOps;
    ComplexNumber c = new ComplexNumber();
    ComplexNumber cj = new ComplexNumber();
    HKL ij = new HKL();
    for (HKL ih : reflectionList.hkllist) {
        double[] fc = hklData[ih.index()];
        if (Double.isNaN(fc[0])) {
            continue;
        }
        // cross validation check!!!
        if (freer != null) {
            if (freer[ih.index()] == flag) {
                nfree++;
                continue;
            }
        }
        c.re(fc[0]);
        c.im(fc[1]);
        // scale
        c.timesIP(2.0 / fftScale);
        // apply symmetry
        for (int j = 0; j < nsym; j++) {
            cj.copy(c);
            crystal.applyTransSymRot(ih, ij, symops.get(j));
            double shift = Crystal.sym_phase_shift(ih, symops.get(j));
            int h = Crystal.mod(ij.h(), fftX);
            int k = Crystal.mod(ij.k(), fftY);
            int l = Crystal.mod(ij.l(), fftZ);
            if (h < halfFFTX + 1) {
                final int ii = iComplex3D(h, k, l, fftX, fftY);
                cj.phaseShiftIP(shift);
                densityGrid[ii] += cj.re();
                densityGrid[ii + 1] += -cj.im();
            } else {
                h = (fftX - h) % fftX;
                k = (fftY - k) % fftY;
                l = (fftZ - l) % fftZ;
                final int ii = iComplex3D(h, k, l, fftX, fftY);
                cj.phaseShiftIP(shift);
                densityGrid[ii] += cj.re();
                densityGrid[ii + 1] += cj.im();
            }
        }
    }
    symtime += System.nanoTime();
    long startTime = System.nanoTime();
    complexFFT3D.ifft(densityGrid);
    long fftTime = System.nanoTime() - startTime;
    /*
         CCP4MapWriter mapout = new CCP4MapWriter(fftX, fftY, fftZ, crystal, "/tmp/foo.map");
         mapout.write(densityGrid);
         */
    startTime = System.nanoTime();
    long permanentDensityTime = 0;
    try {
        if (solvent) {
            solventGradientRegion.setRefinementMode(refinementMode);
            parallelTeam.execute(solventGradientRegion);
        } else {
            for (int i = 0; i < nAtoms; i++) {
                optAtomicGradientWeight.set(i, 0);
            }
            atomicGradientSchedule.updateWeights(previousOptAtomicGradientWeight);
            atomicGradientRegion.setRefinementMode(refinementMode);
            parallelTeam.execute(atomicGradientRegion);
            for (int i = 0; i < nAtoms; i++) {
                previousOptAtomicGradientWeight[i] = optAtomicGradientWeight.get(i);
            }
        }
        permanentDensityTime = System.nanoTime() - startTime;
    } catch (Exception e) {
        String message = "Exception computing atomic gradients.";
        logger.log(Level.SEVERE, message, e);
    }
    if (solvent) {
        sb.append(String.format(" Solvent symmetry: %8.3f\n", symtime * toSeconds));
        sb.append(String.format(" Solvent inverse FFT: %8.3f\n", fftTime * toSeconds));
        sb.append(String.format(" Grid solvent gradients: %8.3f\n", permanentDensityTime * toSeconds));
        sb.append(String.format(" %d reflections ignored (cross validation set)\n", nfree));
    } else {
        sb.append(String.format(" Atomic symmetry: %8.3f\n", symtime * toSeconds));
        sb.append(String.format(" Atomic inverse FFT: %8.3f\n", fftTime * toSeconds));
        sb.append(String.format(" Grid atomic gradients: %8.3f\n", permanentDensityTime * toSeconds));
        sb.append(String.format(" %d reflections ignored (cross validation set)\n", nfree));
    }
    if (logger.isLoggable(Level.INFO) && print) {
        logger.info(sb.toString());
    }
}

Example 18 with HKL

use of ffx.crystal.HKL in project ffx by mjschnie.

the class CIFFilter method getResolution.

