Function updateToFrame has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

  updateToFrame(frameData) {
    // This method looks like a copy paste. However, it
    // was decided to postpone animation refactoring until GFX is fixed.
    const bondsIdc = this._selection.chunks
    const { bonds } = this._selection

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Function _findPairs has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

  _findPairs() {
    const vw = this._complex.getVoxelWorld()
    if (vw === null) {
      return
    }

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Function toURL has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

function toURL(opts) {
  const stringList = []
  let idx = 0

  function checkAndAdd(prefix, value) {

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Function writeString has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

  writeString(string, begin, end) {
    let curStr = this._resultArray[this._currentStr]
    let str

    const curStrLength = curStr ? curStr.length : 0

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Function updateBinaryMode has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

function updateBinaryMode(opts) {
  let { binary } = opts

  // detect by format
  if (opts.fileType !== undefined) {

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Function _extractAtoms has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

  _extractAtoms(complex, complexData) {
    const atomData = complexData.atom_site
    if (!atomData) {
      throw new AtomDataError('CIF parsing error: atom_site is not specified!')
    }

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Function _buildInner has 47 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _buildInner(radOffset, addChunk) {
    const chunksToIdx = this._selection.chunks

    const prevVector = new Vector3()
    const currVector = new Vector3()

Function _parseAtoms has 47 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _parseAtoms(atomsNum, MOL2Data) {
    this._toHeaderString('ATOM', MOL2Data)

    for (let i = 0; i < atomsNum; i++) {
      const parsedStr = splitToFields(MOL2Data[++this._currPosIdx])

Function buildColors has 46 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  buildColors(numVertices, vertices, colors, radiusColorSmoothness) {
    const self = this
    let vx = 0.0
    let vy = 0.0
    let vz = 0.0

Function equalOptions has 46 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function equalOptions(original, generated) {
      function compareAllExceptReps(one, another) {
        const origKeys = Object.keys(one)

        let i

Function _finalize has 45 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _finalize() {
    const self = this
    ;[this._firstAtom] = this._atoms
    this._lastAtom = this._atoms[this._atoms.length - 1]

Function pickObject has 45 lines of code (exceeds 25 allowed). Consider refactoring.

Open

Picker.prototype.pickObject = function (screenPos) {
  if (!this.gfxObj) {
    this.picked = {}
    this.dispatchEvent({ type: 'newpick', obj: {} })
    return

Function _forEachAtomWithinDistFromGroup has 44 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _forEachAtomWithinDistFromGroup(forEachAtom, dist, process) {
    const self = this
    const r2 = dist * dist

    const voxels = []

Function anonymous has 44 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    performAction: function anonymous(
      yytext,
      yyleng,
      yylineno,
      yy,

Function _extractAtoms has 44 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _extractAtoms(complex, complexData) {
    let aids = complexData.atoms && complexData.atoms.aid
    let elements = aids && complexData.atoms.element
    if (!elements || aids.length !== elements.length) {
      throw new Error('Unable to parse atom elements')

Function _onPick has 44 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _onPick(event) {
    if (!settings.now.picking) {
      // picking is disabled
      return
    }

Function getState has 44 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  getState(opts) {
    const state = {}

    opts = defaults(opts, {
      compact: true,

Function checkArg has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

  checkArg(key, arg, modificate) {
    if (key !== undefined && arg !== undefined) {
      if (keyRemap(key) === 'selector') {
        const res = selectors.parse(arg)

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Function deriveDeep has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

function deriveDeep(obj, needZeroOwnProperties) {
  var res = obj;
  var i;
  var n;
  if (obj instanceof Array) {

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Function deriveDeep has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

function deriveDeep(obj, needZeroOwnProperties) {
  var res = obj;
  var i;
  var n;
  if (obj instanceof Array) {

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