@@ -0,0 +1,2081 @@
+package se.raddo.raddose3D;%0A%0Aimport java.util.List;%0A%0Apublic class CoefCalcFromSequenceSAXS extends CoefCalcCompute %7B%0A  /**%0A   * Right angle.%0A   */%0A  protected static final double RIGHT_ANGLE = 90;%0A  %0A  /**%0A   * Default unit cell dimension%0A   */%0A  private static final double   UNIT_CELL_LENGTH = 1000;%0A%0A  /**%0A   * Average molecular mass of an amino acid (daltons = grams/mole)%0A   */%0A  private static final double   AVG_RESIDUE_MASS = 110;%0A%0A  /**%0A   * Conversion factor to convert Angstroms%5E3 to litres%0A   */%0A  private static final double   ANGSTROM_TO_LITRE_VOLUME_CONVERSION = 1e-27;%0A%0A  public CoefCalcFromSequenceSAXS(Double cellA, Double cellB, Double cellC,%0A      Double cellAlpha, Double cellBeta, Double cellGamma, %0A      List%3CString%3E heavyProteinAtomNames, List%3CDouble%3E heavyProteinAtomNums, %0A      List%3CString%3E heavySolutionConcNames, List%3CDouble%3E heavySolutionConcNums, %0A      Double solFrac, Double solventFraction, String sequenceFile) %7B%0A    %0A    /**%0A     * Create local variables for the unit cell parameters.%0A     * These don't have to be given in the input file for this module.%0A     * If these values are null then give suitable defaults.%0A     */%0A    Double a = cellA;%0A    Double b = cellB;%0A    Double c = cellC;%0A    Double alpha = cellAlpha;%0A    Double beta = cellBeta;%0A    Double gamma = cellGamma;%0A%0A    if (alpha == null) %7B%0A      alpha = RIGHT_ANGLE;%0A    %7D%0A    if (beta == null) %7B%0A      beta = RIGHT_ANGLE;%0A    %7D%0A    if (gamma == null) %7B%0A      gamma = RIGHT_ANGLE;%0A    %7D%0A    if (a == null) %7B%0A      a = UNIT_CELL_LENGTH;%0A    %7D%0A    if (b == null) %7B%0A      b = UNIT_CELL_LENGTH;%0A    %7D%0A    if (c == null) %7B%0A      c = UNIT_CELL_LENGTH;%0A    %7D%0A%0A    //Set local variable solvent fraction to minus 1%0A    Double sf = -1.0;%0A%0A    //If actual solvent fraction is given then set the local variable%0A    //sf equal to the actual solvent fraction%0A    if (solventFraction != null) %7B%0A      sf = solventFraction;%0A    %7D%0A%0A    //Calculate the Unit Cell Volume%0A    //This method exists in CoefCalcCompute Class%0A    double unitCellVolume = cellVolume(a, b, c, alpha, beta, gamma);%0A%0A  %7D%0A%0A%7D%0A

Create a module to allow for sequence input with SAXS data. This module is unfinished