/**
 * {@inheritDoc}
 */
@Override
public double getResolution(File cifFile, Crystal crystal) {
    double resolution = Double.POSITIVE_INFINITY;
    try {
        BufferedReader br = new BufferedReader(new FileReader(cifFile));
        String string;
        int nCol = 0;
        boolean inHKL = false;
        while ((string = br.readLine()) != null) {
            String[] strArray = string.split("\\s+");
            if (strArray[0].startsWith("_refln.")) {
                inHKL = true;
                br.mark(0);
                String[] cifArray = strArray[0].split("\\.+");
                switch(Header.toHeader(cifArray[1])) {
                    case index_h:
                        h = nCol;
                        break;
                    case index_k:
                        k = nCol;
                        break;
                    case index_l:
                        l = nCol;
                        break;
                }
                nCol++;
            } else if (inHKL) {
                if (h < 0 || k < 0 || l < 0) {
                    String message = " Fatal error in CIF file - no H K L indexes?\n";
                    logger.log(Level.SEVERE, message);
                    return -1.0;
                }
                break;
            }
        }
        // Go back to where the reflections start.
        br.reset();
        HKL hkl = new HKL();
        while ((string = br.readLine()) != null) {
            // Reached end, break.
            if (string.trim().startsWith("#END")) {
                break;
            } else if (string.trim().startsWith("data")) {
                break;
            } else if (string.trim().startsWith("#")) {
                continue;
            }
            // Some files split data on to multiple lines.
            String[] strArray = string.trim().split("\\s+");
            while (strArray.length < nCol) {
                string = string + " " + br.readLine();
                strArray = string.trim().split("\\s+");
            }
            int ih = Integer.parseInt(strArray[h]);
            int ik = Integer.parseInt(strArray[k]);
            int il = Integer.parseInt(strArray[l]);
            hkl.h(ih);
            hkl.k(ik);
            hkl.l(il);
            resolution = min(resolution, Crystal.res(crystal, hkl));
        }
    } catch (IOException e) {
        String message = " CIF IO Exception.";
        logger.log(Level.WARNING, message, e);
        return -1.0;
    }
    return resolution;
}

Example 19 with HKL

use of ffx.crystal.HKL in project ffx by mjschnie.

the class CIFFilter method readFile.

