eslint src

jol-static.js

@@ -156,9 +156,9 @@ const fullPageIndexHtmlMustache = `
 `
 
 let knownOpts = {
-  'out': [String, null],
-  'browser': [Boolean, false],
-  'embed': [Boolean, true]
+  out: [String, null],
+  browser: [Boolean, false],
+  embed: [Boolean, true]
 }
 let shortHands = {
   o: ['--out'],
@@ -171,7 +171,6 @@ let remain = parsed.argv.remain
 if (remain.length < 1) {
   console.log(doc)
 } else {
-
   const pdb = remain[0]
   let base = path.basename(pdb.replace('.pdb', ''))
   let targetDir = path.join(path.dirname(pdb), base + '-jol')
@@ -197,7 +196,7 @@ if (remain.length < 1) {
     dataServerLoadStr += `"data-server${i}"`
     dataServerArgStr += `dataServer${i}`
     let pdbLines = pdbText.split(/\r?\n/)
-    pdbLines = _.map(pdbLines, (l) => l.replace(/"/g, '\\"'))
+    pdbLines = _.map(pdbLines, l => l.replace(/"/g, '\\"'))
     let pdbId = base
     let viewsJson = pdb.replace('.pdb', '') + '.views.json'
     console.log(`Checking ${viewsJson}`)
@@ -207,9 +206,11 @@ if (remain.length < 1) {
       views = JSON.parse(text)
     }
     let viewsJsonStr = JSON.stringify(views, null, 2)
-    let dataJsText = mustache.render(
-      dataServerMustache,
-      {pdbId, pdbLines, viewsJsonStr})
+    let dataJsText = mustache.render(dataServerMustache, {
+      pdbId,
+      pdbLines,
+      viewsJsonStr
+    })
     fs.writeFileSync(dataJs, dataJsText)
   }
 
@@ -219,39 +220,34 @@ if (remain.length < 1) {
   let htmlText
   if (isFullPage) {
     let user_nickname = 'anonymous'
-    htmlText = mustache.render(
-      fullPageIndexHtmlMustache, {
-        dataServerLoadStr,
-        dataServerArgStr,
-        user_nickname
-      })
+    htmlText = mustache.render(fullPageIndexHtmlMustache, {
+      dataServerLoadStr,
+      dataServerArgStr,
+      user_nickname
+    })
   } else {
-    htmlText = mustache.render(
-      embedIndexHtmlMustache, {
-        dataServerLoadStr,
-        dataServerArgStr,
-      })
+    htmlText = mustache.render(embedIndexHtmlMustache, {
+      dataServerLoadStr,
+      dataServerArgStr
+    })
   }
   fs.writeFileSync(html, htmlText)
 
   let fnames = [
     'dist/jolecule.js',
     'dist/jolecule.js.map',
     'dist/full-page-jolecule.css',
-    'node_modules/requirejs/require.js']
+    'node_modules/requirejs/require.js'
+  ]
 
   for (let fname of fnames) {
     fs.copySync(
       path.join(__dirname, fname),
-      path.join(targetDir, path.basename(fname)))
+      path.join(targetDir, path.basename(fname))
+    )
   }
 
   if (!parsed.browser) {
     opener(html)
   }
 }
-
-
-
-
-

src/animation.js

@@ -20,7 +20,7 @@
  * typically MS_PER_STEP = 17
  */
 
-function loop () {
+function loop() {
   requestAnimationFrame(loop)
 
   if (window.globalWidgets === []) {
@@ -46,7 +46,7 @@ function loop () {
  * run loop() as a singleton by using the global
  * window space to lock one single copy of loop
  */
-function registerGlobalAnimationLoop (widget) {
+function registerGlobalAnimationLoop(widget) {
   // only set once by checking the global window variable
 
   if (typeof window.globalWidgets === 'undefined') {

src/data.js

@@ -66,7 +66,7 @@ for (let [k, v] of _.toPairs(ElementColors)) {
   ElementColors[k] = new THREE.Color(v)
 }
 
