diff --git a/.eslintrc.json b/.eslintrc.json
index 28e80614867167fe9c80bb988dc5fa9114552072..bef255fae52e4dccb7bd4ac7908ec12c3e47cf10 100644
--- a/.eslintrc.json
+++ b/.eslintrc.json
@@ -55,6 +55,9 @@
"error",
"1tbs", { "allowSingleLine": true }
],
+ "comma-spacing": "off",
+ "@typescript-eslint/comma-spacing": "error",
+ "space-infix-ops": "error",
"comma-dangle": "off",
"eqeqeq": [
"error",
diff --git a/src/apps/viewer/extensions/cellpack/color.ts b/src/apps/viewer/extensions/cellpack/color.ts
index 7b3b333d103e797f492a871ad4ab266eb8ccd12b..d14de313246ea5b84d25911a8e3b7c07ea8e39f5 100644
--- a/src/apps/viewer/extensions/cellpack/color.ts
+++ b/src/apps/viewer/extensions/cellpack/color.ts
@@ -52,7 +52,7 @@ export function CellPackColorTheme(ctx: ThemeDataContext, props: PD.Values<CellP
}})
legend = palette.legend
const modelColor = new Map<number, Color>()
- for (let i = 0, il = models.length; i <il; ++i) {
+ for (let i = 0, il = models.length; i < il; ++i) {
const idx = models[i].trajectoryInfo.index;
modelColor.set(models[i].trajectoryInfo.index, palette.color(idx))
}
diff --git a/src/apps/viewer/extensions/cellpack/curve.ts b/src/apps/viewer/extensions/cellpack/curve.ts
index 4b789f7a5cb1755033270839266762a1686da4eb..6a31ac5a78a37700e2d995cba37f9a134407eba2 100644
--- a/src/apps/viewer/extensions/cellpack/curve.ts
+++ b/src/apps/viewer/extensions/cellpack/curve.ts
@@ -119,7 +119,7 @@ function GetSmoothNormals(points: Vec3[]) {
p0 = points[i - 1]
p1 = points[i]
p2 = points[i + 1]
- const t = Vec3.normalize(tmpV1, Vec3.sub(tmpV1, p2 , p0))
+ const t = Vec3.normalize(tmpV1, Vec3.sub(tmpV1, p2, p0))
const b = Vec3.normalize(tmpV2, Vec3.cross(tmpV2, t, prevV))
const n = Vec3.normalize(Vec3(), Vec3.cross(tmpV3, t, b))
Vec3.negate(n, n)
@@ -128,8 +128,8 @@ function GetSmoothNormals(points: Vec3[]) {
}
const last = Vec3()
Vec3.normalize(last, Vec3.cross(last,
- Vec3.sub(tmpV1, points[nP - 3], points[nP-2]),
- Vec3.sub(tmpV2, points[nP-2] , points[nP-1]))
+ Vec3.sub(tmpV1, points[nP - 3], points[nP - 2]),
+ Vec3.sub(tmpV2, points[nP - 2], points[nP - 1]))
)
smoothNormals.push(last)
return smoothNormals;
@@ -168,8 +168,8 @@ function GetMiniFrame(points: Vec3[], normals: Vec3[]) {
const t0 = Vec3.normalize(mfTmpV1, Vec3.sub(mfTmpV1, points[1], points[0]))
frames.push(getFrame(normals[0], t0))
- for (let i = 0; i< points.length-2; ++i) {
- const t2 = Vec3.normalize(mfTmpV1, Vec3.sub(mfTmpV1, points[i+2], points[i+1]))
+ for (let i = 0; i < points.length - 2; ++i) {
+ const t2 = Vec3.normalize(mfTmpV1, Vec3.sub(mfTmpV1, points[i + 2], points[i + 1]))
const v1 = Vec3.sub(mfTmpV2, points[i + 1], points[i]) // this is tangeant
const c1 = Vec3.dot(v1, v1)
// compute r_i^L = R_1 * r_i
@@ -179,10 +179,10 @@ function GetMiniFrame(points: Vec3[], normals: Vec3[]) {
const v1t = Vec3.scale(mfTmpV5, v1, (2.0 / c1) * Vec3.dot(v1, frames[i].t))
const tan_L_i = Vec3.sub(mfTmpV6, frames[i].t, v1t)
// # compute reflection vector of R_2