/**
 * {@inheritDoc}
 */
@Override
public boolean readFile(File cifFile, ReflectionList reflectionList, DiffractionRefinementData refinementData, CompositeConfiguration properties) {
    int nRead, nNAN, nRes;
    int nIgnore, nCIFIgnore;
    int nFriedel, nCut;
    boolean transpose = false;
    boolean intensitiesToAmplitudes = false;
    StringBuilder sb = new StringBuilder();
    sb.append(String.format(" Opening %s\n", cifFile.getName()));
    if (refinementData.rfreeflag < 0) {
        refinementData.setFreeRFlag(1);
        sb.append(format(" Setting R free flag to CIF default: %d\n", refinementData.rfreeflag));
    }
    try {
        BufferedReader br = new BufferedReader(new FileReader(cifFile));
        String string;
        int nCol = 0;
        boolean inHKL = false;
        while ((string = br.readLine()) != null) {
            String[] stringArray = string.split("\\s+");
            if (stringArray[0].startsWith("_refln.")) {
                inHKL = true;
                br.mark(0);
                String[] cifArray = stringArray[0].split("\\.+");
                switch(Header.toHeader(cifArray[1])) {
                    case index_h:
                        h = nCol;
                        break;
                    case index_k:
                        k = nCol;
                        break;
                    case index_l:
                        l = nCol;
                        break;
                    case F_meas:
                    case F_meas_au:
                        fo = nCol;
                        break;
                    case F_meas_sigma:
                    case F_meas_sigma_au:
                        sigFo = nCol;
                        break;
                    case intensity_meas:
                        io = nCol;
                        break;
                    case intensity_sigma:
                        sigIo = nCol;
                        break;
                    case status:
                        rFree = nCol;
                        break;
                }
                nCol++;
            } else if (inHKL) {
                if (h < 0 || k < 0 || l < 0) {
                    String message = " Fatal error in CIF file - no H K L indexes?\n";
                    logger.log(Level.SEVERE, message);
                    return false;
                }
                break;
            }
        }
        if (fo < 0 && sigFo < 0 && io > 0 && sigIo > 0) {
            intensitiesToAmplitudes = true;
        }
        if (fo < 0 && io < 0) {
            logger.severe(" Reflection data (I/F) not found in CIF file!");
        }
        // Go back to where the reflections start.
        br.reset();
        // Check if HKLs need to be transposed or not.
        HKL mate = new HKL();
        int nPosIgnore = 0;
        int nTransIgnore = 0;
        while ((string = br.readLine()) != null) {
            if (string.trim().startsWith("#END")) {
                // Reached end, break.
                break;
            } else if (string.trim().startsWith("data")) {
                break;
            } else if (string.trim().startsWith("#")) {
                continue;
            }
            // Some files split data on to multiple lines.
            String[] strArray = string.trim().split("\\s+");
            while (strArray.length < nCol) {
                string = string + " " + br.readLine();
                strArray = string.trim().split("\\s+");
            }
            if (rFree > 0) {
                // Ignored cases.
                if (strArray[rFree].charAt(0) == 'x' || strArray[rFree].charAt(0) == '<' || strArray[rFree].charAt(0) == '-' || strArray[rFree].charAt(0) == 'h' || strArray[rFree].charAt(0) == 'l') {
                    continue;
                }
            }
            int ih = Integer.parseInt(strArray[h]);
            int ik = Integer.parseInt(strArray[k]);
            int il = Integer.parseInt(strArray[l]);
            boolean friedel = reflectionList.findSymHKL(ih, ik, il, mate, false);
            HKL hklPos = reflectionList.getHKL(mate);
            if (hklPos == null) {
                nPosIgnore++;
            }
            friedel = reflectionList.findSymHKL(ih, ik, il, mate, true);
            HKL hklTrans = reflectionList.getHKL(mate);
            if (hklTrans == null) {
                nTransIgnore++;
            }
        }
        if (nPosIgnore > nTransIgnore) {
            transpose = true;
        }
        // Re-open to start at beginning.
        br = new BufferedReader(new FileReader(cifFile));
        inHKL = false;
        while ((string = br.readLine()) != null) {
            String[] strArray = string.split("\\s+");
            if (strArray[0].startsWith("_refln.")) {
                br.mark(0);
                inHKL = true;
            } else if (inHKL) {
                break;
            }
        }
        // Go back to where the reflections start.
        br.reset();
        // Read in data.
        double[][] anofSigF = new double[refinementData.n][4];
        for (int i = 0; i < refinementData.n; i++) {
            anofSigF[i][0] = anofSigF[i][1] = anofSigF[i][2] = anofSigF[i][3] = Double.NaN;
        }
        nRead = nNAN = nRes = nIgnore = nCIFIgnore = nFriedel = nCut = 0;
        while ((string = br.readLine()) != null) {
            // Reached end, break.
            if (string.trim().startsWith("#END")) {
