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

Example 6 with HKL

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

the class CrystalStats method printSNStats.

/**
 * print signal to noise ratio statistics
 */
public void printSNStats() {
    double[][] res = new double[n][2];
    double[] nhkl = new double[n + 1];
    double[][] sn = new double[n + 1][3];
    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(fo[i][0]) || fo[i][1] <= 0.0) {
            continue;
        }
        // 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;
        }
        // running mean
        nhkl[b]++;
        nhkl[n]++;
        sn[b][0] += (fo[i][0] - sn[b][0]) / nhkl[b];
        sn[b][1] += (fo[i][1] - sn[b][1]) / nhkl[b];
        sn[b][2] += ((fo[i][0] / fo[i][1]) - sn[b][2]) / nhkl[b];
        sn[n][0] += (fo[i][0] - sn[n][0]) / nhkl[b];
        sn[n][1] += (fo[i][1] - sn[n][1]) / nhkl[b];
        sn[n][2] += ((fo[i][0] / fo[i][1]) - sn[n][2]) / nhkl[n];
    }
    StringBuilder sb = new StringBuilder(String.format("\n %15s | %7s | %7s | %7s \n", "Res. Range", "Signal", "Sigma", "S/N"));
    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 | %7.2f\n", sn[i][0], sn[i][1], sn[i][2]));
    }
    sb.append(String.format(" %7.3f %7.3f | ", res[0][0], res[n - 1][1]));
    sb.append(String.format("%7.2f | %7.2f | %7.2f", sn[n][0], sn[n][1], sn[n][2]));
    if (print) {
        logger.info(sb.toString());
    }
}

Example 7 with HKL

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

the class CrystalStats method getR.

/**
 * simply return the current R value
 *
 * @return r value as a percent
 */
public double getR() {
    double numer = 0.0;
    double denom = 0.0;
    double sum = 0.0;
    double sumfo = 0.0;
    double sumall = 0.0;
    double sumfoall = 0.0;
    for (HKL ih : reflectionlist.hkllist) {
        int i = ih.index();
        // 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);
        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]);
        sumall += numer;
        sumfoall += denom;
        if (!refinementdata.isFreeR(i)) {
            sum += numer;
            sumfo += denom;
        }
    }
    rall = (sumall / sumfoall) * 100.0;
    r = (sum / sumfo) * 100.0;
    return r;
}

Example 8 with HKL

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

the class CrystalStats method printDPIStats.

/**
 * output Cruickshank and Blow DPI indices
 *
 * @param natoms number of atoms in the structure
 * @param nnonhatoms number of non-H atoms in the structure
 * @see <a href="http://dx.doi.org/10.1107/S0907444998012645"
 * target="_blank"> D. W. J. Cruickshank, Acta Cryst. (1999). D55,
 * 583-601</a>
 * @see <a href="http://dx.doi.org/10.1107/S0907444902003931"
 * target="_blank"> D. M. Blow, Acta Cryst. (2002). D58, 792-797</a>
 * @see <a href="http://dx.doi.org/10.1107/S0907444998012645"
 * target="_blank"> D. W. J. Cruickshank, Acta Cryst. (1999). D55,
 * 583-601</a>
 * @see <a href="http://dx.doi.org/10.1107/S0907444902003931"
 * target="_blank"> D. M. Blow, Acta Cryst. (2002). D58, 792-797</a>
 */
public void printDPIStats(int natoms, int nnonhatoms) {
    int nhkli = 0;
    int nhklo = refinementdata.n;
    double rfreefrac = getRFree() * 0.01;
    double res = reflectionlist.resolution.resolutionLimit();
    for (HKL ih : reflectionlist.hkllist) {
        int i = ih.index();
        // ignored cases
        if (Double.isNaN(fo[i][0]) || fo[i][1] <= 0.0) {
            continue;
        }
        nhkli++;
    }
    double va = Math.pow(crystal.volume / crystal.spaceGroup.getNumberOfSymOps(), 0.3333);
    blowdpih = 1.28 * Math.sqrt(natoms) * va * Math.pow(nhkli, -0.8333) * rfreefrac;
    blowdpi = 1.28 * Math.sqrt(nnonhatoms) * va * Math.pow(nhkli, -0.8333) * rfreefrac;
    double natni = Math.sqrt((double) natoms / nhkli);
    double noni = Math.pow((double) nhkli / nhklo, -0.3333);
    cruickdpih = natni * noni * rfreefrac * res;
    natni = Math.sqrt((double) nnonhatoms / nhkli);
    cruickdpi = natni * noni * rfreefrac * res;
    StringBuilder sb = new StringBuilder("\n");
    sb.append(String.format(" Blow DPI for all / non-H atoms:        %7.4f / %7.4f\n", blowdpih, blowdpi));
    sb.append(String.format(" Cruickshank DPI for all / non-H atoms: %7.4f / %7.4f", cruickdpih, cruickdpi));
    if (print) {
        logger.info(sb.toString());
    }
}

Example 9 with HKL

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

the class ScaleBulkMinimize method setInitialScale.

private void setInitialScale() {
    double[][] fc = refinementData.fc;
    double[][] fo = refinementData.fsigf;
    double e = bulkSolventEnergy.energyAndGradient(x, grad);
    double fct, sumfofc, sumfc;
    sumfofc = sumfc = 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;
        }
        fct = refinementData.fcTotF(i);
        sumfofc += fo[i][0] * fct;
        sumfc += fct * fct;
    }
    x[0] = Math.log(4.0 * sumfofc / sumfc);
}

Example 10 with HKL

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

the class MTZFilterTest method testMTZHKL.

@Test
public void testMTZHKL() {
    MTZFilter mtzFilter = new MTZFilter();
    assertTrue("mtz file errors", mtzFilter.readFile(mtzFile, reflectionList, refinementData, null));
    HKL hkl = reflectionList.getHKL(-10, 1, 1);
    assertEquals("-10 1 1 FP value", 229.90, refinementData.getF(hkl.index()), 0.02);
    assertEquals("-10 1 1 SIGFP value", 2.50, refinementData.getSigF(hkl.index()), 0.02);
    assertEquals("-10 1 1 FREE value", 1, refinementData.getFreeR(hkl.index()));
    hkl = reflectionList.getHKL(-10, 1, 10);
    assertEquals("-10 1 10 FP value should be NaN", Double.NaN, refinementData.getF(hkl.index()), 0.1);
    assertEquals("-10 1 10 SIGFP value should be NaN", Double.NaN, refinementData.getSigF(hkl.index()), 0.1);
}