- const v2 = Vec3.sub(mfTmpV7, t2 , tan_L_i)
+ const v2 = Vec3.sub(mfTmpV7, t2, tan_L_i)
const c2 = Vec3.dot(v2, v2)
// compute r_(i+1) = R_2 * r_i^L
- const v2l = Vec3.scale(mfTmpV8, v1, (2.0/c2) * Vec3.dot(v2, ref_L_i))
+ const v2l = Vec3.scale(mfTmpV8, v1, (2.0 / c2) * Vec3.dot(v2, ref_L_i))
const ref_next = Vec3.sub(mfTmpV9, ref_L_i, v2l) // ref_L_i - (2 / c2) * v2.dot(ref_L_i) * v2
frames.push(getFrame(ref_next, t2)) // frames.append(Frame(ref_next, tangents[i+1]))
}
@@ -199,13 +199,13 @@ export function getMatFromResamplePoints(points: NumberArray, segmentLength: num
const limit = npoints
const transforms: Mat4[] = []
const pti = Vec3.copy(rpTmpVec1, new_points[0]);
- for (let i = 0; i<npoints-2; ++i) {
- const pti1: Vec3 = new_points[i+1] // Vec3.create(points[(i+1)*3],points[(i+1)*3+1],points[(i+1)*3+2]);
+ for (let i = 0; i < npoints - 2; ++i) {
+ const pti1: Vec3 = new_points[i + 1] // Vec3.create(points[(i+1)*3],points[(i+1)*3+1],points[(i+1)*3+2]);
const d = Vec3.distance(pti, pti1)
if (d >= segmentLength) {
// use twist or random?
const quat = Quat.rotationTo(Quat.zero(), Vec3.create(0, 0, 1), frames[i].t) // Quat.rotationTo(Quat.zero(), Vec3.create(0,0,1),new_normal[i]);//Quat.rotationTo(Quat.zero(), Vec3.create(0,0,1),direction);new_normal
- const rq = Quat.setAxisAngle(Quat.zero(), frames[i].t, Math.random()*3.60 ) // Quat.setAxisAngle(Quat.zero(),direction, Math.random()*3.60 );//Quat.identity();//
+ const rq = Quat.setAxisAngle(Quat.zero(), frames[i].t, Math.random() * 3.60 ) // Quat.setAxisAngle(Quat.zero(),direction, Math.random()*3.60 );//Quat.identity();//
const m = Mat4.fromQuat(Mat4.zero(), Quat.multiply(Quat.zero(), rq, quat)) // Mat4.fromQuat(Mat4.zero(),Quat.multiply(Quat.zero(),quat1,quat2));//Mat4.fromQuat(Mat4.zero(),quat);//Mat4.identity();//Mat4.fromQuat(Mat4.zero(),Quat.multiply(Quat.zero(),rq,quat));
// let pos:Vec3 = Vec3.add(Vec3.zero(),pti1,pti)
// pos = Vec3.scale(pos,pos,1.0/2.0);
diff --git a/src/apps/viewer/extensions/cellpack/model.ts b/src/apps/viewer/extensions/cellpack/model.ts
index 5ef48f02eff4e741a53a8b8f59350e9f5c413b96..6dbc3b59acfbbaff066231ade01a081eb10fc9fa 100644
--- a/src/apps/viewer/extensions/cellpack/model.ts
+++ b/src/apps/viewer/extensions/cellpack/model.ts
@@ -49,7 +49,6 @@ async function getModel(id: string, model_id: number, baseUrl: string, file?: Fi
throw new Error(`unsupported file type '${file.name}'`)
}
} else if (id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) {
- // return
const cif = await getFromPdb(id)
model = (await trajectoryFromMmCIF(cif).run())[model_id]
} else {
@@ -68,7 +67,7 @@ async function getStructure(model: Model, source: IngredientSource, props: { ass
}
let query;
if (source.selection){
- const asymIds: string[] = source.selection.replace(' :','').split(' or')
+ const asymIds: string[] = source.selection.replace(' :', '').split(' or')
query = MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
@@ -102,7 +101,7 @@ function getTransformLegacy(trans: Vec3, rot: Quat) {
