epam/miew

import { isString } from 'lodash'
import Parser from './Parser'
import chem from '../../chem'
import { Vector3 } from 'three'

const { Complex, Element, Molecule } = chem

class XYZParser extends Parser {
  constructor(data, options) {
    super(data, options)

    this._complex = null
    this._atomsInf = null

    this._options.fileType = 'xyz'
    this._fileName = options.name
  }

  static canProbablyParse(data) {
    return isString(data) && /^\s*\d+ *\n[^\n]*\n\s*\w{1,3}\s+-?\d/.test(data)
  }

  _parseToAtomsInf(source) {
    const endnAtoms = source.indexOf('\n')
    const nAtoms = parseInt(source.substring(0, endnAtoms), 10)
    const endComment = source.indexOf('\n', endnAtoms + 1)
    let comment = source.slice(endnAtoms + 1, endComment).trim()
    if (comment.length === 0) {
      comment = this._fileName
    }

    const startAtomsInf = endComment + source.substring(endComment).search(/\S/)
    this._atomsInf = source.substring(startAtomsInf).split(/[\s,]*\n[\s,]*/)
    if (!Number.isNaN(nAtoms) && this._atomsInf.length - 1 !== nAtoms) {
      this._complex.error = {
        message: 'wrong number of atoms'
      }
      return
    }

    this._complex.metadata.format = 'xyz'
    this._complex.name = comment
  }

  _parseAtomsInf() {
    const het = true
    const altLoc = ' '
    const occupancy = 1
    const tempFactor = 1
    const charge = 0

    const chain = this._complex.addChain('A')
    const residue = chain.addResidue('UNK', 1, ' ')

    for (let i = 0; i < this._atomsInf.length - 1; i++) {
      const words = this._atomsInf[i].split(/[\s,]+/)

      if (words.length !== 4) {
        this._complex.error = {
          message: 'missed parameters'
        }
        break
      }

      const serial = i + 1
      const name = words[0]
      const xyz = new Vector3(
        parseFloat(words[1]),
        parseFloat(words[2]),
        parseFloat(words[3])
      )
      const type = Element.getByName(name)
      const role = undefined

      residue.addAtom(
        name,
        type,
        xyz,
        role,
        het,
        serial,
        altLoc,
        occupancy,
        tempFactor,
        charge
      )
    }

    const molecule = new Molecule(this._complex, this._complex.name, 1)
    molecule.residues = residue
    this._complex._molecules[0] = molecule
  }

  parseSync() {
    const result = (this._complex = new Complex())

    this._parseToAtomsInf(this._data)
    this._parseAtomsInf()

    this._complex.finalize({
      needAutoBonding: true,
      detectAromaticLoops: this.settings.now.aromatic,
      enableEditing: this.settings.now.editing,
      serialAtomMap: this._serialAtomMap
    })

    this._complex = null
    this._atomsInf = null

    if (result.error) {
      throw new Error(result.error.message)
    }
    return result
  }

  static formats = ['xyz']

  static extensions = ['.xyz']
}

export default XYZParser