src/align/align-utils.js

/**
 * @file Align Utils
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 * @private
 */

import { defaults } from '../utils.js'
import Selection from '../selection/selection.js'
import Alignment from './alignment.js'
import Superposition from './superposition.js'

/**
 * Perform structural superposition of two structures,
 * optionally guided by a sequence alignment
 * @param  {Structure|StructureView} s1 - structure 1 which is superposed onto structure 2
 * @param  {Structure|StructureView} s2 - structure 2 onto which structure 1 is superposed
 * @param  {Boolean} [align] - guide the superposition by a sequence alignment
 * @param  {String} [sele1] - selection string for structure 1
 * @param  {String} [sele2] - selection string for structure 2
 * @return {undefined}
 */
function superpose (s1, s2, align, sele1, sele2) {
  align = defaults(align, false)
  sele1 = defaults(sele1, '')
  sele2 = defaults(sele2, '')

  var i, j, n, atoms1, atoms2

  if (align) {
    var _s1 = s1
    var _s2 = s2

    if (sele1 && sele2) {
      _s1 = s1.getView(new Selection(sele1))
      _s2 = s2.getView(new Selection(sele2))
    }

    var seq1 = _s1.getSequence()
    var seq2 = _s2.getSequence()

    // Log.log( seq1.join("") );
    // Log.log( seq2.join("") );

    var ali = new Alignment(seq1.join(''), seq2.join(''))

    ali.calc()
    ali.trace()

    // Log.log( "superpose alignment score", ali.score );

    // Log.log( ali.ali1 );
    // Log.log( ali.ali2 );

    var l, _i, _j, x, y
    i = 0
    j = 0
    n = ali.ali1.length
    var aliIdx1 = []
    var aliIdx2 = []

    for (l = 0; l < n; ++l) {
      x = ali.ali1[ l ]
      y = ali.ali2[ l ]

      _i = 0
      _j = 0

      if (x === '-') {
        aliIdx2[ j ] = false
      } else {
        aliIdx2[ j ] = true
        _i = 1
      }

      if (y === '-') {
        aliIdx1[ i ] = false
      } else {
        aliIdx1[ i ] = true
        _j = 1
      }

      i += _i
      j += _j
    }

    // Log.log( i, j );

    // Log.log( aliIdx1 );
    // Log.log( aliIdx2 );

    var _atoms1 = []
    var _atoms2 = []
    var ap1 = _s1.getAtomProxy()
    var ap2 = _s2.getAtomProxy()

    i = 0
    _s1.eachResidue(function (r) {
      if (r.traceAtomIndex === undefined ||
            r.traceAtomIndex !== r.getAtomIndexByName('CA')) return

      if (aliIdx1[ i ]) {
        ap1.index = r.getAtomIndexByName('CA')
        _atoms1.push(ap1.x, ap1.y, ap1.z)
      }
      i += 1
    })

    i = 0
    _s2.eachResidue(function (r) {
      if (r.traceAtomIndex === undefined ||
            r.traceAtomIndex !== r.getAtomIndexByName('CA')) return

      if (aliIdx2[ i ]) {
        ap2.index = r.getAtomIndexByName('CA')
        _atoms2.push(ap2.x, ap2.y, ap2.z)
      }
      i += 1
    })

    atoms1 = new Float32Array(_atoms1)
    atoms2 = new Float32Array(_atoms2)
  } else {
    var sviewCa1 = s1.getView(new Selection(sele1 + ' and .CA'))
    var sviewCa2 = s2.getView(new Selection(sele2 + ' and .CA'))

    atoms1 = sviewCa1
    atoms2 = sviewCa2
  }

  var superpose = new Superposition(atoms1, atoms2)
  superpose.transform(s1)
  s1.refreshPosition()
}

export {
  superpose
}