function getTransform(trans: Vec3, rot: Quat) {
const q: Quat = Quat.create(rot[0], rot[1], rot[2], rot[3])
const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q)
- const p: Vec3 = Vec3.create(trans[0],trans[1],trans[2])
+ const p: Vec3 = Vec3.create(trans[0], trans[1], trans[2])
Mat4.setTranslation(m, p)
return m
}
@@ -116,7 +115,11 @@ function getResultTransforms(results: Ingredient['results'], legacy: boolean) {
function getCurveTransforms(ingredient: Ingredient) {
const n = ingredient.nbCurve || 0
const instances: Mat4[] = []
- const segmentLength = (ingredient.radii)? ((ingredient.radii[0].radii)?ingredient.radii[0].radii[0]*2.0:3.4):3.4;
+ const segmentLength = ingredient.radii
+ ? (ingredient.radii[0].radii
+ ? ingredient.radii[0].radii[0] * 2.0
+ : 3.4)
+ : 3.4;
for (let i = 0; i < n; ++i) {
const cname = `curve${i}`
if (!(cname in ingredient)) {
@@ -130,7 +133,7 @@ function getCurveTransforms(ingredient: Ingredient) {
}
const points = new Float32Array(_points.length * 3)
for (let i = 0, il = _points.length; i < il; ++i) Vec3.toArray(_points[i], points, i * 3)
- const newInstances = getMatFromResamplePoints(points,segmentLength)
+ const newInstances = getMatFromResamplePoints(points, segmentLength)
instances.push(...newInstances)
}
@@ -273,8 +276,8 @@ async function getIngredientStructure(ingredient: Ingredient, baseUrl: string, i
}
// model id in case structure is NMR
- const model_id = (ingredient.source.model)? parseInt(ingredient.source.model) : 0;
- const model = await getModel(source.pdb || name,model_id, baseUrl, file)
+ const model_id = (ingredient.source.model) ? parseInt(ingredient.source.model) : 0;
+ const model = await getModel(source.pdb || name, model_id, baseUrl, file)
if (!model) return
if (nbCurve) {
@@ -288,35 +291,35 @@ async function getIngredientStructure(ingredient: Ingredient, baseUrl: string, i
bu = bu.slice(2)
}
}
- let structure = await getStructure(model,source, { assembly: bu })
+ let structure = await getStructure(model, source, { assembly: bu })
// transform with offset and pcp
let legacy: boolean = true
if (ingredient.offset || ingredient.principalAxis){
// center the structure
- legacy=false
+ legacy = false
const boundary = structure.boundary
let structureCenter: Vec3 = Vec3.zero()
- Vec3.negate(structureCenter,boundary.sphere.center)
+ Vec3.negate(structureCenter, boundary.sphere.center)
const m1: Mat4 = Mat4.identity()
Mat4.setTranslation(m1, structureCenter)
- structure = Structure.transform(structure,m1)
+ structure = Structure.transform(structure, m1)
if (ingredient.offset){
- if (!Vec3.exactEquals(ingredient.offset,Vec3.zero())){
+ if (!Vec3.exactEquals(ingredient.offset, Vec3.zero())){
const m: Mat4 = Mat4.identity();
Mat4.setTranslation(m, ingredient.offset)
- structure = Structure.transform(structure,m);
+ structure = Structure.transform(structure, m);
}
}
if (ingredient.principalAxis){
- if (!Vec3.exactEquals(ingredient.principalAxis,Vec3.unitZ)){
