lint: add no-multi-spaces rule

.eslintrc.json

@@ -50,7 +50,8 @@
             "ignoreReadBeforeAssign": false
         }],
         "space-before-function-paren": "off",
-        "func-call-spacing": "off"
+        "func-call-spacing": "off",
+        "no-multi-spaces": "error"
     },
     "overrides": [
         {

src/cli/chem-comp-dict/create-table.ts

@@ -171,7 +171,7 @@ async function createBonds(
         pdbx_aromatic_flag, pdbx_stereo_config, molstar_protonation_variant
     });
 
-    const bondDatabase =  Database.ofTables(
+    const bondDatabase = Database.ofTables(
         CCB_TABLE_NAME,
         { chem_comp_bond: mmCIF_chemCompBond_schema },
         { chem_comp_bond: bondTable }

src/cli/cifschema/util/cif-dic.ts

@@ -316,7 +316,7 @@ export function generateSchema(frames: CifFrame[], imports: Imports = new Map())
     frames.forEach(d => {
         // category definitions in mmCIF start with '_' and don't include a '.'
         // category definitions in cifCore don't include a '.'
-        if (d.header[0] === '_'  || d.header.includes('.')) return;
+        if (d.header[0] === '_' || d.header.includes('.')) return;
         const categoryName = d.header.toLowerCase();
         // console.log(d.header, d.categoryNames, d.categories)
         let descriptionField: Data.CifField | undefined;

src/examples/domain-annotation-server/mapping.ts

@@ -38,7 +38,7 @@ type MappingRow = Table.Row<S.mapping>;
 
 function writeDomain(enc: CifWriter.Encoder, domain: DomainAnnotation | undefined) {
     if (!domain) return;
-    enc.writeCategory({ name: `pdbx_${domain.name}_domain_annotation`, instance: () =>  CifWriter.Category.ofTable(domain.domains) });
+    enc.writeCategory({ name: `pdbx_${domain.name}_domain_annotation`, instance: () => CifWriter.Category.ofTable(domain.domains) });
     enc.writeCategory({ name: `pdbx_${domain.name}_domain_mapping`, instance: () => CifWriter.Category.ofTable(domain.mappings) });
 }
 

src/examples/proteopedia-wrapper/index.ts

@@ -250,7 +250,7 @@ class MolStarProteopediaWrapper {
     setBackground(color: number) {
         if (!this.plugin.canvas3d) return;
         const renderer = this.plugin.canvas3d.props.renderer;
-        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: { ...renderer,  backgroundColor: Color(color) } } });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: Color(color) } } });
     }
 
     toggleSpin() {

src/extensions/anvil/algorithm.ts

@@ -183,7 +183,7 @@ export async function calculate(runtime: RuntimeContext, structure: Structure, p
     }
 
     const normalVector = v3zero();
-    const center =  v3zero();
+    const center = v3zero();
     v3sub(normalVector, membrane.planePoint1, membrane.planePoint2);
     v3normalize(normalVector, normalVector);
 
@@ -404,7 +404,7 @@ function membraneSegments(ctx: ANVILContext, membrane: MembraneCandidate): Array
                 }
                 lastAuthSeqId = authSeqId;
                 endOffset = k;
-            } else  {
+            } else {
                 lastAuthSeqId++;
                 endOffset++;
             }

src/extensions/anvil/behavior.ts

@@ -150,7 +150,7 @@ export const MembraneOrientationPreset = StructureRepresentationPresetProvider({
     params: () => StructureRepresentationPresetProvider.CommonParams,
     async apply(ref, params, plugin) {
         const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        const structure  = structureCell?.obj?.data;
+        const structure = structureCell?.obj?.data;
         if (!structureCell || !structure) return {};
 
         if (!MembraneOrientationProvider.get(structure).value) {

src/extensions/cellpack/curve.ts

@@ -111,7 +111,7 @@ function GetSmoothNormals(points: Vec3[]) {
     let p1 = points[1];
     let p2 = points[2];
     const p21 = Vec3.sub(tmpV1, p2, p1);
-    const p01 =  Vec3.sub(tmpV2, p0, p1);
+    const p01 = Vec3.sub(tmpV2, p0, p1);
     const p0121 = Vec3.cross(tmpV3, p01, p21);
     Vec3.normalize(prevV, p0121);
     smoothNormals.push(Vec3.clone(prevV));
@@ -179,7 +179,7 @@ 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));