                break;
            } else if (string.trim().startsWith("data")) {
                break;
            } else if (string.trim().startsWith("#")) {
                continue;
            }
            // Some files split data on to multiple lines.
            String[] strArray = string.trim().split("\\s+");
            while (strArray.length < nCol) {
                string = string + " " + br.readLine();
                strArray = string.trim().split("\\s+");
            }
            int ih = Integer.parseInt(strArray[h]);
            int ik = Integer.parseInt(strArray[k]);
            int il = Integer.parseInt(strArray[l]);
            boolean friedel = reflectionList.findSymHKL(ih, ik, il, mate, transpose);
            HKL hkl = reflectionList.getHKL(mate);
            if (hkl != null) {
                boolean isnull = false;
                if (rFree > 0) {
                    if (strArray[rFree].charAt(0) == 'o') {
                        refinementData.setFreeR(hkl.index(), 0);
                    } else if (strArray[rFree].charAt(0) == 'f') {
                        refinementData.setFreeR(hkl.index(), 1);
                    } else if (strArray[rFree].charAt(0) == 'x') {
                        isnull = true;
                        nNAN++;
                    } else if (strArray[rFree].charAt(0) == '<' || strArray[rFree].charAt(0) == '-' || strArray[rFree].charAt(0) == 'h' || strArray[rFree].charAt(0) == 'l') {
                        isnull = true;
                        nCIFIgnore++;
                    } else {
                        refinementData.setFreeR(hkl.index(), Integer.parseInt(strArray[rFree]));
                    }
                }
                if (!intensitiesToAmplitudes && !isnull) {
                    if (strArray[fo].charAt(0) == '?' || strArray[sigFo].charAt(0) == '?') {
                        isnull = true;
                        nNAN++;
                        continue;
                    }
                    if (refinementData.fsigfcutoff > 0.0) {
                        double f1 = Double.parseDouble(strArray[fo]);
                        double sigf1 = Double.parseDouble(strArray[sigFo]);
                        if ((f1 / sigf1) < refinementData.fsigfcutoff) {
                            nCut++;
                            continue;
                        }
                    }
                    if (friedel) {
                        anofSigF[hkl.index()][2] = Double.parseDouble(strArray[fo]);
                        anofSigF[hkl.index()][3] = Double.parseDouble(strArray[sigFo]);
                        nFriedel++;
                    } else {
                        anofSigF[hkl.index()][0] = Double.parseDouble(strArray[fo]);
                        anofSigF[hkl.index()][1] = Double.parseDouble(strArray[sigFo]);
                    }
                }
                if (intensitiesToAmplitudes && !isnull) {
                    if (strArray[io].charAt(0) == '?' || strArray[sigIo].charAt(0) == '?') {
                        isnull = true;
                        nNAN++;
                        continue;
                    }
                    if (friedel) {
                        anofSigF[hkl.index()][2] = Double.parseDouble(strArray[io]);
                        anofSigF[hkl.index()][3] = Double.parseDouble(strArray[sigIo]);
                        nFriedel++;
                    } else {
                        anofSigF[hkl.index()][0] = Double.parseDouble(strArray[io]);
                        anofSigF[hkl.index()][1] = Double.parseDouble(strArray[sigIo]);
                    }
                }
                nRead++;
            } else {
                HKL tmp = new HKL(ih, ik, il);
                if (!reflectionList.resolution.inInverseResSqRange(Crystal.invressq(reflectionList.crystal, tmp))) {
                    nRes++;
                } else {
                    nIgnore++;
                }
            }
        }
        br.close();
        // Set up fsigf from F+ and F-.
        refinementData.generate_fsigf_from_anofsigf(anofSigF);
        if (intensitiesToAmplitudes) {
            refinementData.intensities_to_amplitudes();
        }
    } catch (IOException ioe) {
        System.out.println("IO Exception: " + ioe.getMessage());
        return false;
    }
    sb.append(String.format(" HKL data is %s\n", transpose ? "transposed" : "not transposed"));
    sb.append(String.format(" HKL read in:                             %d\n", nRead));
    sb.append(String.format(" HKL read as friedel mates:               %d\n", nFriedel));
    sb.append(String.format(" HKL with NaN (ignored):                  %d\n", nNAN));
    sb.append(String.format(" HKL NOT read in (status <, -, h or l):   %d\n", nCIFIgnore));
    sb.append(String.format(" HKL NOT read in (too high resolution):   %d\n", nRes));
    sb.append(String.format(" HKL NOT read in (not in internal list?): %d\n", nIgnore));
    sb.append(String.format(" HKL NOT read in (F/sigF cutoff):         %d\n", nCut));
    sb.append(String.format(" HKL in internal list:                    %d\n", reflectionList.hkllist.size()));
    if (logger.isLoggable(Level.INFO)) {
        logger.info(sb.toString());
    }
    String doRFree = System.getProperty("generate-rfree", "false");
    if (doRFree.equalsIgnoreCase("true")) {
        refinementData.generateRFree();
    }
    return true;
}

