src/utils/radius-factory.js

/**
 * @file Radius Factory
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 * @private
 */

import {
    VdwRadii, DefaultVdwRadius, CovalentRadii, DefaultCovalentRadius,
    NucleicBackboneAtoms
} from '../structure/structure-constants'

function RadiusFactory (type, scale) {
  this.type = type
  this.scale = scale || 1.0

  this.max = 10
}

RadiusFactory.prototype = {

  constructor: RadiusFactory,

  atomRadius: function (a) {
    var type = this.type
    var scale = this.scale

    var r

    switch (type) {
      case 'vdw':

        r = VdwRadii[ a.element ] || DefaultVdwRadius
        break

      case 'covalent':

        r = CovalentRadii[ a.element ] || DefaultCovalentRadius
        break

      case 'bfactor':

        r = a.bfactor || 1.0
        break

      case 'sstruc':

        var sstruc = a.sstruc
        if (sstruc === 'h') {
          r = 0.25
        } else if (sstruc === 'g') {
          r = 0.25
        } else if (sstruc === 'i') {
          r = 0.25
        } else if (sstruc === 'e') {
          r = 0.25
        } else if (sstruc === 'b') {
          r = 0.25
        } else if (NucleicBackboneAtoms.includes(a.atomname)) {
          r = 0.4
        } else {
          r = 0.1
        }
        break

      default:

        r = type || 1.0
        break
    }

    return Math.min(r * scale, this.max)
  }

}

RadiusFactory.types = {

  '': '',
  'vdw': 'by vdW radius',
  'covalent': 'by covalent radius',
  'sstruc': 'by secondary structure',
  'bfactor': 'by bfactor',
  'size': 'size'

}

export default RadiusFactory