src/extensions/cellpack/data.ts

@@ -73,9 +73,9 @@ export interface Ingredient {
 
 export interface IngredientSource {
     pdb: string;
-    bu?: string;  /** biological unit e.g AU,BU1,etc.. */
+    bu?: string; /** biological unit e.g AU,BU1,etc.. */
     selection?: string; /** NGL selection or :A or :B etc.. */
-    model?: string;     /** model number e.g 0,1,2... */
+    model?: string; /** model number e.g 0,1,2... */
     transform: {
         center: boolean;
         translate?: Vec3;

src/extensions/dnatco/confal-pyramids/behavior.ts

@@ -41,10 +41,10 @@ export const DnatcoConfalPyramidsPreset = StructureRepresentationPresetProvider(
 
         let pyramidsRepr;
         if (representations)
-            pyramidsRepr = builder.buildRepresentation(update, pyramids,  { type: ConfalPyramidsRepresentationProvider, typeParams, color: ConfalPyramidsColorThemeProvider }, { tag: 'confal-pyramdis' });
+            pyramidsRepr = builder.buildRepresentation(update, pyramids, { type: ConfalPyramidsRepresentationProvider, typeParams, color: ConfalPyramidsColorThemeProvider }, { tag: 'confal-pyramdis' });
 
         await update.commit({ revertOnError: true });
-        return  { components: { ...components, pyramids }, representations: { ...representations, pyramidsRepr } };
+        return { components: { ...components, pyramids }, representations: { ...representations, pyramidsRepr } };
     }
 });
 

src/extensions/dnatco/confal-pyramids/color.ts

@@ -27,7 +27,7 @@ const ColorMapping: ReadonlyMap<ConformerClasses, Color> = new Map([
     ['B', Color(0xC8CFFF)],
     ['BII', Color(0x0059DA)],
     ['miB', Color(0x3BE8FB)],
-    ['Z',  Color(0x01F60E)],
+    ['Z', Color(0x01F60E)],
     ['IC', Color(0xFA5CFB)],
     ['OPN', Color(0xE90000)],
     ['SYN', Color(0xFFFF01)],

src/extensions/dnatco/confal-pyramids/util.ts

@@ -95,7 +95,7 @@ export namespace ConfalPyramidsUtil {
             const first = residueInfoFromLocation(locFirst);
             const second = residueInfoFromLocation(locSecond);
             const model_id = this.hasMultipleModels ? `-m${modelNum}` : '';
-            const alt_id_1 =  fakeAltId_1 !== '' ? `.${fakeAltId_1}` : (first.alt_id.length ? `.${first.alt_id}` : '');
+            const alt_id_1 = fakeAltId_1 !== '' ? `.${fakeAltId_1}` : (first.alt_id.length ? `.${first.alt_id}` : '');
             const alt_id_2 = fakeAltId_2 !== '' ? `.${fakeAltId_2}` : (second.alt_id.length ? `.${second.alt_id}` : '');
             const ins_code_1 = first.ins_code.length ? `.${first.ins_code}` : '';
             const ins_code_2 = second.ins_code.length ? `.${second.ins_code}` : '';

src/extensions/g3d/model.ts

@@ -61,7 +61,7 @@ function getColumns(block: G3dDataBlock) {
     objectForEach(data, (hs, h) => {
         objectForEach(hs, (chs, ch) => {
             const entity_id = `${ch}-${h}`;
-            const l =  chs.start.length;
+            const l = chs.start.length;
             if (l === 0) return;
 
             let x = chs.x[0];

src/extensions/pdbe/preferred-assembly.ts

@@ -62,7 +62,7 @@ export namespace PDBePreferredAssembly {
         if (model.customProperties.has(Descriptor)) return true;
 
         let asmName: string | undefined = fromCifData(model);
-        if (asmName === void 0 &&  params.PDBe_apiSourceJson) {
+        if (asmName === void 0 && params.PDBe_apiSourceJson) {
             const data = await params.PDBe_apiSourceJson(model);
             if (!data) return false;
             asmName = asmNameFromJson(model, data);

src/extensions/pdbe/structure-quality-report/color.ts

@@ -87,7 +87,7 @@ export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: P
     };
 }
 