+ if (!Vec3.exactEquals(ingredient.principalAxis, Vec3.unitZ)){
const q: Quat = Quat.identity();
- Quat.rotationTo(q,ingredient.principalAxis,Vec3.unitZ)
+ Quat.rotationTo(q, ingredient.principalAxis, Vec3.unitZ)
const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q)
- structure = Structure.transform(structure,m);
+ structure = Structure.transform(structure, m);
}
}
}
- return getAssembly(getResultTransforms(results,legacy), structure)
+ return getAssembly(getResultTransforms(results, legacy), structure)
}
}
@@ -388,7 +391,7 @@ async function loadMembrane(name: string, plugin: PluginContext, runtime: Runtim
}
const url = `${params.baseUrl}/membranes/${name}.bcif`
//
- const file = (ingredientFiles)?ingredientFiles[fname]:null;
+ const file = (ingredientFiles) ? ingredientFiles[fname] : null;
// can we check if url exist
let membrane
if (!file) {
diff --git a/src/mol-plugin-ui/controls.tsx b/src/mol-plugin-ui/controls.tsx
index 63409ca18b847924a66639e1fadcbf01d42cdff7..34661f0cf1c0749cdc7bc55c00f64e117493d6da 100644
--- a/src/mol-plugin-ui/controls.tsx
+++ b/src/mol-plugin-ui/controls.tsx
@@ -237,7 +237,7 @@ export class AnimationViewportControls extends PluginUIComponent<{}, { isEmpty:
<div className='msp-semi-transparent-background' />
<IconButton icon={isAnimating || isPlaying ? 'stop' : 'tape'} transparent title={isAnimating ? 'Stop' : 'Select Animation'}
onClick={isAnimating || isPlaying ? this.stop : this.toggleExpanded}
- disabled={isAnimating|| isPlaying ? false : this.state.isBusy || this.state.isPlaying || this.state.isEmpty} />
+ disabled={isAnimating || isPlaying ? false : this.state.isBusy || this.state.isPlaying || this.state.isEmpty} />
</div>
{(this.state.isExpanded && !this.state.isBusy) && <div className='msp-animation-viewport-controls-select'>
<AnimationControls onStart={this.toggleExpanded} />
diff --git a/src/mol-util/uuid.ts b/src/mol-util/uuid.ts
index 541489a5f5f57d439bff87bdee88381c9eb5cc6e..e1dc052b87920f345d11ab9439d8a21605c0eedc 100644
--- a/src/mol-util/uuid.ts
+++ b/src/mol-util/uuid.ts
@@ -17,8 +17,8 @@ namespace UUID {
export function create22(): UUID {
let d = (+new Date()) + now();
for (let i = 0; i < 16; i++) {
- chars[i] = String.fromCharCode((d + Math.random()*0xff)%0xff | 0);
- d = Math.floor(d/0xff);
+ chars[i] = String.fromCharCode((d + Math.random() * 0xff) % 0xff | 0);
+ d = Math.floor(d / 0xff);
}
return _btoa(chars.join('')).replace(/\+/g, '-').replace(/\//g, '_').substr(0, 22) as UUID;
}
@@ -26,9 +26,9 @@ namespace UUID {
export function createv4(): UUID {
let d = (+new Date()) + now();
const uuid = 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'.replace(/[xy]/g, function(c) {
- const r = (d + Math.random()*16)%16 | 0;
- d = Math.floor(d/16);
- return (c==='x' ? r : (r&0x3|0x8)).toString(16);
+ const r = (d + Math.random() * 16) % 16 | 0;
+ d = Math.floor(d / 16);
+ return (c === 'x' ? r : (r & 0x3 | 0x8)).toString(16);
});
return uuid as any;
}