-function getSsColor (ss) {
+function getSsColor(ss) {
   if (ss === 'E') {
     return yellow
   } else if (ss === 'H') {
@@ -127,26 +127,26 @@ const backboneAtomTypes = [
   'HA',
   'CA',
   'OXT',
-  'C3\'',
+  "C3'",
   'P',
   'OP1',
-  'O5\'',
+  "O5'",
   'OP2',
-  'C5\'',
-  'O5\'',
-  'O3\'',
-  'C4\'',
-  'O4\'',
-  'C1\'',
-  'C2\'',
-  'O2\'',
-  'H2\'',
-  'H2\'\'',
-  'H3\'',
-  'H4\'',
-  'H5\'',
-  'H5\'\'',
-  'HO3\''
+  "C5'",
+  "O5'",
+  "O3'",
+  "C4'",
+  "O4'",
+  "C1'",
+  "C2'",
+  "O2'",
+  "H2'",
+  "H2''",
+  "H3'",
+  "H4'",
+  "H5'",
+  "H5''",
+  "HO3'"
 ]
 
 // Cartoon cross-sections
@@ -171,14 +171,14 @@ const fatCoilFace = new THREE.Shape([
   new THREE.Vector2(+0.25, -0.25)
 ])
 
-function getSsFace (ss) {
+function getSsFace(ss) {
   if (ss === 'C' || ss === '-') {
     return coilFace
   }
   return ribbonFace
 }
 
-function getNucleotideBaseAtomTypes (resType) {
+function getNucleotideBaseAtomTypes(resType) {
   let atomTypes = []
   if (resType === 'DA' || resType === 'A') {
     atomTypes = ['N9', 'C8', 'N7', 'C5', 'C6', 'N1', 'C2', 'N3', 'C4']
@@ -192,16 +192,16 @@ function getNucleotideBaseAtomTypes (resType) {
   return atomTypes
 }
 
-function getNucleotideConnectorBondAtomTypes (resType) {
+function getNucleotideConnectorBondAtomTypes(resType) {
   let bondTypes = []
   if (resType === 'DA' || resType === 'A') {
-    bondTypes = [['C3\'', 'C2\''], ['C2\'', 'C1\''], ['C1\'', 'N9']]
+    bondTypes = [["C3'", "C2'"], ["C2'", "C1'"], ["C1'", 'N9']]
   } else if (resType === 'DG' || resType === 'G') {
-    bondTypes = [['C3\'', 'C2\''], ['C2\'', 'C1\''], ['C1\'', 'N9']]
+    bondTypes = [["C3'", "C2'"], ["C2'", "C1'"], ["C1'", 'N9']]
   } else if (resType === 'DT' || resType === 'U') {
-    bondTypes = [['C3\'', 'C2\''], ['C2\'', 'C1\''], ['C1\'', 'N1']]
+    bondTypes = [["C3'", "C2'"], ["C2'", "C1'"], ["C1'", 'N1']]
   } else if (resType === 'DC' || resType === 'C') {
-    bondTypes = [['C3\'', 'C2\''], ['C2\'', 'C1\''], ['C1\'', 'N1']]
+    bondTypes = [["C3'", "C2'"], ["C2'", "C1'"], ["C1'", 'N1']]
   }
   return bondTypes
 }

src/embed-widget.js

@@ -32,11 +32,11 @@ let defaultArgs = {
 }
 
 class EmbedJolecule {
-  constructor (params) {
+  constructor(params) {
     this.params = _.cloneDeep(defaultArgs)
     _.assign(this.params, params)
     console.log('EmbedJolecule.constructor', this.params)
-    this.isProcessing = {flag: false}
+    this.isProcessing = { flag: false }
 
     this.divTag = this.params.divTag
     this.div = $(this.params.divTag)
@@ -66,7 +66,7 @@ class EmbedJolecule {
     resizeFn()
   }
 
-  async asyncAddDataServer (dataServer) {
+  async asyncAddDataServer(dataServer) {
     while (this.isProcessing.flag) {
       await delay(100)
     }
@@ -121,13 +121,13 @@ class EmbedJolecule {
     this.isProcessing.flag = false
   }
 
-  clear () {
+  clear() {
     while (this.soupWidget.soup.structureIds.length > 0) {
       this.soupWidget.deleteStructure(0)
     }
   }
 
-  createDivs () {
+  createDivs() {
     this.headerDiv = $('<div>').attr('id', `${this.divId}-sequence-widget`)
 
     this.bodyDiv = $('<div>')
@@ -331,7 +331,7 @@ class EmbedJolecule {
     }
   }
 
-  resize () {
+  resize() {
     this.bodyDiv.width(this.div.outerWidth())
 
     let height = this.div.outerHeight()
@@ -348,7 +348,4 @@ class EmbedJolecule {
   }
 }
 
-export {
-  EmbedJolecule,
-  defaultArgs
-}
+export { EmbedJolecule, defaultArgs }