-export const StructureQualityReportColorThemeProvider: ColorTheme.Provider<Params, 'pdbe-structure-quality-report'> =  {
+export const StructureQualityReportColorThemeProvider: ColorTheme.Provider<Params, 'pdbe-structure-quality-report'> = {
     name: 'pdbe-structure-quality-report',
     label: 'Structure Quality Report',
     category: ColorTheme.Category.Validation,

src/extensions/rcsb/assembly-symmetry/ui.tsx

@@ -7,7 +7,7 @@
 import { CollapsableState, CollapsableControls } from '../../../mol-plugin-ui/base';
 import { ApplyActionControl } from '../../../mol-plugin-ui/state/apply-action';
 import { InitAssemblySymmetry3D, AssemblySymmetry3D, AssemblySymmetryPreset, tryCreateAssemblySymmetry } from './behavior';
-import { AssemblySymmetryProvider,  AssemblySymmetryProps, AssemblySymmetryDataProvider, AssemblySymmetry } from './prop';
+import { AssemblySymmetryProvider, AssemblySymmetryProps, AssemblySymmetryDataProvider, AssemblySymmetry } from './prop';
 import { ParameterControls } from '../../../mol-plugin-ui/controls/parameters';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { StructureHierarchyManager } from '../../../mol-plugin-state/manager/structure/hierarchy';

src/extensions/rcsb/validation-report/representation.ts

@@ -107,7 +107,7 @@ function getIntraClashLabel(structure: Structure, unit: Unit.Atomic, clashes: In
 
 function IntraClashLoci(structure: Structure, unit: Unit.Atomic, clashes: IntraUnitClashes, elements: number[]) {
     return DataLoci('intra-clashes', { unit, clashes }, elements,
-        (boundingSphere: Sphere3D) =>  getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere),
+        (boundingSphere: Sphere3D) => getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere),
         () => getIntraClashLabel(structure, unit, clashes, elements));
 }
 
@@ -226,7 +226,7 @@ function getInterClashLabel(structure: Structure, clashes: InterUnitClashes, ele
 
 function InterClashLoci(structure: Structure, clashes: InterUnitClashes, elements: number[]) {
     return DataLoci('inter-clashes', clashes, elements,
-        (boundingSphere: Sphere3D) =>  getInterClashBoundingSphere(structure, clashes, elements, boundingSphere),
+        (boundingSphere: Sphere3D) => getInterClashBoundingSphere(structure, clashes, elements, boundingSphere),
         () => getInterClashLabel(structure, clashes, elements));
 }
 

src/mol-canvas3d/passes/draw.ts

@@ -58,8 +58,8 @@ const CopySchema = {
     tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     uTexSize: UniformSpec('v2'),
 };
-const  CopyShaderCode = ShaderCode('copy', quad_vert, copy_frag);
-type  CopyRenderable = ComputeRenderable<Values<typeof CopySchema>>
+const CopyShaderCode = ShaderCode('copy', quad_vert, copy_frag);
+type CopyRenderable = ComputeRenderable<Values<typeof CopySchema>>
 
 function getCopyRenderable(ctx: WebGLContext, colorTexture: Texture): CopyRenderable {
     const values: Values<typeof CopySchema> = {

src/mol-data/int/impl/sorted-array.ts

@@ -25,7 +25,7 @@ export function is(xs: any): xs is Nums { return xs && (Array.isArray(xs) || !!x
 export function isRange(xs: Nums) { return xs[xs.length - 1] - xs[0] + 1 === xs.length; }
 
 export function start(xs: Nums) { return xs[0]; }
-export function end(xs: Nums) { return xs[xs.length - 1] + 1;  }
+export function end(xs: Nums) { return xs[xs.length - 1] + 1; }
 export function min(xs: Nums) { return xs[0]; }
 export function max(xs: Nums) { return xs[xs.length - 1]; }
 export function size(xs: Nums) { return xs.length; }

src/mol-data/util/_spec/chunked-array.spec.ts

@@ -8,14 +8,14 @@ import { ChunkedArray } from '../chunked-array';
 
