src/parser/cube-parser.js

/**
 * @file Cube Parser
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 * @private
 */
 
import { Matrix4, Vector3 } from '../../lib/three.es6.js'
 
import { Debug, Log, ParserRegistry } from '../globals.js'
import VolumeParser from './volume-parser.js'
 
// @author Johanna Tiemann <johanna.tiemann@googlemail.com>
// @author Alexander Rose <alexander.rose@weirdbyte.de>
 
const reWhitespace = /\s+/
const reScientificNotation = /-?\d+(?:\.\d*)?(?:[eE][+-]?\d+)?/g
const bohrToAngstromFactor = 0.529177210859
 
class CubeParser extends VolumeParser {
  get type () { return 'cube' }
 
  _parse () {
    // http://paulbourke.net/dataformats/cube/
 
    if (Debug) Log.time('CubeParser._parse ' + this.name)
 
    const v = this.volume
    const headerLines = this.streamer.peekLines(6)
    const header = {}
 
    const scaleFactor = bohrToAngstromFactor * this.voxelSize
 
    function h (k, l) {
      var field = headerLines[ k ].trim().split(reWhitespace)[ l ]
      return parseFloat(field)
    }
 
    header.atomCount = Math.abs(h(2, 0))  // Number of atoms
    header.originX = h(2, 1) * bohrToAngstromFactor  // Position of origin of volumetric data
    header.originY = h(2, 2) * bohrToAngstromFactor
    header.originZ = h(2, 3) * bohrToAngstromFactor
    header.NVX = h(3, 0)  // Number of voxels
    header.NVY = h(4, 0)
    header.NVZ = h(5, 0)
 
    header.basisX = new Vector3(h(3, 1), h(3, 2), h(3, 3))
      .multiplyScalar(scaleFactor)
    header.basisY = new Vector3(h(4, 1), h(4, 2), h(4, 3))
      .multiplyScalar(scaleFactor)
    header.basisZ = new Vector3(h(5, 1), h(5, 2), h(5, 3))
      .multiplyScalar(scaleFactor)
 
    const data = new Float32Array(header.NVX * header.NVY * header.NVZ)
    let count = 0
    let lineNo = 0
    const oribitalFlag = h(2, 0) > 0 ? 0 : 1
 
    function _parseChunkOfLines (_i, _n, lines) {
      for (let i = _i; i < _n; ++i) {
        const line = lines[ i ].trim()
 
        if (line !== '' && lineNo >= header.atomCount + 6 + oribitalFlag) {
          const m = line.match(reScientificNotation)
          for (let j = 0, lj = m.length; j < lj; ++j) {
            data[ count ] = parseFloat(m[ j ])
            ++count
          }
        }
 
        ++lineNo
      }
    }
 
    this.streamer.eachChunkOfLines(function (lines/*, chunkNo, chunkCount */) {
      _parseChunkOfLines(0, lines.length, lines)
    })
 
    v.header = header
    v.setData(data, header.NVZ, header.NVY, header.NVX)
 
    if (Debug) Log.timeEnd('CubeParser._parse ' + this.name)
  }
 
  getMatrix () {
    const h = this.volume.header
    const matrix = new Matrix4()
 
    matrix.multiply(
      new Matrix4().makeTranslation(
        h.originX, h.originY, h.originZ
      )
    )
 
    matrix.multiply(
      new Matrix4().makeBasis(
        h.basisZ, h.basisY, h.basisX
      )
    )
 
    return matrix
  }
}
 
ParserRegistry.add('cub', CubeParser)
ParserRegistry.add('cube', CubeParser)
 
export default CubeParser