Function addVertexToGeo has 58 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  addVertexToGeo(geoOut, vAdd) {
    let entry
    const oneHynberes = 0.01
    const n815851 = 815851
    const n37633 = 37633

Function buildNormals has 57 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  buildNormals(numVertices, vertices, normals) {
    const self = this
    let numCloseAtoms = 0
    let vx = 0
    let vy = 0

Function _parseAtom has 57 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _parseAtom(line) {
    this._residueNumber = line.readInt(1, 5)
    this._residueName = line.readString(6, 10).trim()
    this._atomName = line.readString(11, 15).trim()
    this._atomNumber = line.readInt(16, 20)

Function getMiewWithCli has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

var getMiewWithCli = function getMiewWithCli(miewInstance) {
  var obj = Object.create(miewInstance);
  obj.script = function (script, _printCallback, _errorCallback) {
    MiewCLIParser.parser.yy.miew = obj;
    MiewCLIParser.parser.yy.echo = _printCallback;

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Function getMiewWithCli has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

var getMiewWithCli = function getMiewWithCli(miewInstance) {
  var obj = Object.create(miewInstance);
  obj.script = function (script, _printCallback, _errorCallback) {
    MiewCLIParser.parser.yy.miew = obj;
    MiewCLIParser.parser.yy.echo = _printCallback;

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Function getMiewWithCli has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

export const getMiewWithCli = (miewInstance) => {
  const obj = Object.create(miewInstance)

  obj.script = function (script, _printCallback, _errorCallback) {
    parsercli.yy.miew = obj

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Function computeBoundaries has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

  computeBoundaries() {
    const atoms = this._complex._atoms
    const n = atoms.length
    const selector = this._selector

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Function _updateInfoPanel has 56 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _updateInfoPanel() {
    const info = this._msgAtomInfo.getElementsByTagName('p')[0]
    let atom
    let residue

Function _copyCurReprListItem has 55 lines of code (exceeds 25 allowed). Consider refactoring.

Open

Menu.prototype._copyCurReprListItem = function (index) {
  const self = this
  const reprList = $(
    `${self._menuId} .panel-menu[data-panel-type=miew-menu-panel-representation] .miew-repr-list`
  )

Function _initPresetsPanelActions has 55 lines of code (exceeds 25 allowed). Consider refactoring.

Open

Menu.prototype._initPresetsPanelActions = function () {
  const self = this

  self.presetsPanel.actions.pdb.inputs.refresh =
    self._presetsPanelActionsPdbInputsRefresh // check input box?

Function show has 55 lines of code (exceeds 25 allowed). Consider refactoring.

Open

Menu.prototype.show = function (panelID, menuItem) {
  const self = this

  this.setBlur(true)
  this._titlebar.hide()

Function _parseValue has 55 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  function _parseValue() {
    let val
    if (
      (code === 46 || code === 63) &&
      (i + 1 >= n || _isWhitespace(source.charCodeAt(i + 1)))

File MOL2Parser.js has 258 lines of code (exceeds 250 allowed). Consider refactoring.

Open

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

const { Complex, Element, Bond, Molecule } = chem

File PDBExporter.js has 257 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import { invert } from 'lodash'
import Complex from '../../chem/Complex'
import Exporter from './Exporter'
import PDBResult from './PDBResult'
import Assembly from '../../chem/Assembly'

Function next has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      next: function () {
        if (this.done) {
          return this.EOF
        }
        if (!this._input) {

Function updateToFrame has 54 lines of code (exceeds 25 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

Function _buildVW has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _buildVW() {
    const self = this
    const residues = this._complex._residues
    let ri
    let preri

Function _prepareBuffer has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _prepareBuffer(framesStart, framesEnd) {
    if (framesStart === undefined || framesStart === null) {
      framesStart = 0
    }
    if (framesEnd === undefined || framesEnd === null) {

Function buildTiledTexture has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  buildTiledTexture() {
    let tilesX = Math.ceil(Math.sqrt((this._dimZ * this._dimY) / this._dimX))

    let width = tilesX * (this._dimX + 2) - 1
    width = pow2ceil(width)

Function next has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      next: function () {
        if (this.done) {
          return this.EOF
        }
        if (!this._input) {