 describe('Chunked Array', () => {
     it('creation', () => {
-        const arr  = ChunkedArray.create<number, 2>(Array, 2, 2);
+        const arr = ChunkedArray.create<number, 2>(Array, 2, 2);
         ChunkedArray.add2(arr, 1, 2);
         ChunkedArray.add2(arr, 3, 4);
         expect(ChunkedArray.compact(arr)).toEqual([1, 2, 3, 4]);
     });
 
     it('initial', () => {
-        const arr  = ChunkedArray.create(Int32Array, 2, 6, new Int32Array([1, 2, 3, 4]));
+        const arr = ChunkedArray.create(Int32Array, 2, 6, new Int32Array([1, 2, 3, 4]));
         ChunkedArray.add2(arr, 4, 3);
         ChunkedArray.add2(arr, 2, 1);
         ChunkedArray.add2(arr, 5, 6);
@@ -23,13 +23,13 @@ describe('Chunked Array', () => {
     });
 
     it('add many', () => {
-        const arr  = ChunkedArray.create<number, 2>(Array, 2, 2);
+        const arr = ChunkedArray.create<number, 2>(Array, 2, 2);
         ChunkedArray.addMany(arr, [1, 2, 3, 4]);
         expect(ChunkedArray.compact(arr)).toEqual([1, 2, 3, 4]);
     });
 
     it('resize', () => {
-        const arr  = ChunkedArray.create<number, 2>(Int32Array, 2, 2);
+        const arr = ChunkedArray.create<number, 2>(Int32Array, 2, 2);
         ChunkedArray.add2(arr, 1, 2);
         ChunkedArray.add2(arr, 3, 4);
         ChunkedArray.add2(arr, 5, 6);
@@ -39,7 +39,7 @@ describe('Chunked Array', () => {
     });
 
     it('resize-fraction', () => {
-        const arr  = ChunkedArray.create<number, 2>(Int32Array, 2, 2.5);
+        const arr = ChunkedArray.create<number, 2>(Int32Array, 2, 2.5);
         ChunkedArray.add2(arr, 1, 2);
         ChunkedArray.add2(arr, 3, 4);
         ChunkedArray.add2(arr, 5, 6);

src/mol-geo/geometry/mesh/mesh-builder.ts

@@ -61,8 +61,8 @@ export namespace MeshBuilder {
 
         v3triangleNormal(tmpV, a, b, c);
         for (let i = 0; i < 3; ++i) {
-            caAdd3(normals, tmpV[0], tmpV[1], tmpV[2]);  // normal
-            caAdd(groups, currentGroup);  // group
+            caAdd3(normals, tmpV[0], tmpV[1], tmpV[2]); // normal
+            caAdd(groups, currentGroup); // group
         }
         caAdd3(indices, offset, offset + 1, offset + 2);
     }

src/mol-geo/geometry/text/text-builder.ts

@@ -69,7 +69,7 @@ export namespace TextBuilder {
                 } else if (attachment.startsWith('middle')) {
                     yShift = bHeight / 2;
                 } else {
-                    yShift = 0;  // "bottom"
+                    yShift = 0; // "bottom"
                 }
                 // horizontal
                 if (attachment.endsWith('right')) {
@@ -77,7 +77,7 @@ export namespace TextBuilder {
                 } else if (attachment.endsWith('center')) {
                     xShift = bWidth / 2;
                 } else {
-                    xShift = 0;  // "left"
+                    xShift = 0; // "left"
                 }
 
                 if (tether) {

src/mol-geo/primitive/box.ts

@@ -73,18 +73,18 @@ let boxCage: Cage;
 export function BoxCage() {
     if (!boxCage) {
         boxCage = createCage([
-            0.5,  0.5, -0.5, // bottom
-            -0.5,  0.5, -0.5,
+            0.5, 0.5, -0.5, // bottom
+            -0.5, 0.5, -0.5,
             -0.5, -0.5, -0.5,
             0.5, -0.5, -0.5,
-            0.5,  0.5, 0.5,  // top
-            -0.5,  0.5, 0.5,
+            0.5, 0.5, 0.5, // top
+            -0.5, 0.5, 0.5,
             -0.5, -0.5, 0.5,
             0.5, -0.5, 0.5
         ], [
-            0, 4,  1, 5,  2, 6,  3, 7, // sides
-            0, 1,  1, 2,  2, 3,  3, 0,  // bottom base
-            4, 5,  5, 6,  6, 7,  7, 4   // top base
+            0, 4, 1, 5, 2, 6, 3, 7, // sides
+            0, 1, 1, 2, 2, 3, 3, 0, // bottom base
+            4, 5, 5, 6, 6, 7, 7, 4 // top base
         ]);
     }
     return boxCage;

