Function _calcHBondEnergy has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

  _calcHBondEnergy(predonor, donor, acceptor) {
    let result = 0

    if (predonor === null) {
      return result

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Function updateSelectionMask has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

  updateSelectionMask(pickedObj) {
    const self = this
    const { atom } = pickedObj
    let { residue, chain, molecule } = pickedObj
    const setMask = 1 << this._selectionBit

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Function _parseSTRUCTURE has 77 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _parseSTRUCTURE(stream, pars, adder) {
    const startId = 0
    const startIndex = 1
    const endId = 2
    const endIndex = 3

File Residue.js has 294 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import Atom from './Atom'
import Element from './Element'
import { Vector3 } from 'three'

const cNucleicControlNames = ["C3'", 'C3*', 'P', 'H5T', 'H3T']

Function _fillCombo has 75 lines of code (exceeds 25 allowed). Consider refactoring.

Open

Menu.prototype._fillCombo = function (type, name, path, entityList) {
  const self = this
  const frag = document.createDocumentFragment()
  let newItem

Function _renderObject has 74 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _renderObject(object, camera, scene) {
    function lerpColorAsHex(a, b, t) {
      tempColor.setHex(a)
      tempColor.lerp(b, t)
      return `#${tempColor.getHexString()}`

Function _performAO has 74 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _performAO(
    srcColorBuffer,
    normalBuffer,
    srcDepthTexture,
    targetBuffer,

File selectArgs.test.js has 289 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import chai, { expect } from 'chai'
import dirtyChai from 'dirty-chai'
import { Range, RangeList, ValueList } from './selectArgs'

chai.use(dirtyChai)

Function getMiewWithCli has 73 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

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

Function RepresentationMap has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

var RepresentationMap = function () {
  function RepresentationMap() {
    _classCallCheck(this, RepresentationMap);
    this.representationMap = {};
    this.representationID = {};

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Function RepresentationMap has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

var RepresentationMap = function () {
  function RepresentationMap() {
    _classCallCheck(this, RepresentationMap);
    this.representationMap = {};
    this.representationID = {};

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Function getNumIntersectedCells has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

  getNumIntersectedCells(side, numCells, corners, cube) {
    const side2 = side * side
    const cNumVerts = 8
    let numIntersectedCells = 0

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Function _renderObject has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

  _renderObject(object, camera, scene) {
    function lerpColorAsHex(a, b, t) {
      tempColor.setHex(a)
      tempColor.lerp(b, t)
      return `#${tempColor.getHexString()}`

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Function _breadWidthSearch has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

  _breadWidthSearch(atoms, molID) {
    const atomLabels = new Array(atoms.length)

    let id
    for (id = 0; id < atomLabels.length; id++) {

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Function _extractSGroup has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

  _extractSGroup(molecule, moleculeArr) {
    if (!Array.isArray(moleculeArr)) {
      moleculeArr = []
    }

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Function _extractOperations has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

function _extractOperations(assemblyGen, opsDict) {
  assemblyGen = isString(assemblyGen) ? assemblyGen : `${assemblyGen}`
  const l = assemblyGen.replace(/\)\s*\(/g, '!').replace(/[()']/g, '')
  const groupStr = l.split('!')
  const gps = []

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Function gaussdensity has 72 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  gaussdensity(surface, packedArrays, atomicNum, params) {
    const numAtoms = packedArrays.posRad.length / 4
    const { posRad, colors } = packedArrays
    const { numVoxels } = this
    const { radScale, gaussLim, gridSpacing } = params

Function _init has 70 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _init(instanceCount, cylinderGeo, useZSprites) {
    this.copy(cylinderGeo)
    this._matVector1 = utils.allocateTyped(
      Float32Array,
      instanceCount * OFFSET_SIZE

Function _extractConfs has 70 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _extractConfs(complex, helicesData) {
    const { asymDict } = this
    if (
      !helicesData.conf_type_id ||
      !helicesData.beg_label_seq_id ||

Function projectPoints has 69 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  function projectPoints() {
    // For each atom:
    //     Iterate over a subsection of the grid, for each point:
    //         If current value < 0.0, unvisited, set positive
    //