Example 20 with HKL

use of ffx.crystal.HKL in project ffx by mjschnie.

the class CrystalStats method printRStats.

/**
 * print R factors and associated statistics in a binned fashion
 */
public void printRStats() {
    double[][] res = new double[n][2];
    double[] nhkl = new double[n + 1];
    double[][] rb = new double[n + 1][2];
    double[][] sumfo = new double[n + 1][2];
    double[][] s = new double[n + 1][4];
    double numer = 0.0;
    double denom = 0.0;
    double sumall = 0.0;
    double sumfoall = 0.0;
    ReflectionSpline sigmaaspline = new ReflectionSpline(reflectionlist, refinementdata.sigmaa.length);
    for (int i = 0; i < n; i++) {
        res[i][0] = Double.NEGATIVE_INFINITY;
        res[i][1] = Double.POSITIVE_INFINITY;
    }
    for (HKL ih : reflectionlist.hkllist) {
        int i = ih.index();
        int b = ih.bin();
        // ignored cases
        if (Double.isNaN(fc[i][0]) || Double.isNaN(fo[i][0]) || fo[i][1] <= 0.0) {
            continue;
        }
        // spline setup
        double ss = Crystal.invressq(crystal, ih);
        double fh = spline.f(ss, refinementdata.spline);
        double sa = sigmaaspline.f(ss, refinementdata.sigmaa);
        double wa = sigmaaspline.f(ss, refinementdata.sigmaw);
        double eoscale = sigmaaspline.f(ss, refinementdata.foesq);
        // determine res limits of each bin
        double rs = Crystal.res(crystal, ih);
        if (rs > res[b][0]) {
            res[b][0] = rs;
        }
        if (rs < res[b][1]) {
            res[b][1] = rs;
        }
        ComplexNumber c = new ComplexNumber(fc[i][0], fc[i][1]);
        numer = abs(abs(fo[i][0]) - fh * abs(c.abs()));
        denom = abs(fo[i][0]);
        if (refinementdata.isFreeR(i)) {
            rb[b][1] += numer;
            sumfo[b][1] += denom;
            rb[n][1] += numer;
            sumfo[n][1] += denom;
            sumall += numer;
            sumfoall += denom;
        } else {
            rb[b][0] += numer;
            sumfo[b][0] += denom;
            rb[n][0] += numer;
            sumfo[n][0] += denom;
            sumall += numer;
            sumfoall += denom;
        }
        nhkl[b]++;
        nhkl[n]++;
        s[b][0] += (sa - s[b][0]) / nhkl[b];
        s[b][1] += (wa - s[b][1]) / nhkl[b];
        s[b][2] += ((wa / Math.sqrt(eoscale)) - s[b][2]) / nhkl[b];
        s[b][3] += (fomphi[i][0] - s[b][3]) / nhkl[b];
        s[n][0] += (sa - s[n][0]) / nhkl[n];
        s[n][1] += (wa - s[n][1]) / nhkl[n];
        s[n][2] += ((wa / Math.sqrt(eoscale)) - s[n][2]) / nhkl[n];
        s[n][3] += (fomphi[i][0] - s[n][3]) / nhkl[n];
    }
    StringBuilder sb = new StringBuilder(String.format("\n %15s | %7s | %7s | %7s | %7s | %7s | %7s\n", "Res. Range", "  R", "Rfree", "s", "w(E)", "w(F)", "FOM"));
    for (int i = 0; i < n; i++) {
        sb.append(String.format(" %7.3f %7.3f | ", res[i][0], res[i][1]));
        sb.append(String.format("%7.2f | %7.2f | %7.4f | %7.4f | %7.2f | %7.4f\n", (rb[i][0] / sumfo[i][0]) * 100.0, (rb[i][1] / sumfo[i][1]) * 100.0, s[i][0], s[i][1], s[i][2], s[i][3]));
    }
    sb.append(String.format(" %7.3f %7.3f | ", res[0][0], res[n - 1][1]));
    sb.append(String.format("%7.2f | %7.2f | %7.4f | %7.4f | %7.2f | %7.4f\n", (rb[n][0] / sumfo[n][0]) * 100.0, (rb[n][1] / sumfo[n][1]) * 100.0, s[n][0], s[n][1], s[n][2], s[n][3]));
    sb.append(" s and w are analagous to D and sum_wc");
    reslow = res[0][0];
    reshigh = res[n - 1][1];
    highreslow = res[n - 1][0];
    highreshigh = res[n - 1][1];
    r = (rb[n][0] / sumfo[n][0]) * 100.0;
    rfree = (rb[n][1] / sumfo[n][1]) * 100.0;
    rall = (sumall / sumfoall) * 100.0;
    highr = (rb[n - 1][0] / sumfo[n - 1][0]) * 100.0;
    highrfree = (rb[n - 1][1] / sumfo[n - 1][1]) * 100.0;
    if (print) {
        logger.info(sb.toString());
    }
}