src/mol-geo/primitive/dodecahedron.ts

@@ -14,10 +14,10 @@ const b = 1 / t;
 const c = 2 - t;
 
 export const dodecahedronVertices: ReadonlyArray<number> = [
-    c, 0, a,    -c, 0, a,    -b, b, b,    0, a, c,     b, b, b,
-    b, -b, b,    0, -a, c,   -b, -b, b,   c, 0, -a,   -c, 0, -a,
-    -b, -b, -b,   0, -a, -c,   b, -b, -b,  b,  b, -b,   0, a, -c,
-    -b, b, -b,    a, c, 0,    -a, c, 0,   -a, -c, 0,    a, -c, 0
+    c, 0, a, -c, 0, a, -b, b, b, 0, a, c, b, b, b,
+    b, -b, b, 0, -a, c, -b, -b, b, c, 0, -a, -c, 0, -a,
+    -b, -b, -b, 0, -a, -c, b, -b, -b, b, b, -b, 0, a, -c,
+    -b, b, -b, a, c, 0, -a, c, 0, -a, -c, 0, a, -c, 0
 ];
 
 /** indices of pentagonal faces, groups of five  */
@@ -36,25 +36,25 @@ export const dodecahedronFaces: ReadonlyArray<number> = [
     7, 1, 2, 17, 18
 ];
 
-const dodecahedronIndices: ReadonlyArray<number> = [  // pentagonal faces
-    4, 3, 2,     2, 1, 0,     4, 2, 0,    // 4, 3, 2, 1, 0
-    7, 6, 5,     5, 0, 1,     7, 5, 1,    // 7, 6, 5, 0, 1
-    12, 11, 10,  10, 9, 8,    12, 10, 8,   // 12, 11, 10, 9, 8
-    15, 14, 13,  13, 8, 9,    15, 13, 9,   // 15, 14, 13, 8, 9
-    14, 3, 4,     4, 16, 13,  14, 4, 13,   // 14, 3, 4, 16, 13
-    3, 14, 15,   15, 17, 2,   3, 15, 2,   // 3, 14, 15, 17, 2
-    11, 6, 7,     7, 18, 10,  11, 7, 10,   // 11, 6, 7, 18, 10
-    6, 11, 12,  12, 19, 5,    6, 12, 5,   // 6, 11, 12, 19, 5
-    4, 0, 5,     5, 19, 16,   4, 5, 16,   // 4, 0, 5, 19, 16
-    12, 8, 13,   13, 16, 19,  12, 13, 19,  // 12, 8, 13, 16, 19
-    15, 9, 10,   10, 18, 17,  15, 10, 17,  // 15, 9, 10, 18, 17
-    7, 1, 2,     2, 17, 18,   7, 2, 18,   // 7, 1, 2, 17, 18
+const dodecahedronIndices: ReadonlyArray<number> = [ // pentagonal faces
+    4, 3, 2, 2, 1, 0, 4, 2, 0, // 4, 3, 2, 1, 0
+    7, 6, 5, 5, 0, 1, 7, 5, 1, // 7, 6, 5, 0, 1
+    12, 11, 10, 10, 9, 8, 12, 10, 8, // 12, 11, 10, 9, 8
+    15, 14, 13, 13, 8, 9, 15, 13, 9, // 15, 14, 13, 8, 9
+    14, 3, 4, 4, 16, 13, 14, 4, 13, // 14, 3, 4, 16, 13
+    3, 14, 15, 15, 17, 2, 3, 15, 2, // 3, 14, 15, 17, 2
+    11, 6, 7, 7, 18, 10, 11, 7, 10, // 11, 6, 7, 18, 10
+    6, 11, 12, 12, 19, 5, 6, 12, 5, // 6, 11, 12, 19, 5
+    4, 0, 5, 5, 19, 16, 4, 5, 16, // 4, 0, 5, 19, 16
+    12, 8, 13, 13, 16, 19, 12, 13, 19, // 12, 8, 13, 16, 19
+    15, 9, 10, 10, 18, 17, 15, 10, 17, // 15, 9, 10, 18, 17
+    7, 1, 2, 2, 17, 18, 7, 2, 18, // 7, 1, 2, 17, 18
 ];
 
