uglymol/src/unitcell.js

Macromolecular Viewer for Crystallographers

// @flow

export class UnitCell {
  /*::
  parameters: number[]
  orth: number[]
  frac: number[]
  */
  // eslint-disable-next-line max-params
  constructor(a /*:number*/, b /*:number*/, c /*:number*/,
              alpha /*:number*/, beta /*:number*/, gamma /*:number*/) {
    if (a <= 0 || b <= 0 || c <= 0 || alpha <= 0 || beta <= 0 || gamma <= 0) {
      throw Error('Zero or negative unit cell parameter(s).');
    }
    this.parameters = [a, b, c, alpha, beta, gamma];
    const deg2rad = Math.PI / 180.0;
    const cos_alpha = Math.cos(deg2rad * alpha);
    const cos_beta = Math.cos(deg2rad * beta);
    const cos_gamma = Math.cos(deg2rad * gamma);
    const sin_alpha = Math.sin(deg2rad * alpha);
    const sin_beta = Math.sin(deg2rad * beta);
    const sin_gamma = Math.sin(deg2rad * gamma);
    if (sin_alpha === 0 || sin_beta === 0 || sin_gamma === 0) {
      throw Error('Impossible angle - N*180deg.');
    }
    const cos_alpha_star_sin_beta = (cos_beta * cos_gamma - cos_alpha) /
                                    sin_gamma;
    const cos_alpha_star = cos_alpha_star_sin_beta / sin_beta;
    const s1rca2 = Math.sqrt(1.0 - cos_alpha_star * cos_alpha_star);
    // The orthogonalization matrix we use is described in ITfC B p.262:
    // "An alternative mode of orthogonalization, used by the Protein
    // Data Bank and most programs, is to align the a1 axis of the unit
    // cell with the Cartesian X_1 axis, and to align the a*_3 axis with the
    // Cartesian X_3 axis."
    //
    // Zeros in the matrices below are kept to make matrix multiplication
    // faster: they make extract_block() 2x (!) faster on V8 4.5.103,
    // no difference on FF 50.
    /* eslint-disable no-multi-spaces, comma-spacing */
    this.orth = [a,   b * cos_gamma,  c * cos_beta,
                 0.0, b * sin_gamma, -c * cos_alpha_star_sin_beta,
                 0.0, 0.0          ,  c * sin_beta * s1rca2];
    // based on xtal.js which is based on cctbx.uctbx
    this.frac = [
      1.0 / a,
      -cos_gamma / (sin_gamma * a),
      -(cos_gamma * cos_alpha_star_sin_beta + cos_beta * sin_gamma) /
          (sin_beta * s1rca2 * sin_gamma * a),
      0.0,
      1.0 / (sin_gamma * b),
      cos_alpha_star / (s1rca2 * sin_gamma * b),
      0.0,
      0.0,
      1.0 / (sin_beta * s1rca2 * c),
    ];
  }

  fractionalize(xyz /*:[number,number,number]*/) {
    return multiply(xyz, this.frac);
  }

  orthogonalize(xyz /*:[number,number,number]*/) {
    return multiply(xyz, this.orth);
  }
}

// This function is only used with matrices frac and orth, which have 3 zeros.
// We skip these elements, but it doesn't affect performance (on FF50 and V8).
function multiply(xyz, mat) {
  /* eslint-disable indent */
  return [mat[0] * xyz[0]  + mat[1] * xyz[1]  + mat[2] * xyz[2],
        /*mat[3] * xyz[0]*/+ mat[4] * xyz[1]  + mat[5] * xyz[2],
        /*mat[6] * xyz[0]  + mat[7] * xyz[1]*/+ mat[8] * xyz[2]];
}