 const dodecahedronEdges: ReadonlyArray<number> = [
-    0, 1,   0, 4,    0, 5,    1, 2,    1, 7,    2, 3,    2, 17,   3, 4,    3, 14,   4, 16,
-    5, 6,   5, 19,   6, 7,    6, 11,   7, 18,   8, 9,    8, 12,   8, 13,   9, 10,   9, 15,
-    10, 11, 10, 18,  11, 12,  12, 19,  13, 14,  13, 16,  14, 15,  15, 17,  16, 19,  17, 18,
+    0, 1, 0, 4, 0, 5, 1, 2, 1, 7, 2, 3, 2, 17, 3, 4, 3, 14, 4, 16,
+    5, 6, 5, 19, 6, 7, 6, 11, 7, 18, 8, 9, 8, 12, 8, 13, 9, 10, 9, 15,
+    10, 11, 10, 18, 11, 12, 12, 19, 13, 14, 13, 16, 14, 15, 15, 17, 16, 19, 17, 18,
 ];
 
 let dodecahedron: Primitive;

src/mol-geo/primitive/icosahedron.ts

@@ -10,22 +10,22 @@ import { Cage, createCage } from './cage';
 const t = (1 + Math.sqrt(5)) / 2;
 
 const icosahedronVertices: ReadonlyArray<number> = [
-    -1, t, 0,   1, t, 0,  -1, -t, 0,   1, -t, 0,
-    0, -1, t,  0, 1, t,   0, -1, -t,  0, 1, -t,
-    t, 0, -1,  t, 0, 1,  -t, 0, -1,  -t, 0, 1
+    -1, t, 0, 1, t, 0, -1, -t, 0, 1, -t, 0,
+    0, -1, t, 0, 1, t, 0, -1, -t, 0, 1, -t,
+    t, 0, -1, t, 0, 1, -t, 0, -1, -t, 0, 1
 ];
 
 const icosahedronIndices: ReadonlyArray<number> = [
-    0, 11, 5,  0, 5, 1,    0, 1, 7,    0, 7, 10,  0, 10, 11,
-    1, 5, 9,   5, 11, 4,  11, 10, 2,  10, 7, 6,   7, 1, 8,
-    3, 9, 4,   3, 4, 2,    3, 2, 6,    3, 6, 8,   3, 8, 9,
-    4, 9, 5,   2, 4, 11,   6, 2, 10,   8, 6, 7,   9, 8, 1
+    0, 11, 5, 0, 5, 1, 0, 1, 7, 0, 7, 10, 0, 10, 11,
+    1, 5, 9, 5, 11, 4, 11, 10, 2, 10, 7, 6, 7, 1, 8,
+    3, 9, 4, 3, 4, 2, 3, 2, 6, 3, 6, 8, 3, 8, 9,
+    4, 9, 5, 2, 4, 11, 6, 2, 10, 8, 6, 7, 9, 8, 1
 ];
 
 const icosahedronEdges: ReadonlyArray<number> = [
-    0, 11,  5, 11,  0, 5,   1, 5,  0, 1,  1, 7,  0, 7,   7, 10,  0, 10,  10, 11,
-    5, 9,   4, 11,  2, 10,  6, 7,  1, 8,  3, 9,  4, 9,   3, 4,   2, 4,   2, 3,
-    2, 6,   3, 6,   6, 8,   3, 8,  8, 9,  4, 5,  2, 11,  6, 10,  7, 8,   1, 9
+    0, 11, 5, 11, 0, 5, 1, 5, 0, 1, 1, 7, 0, 7, 7, 10, 0, 10, 10, 11,
+    5, 9, 4, 11, 2, 10, 6, 7, 1, 8, 3, 9, 4, 9, 3, 4, 2, 4, 2, 3,
+    2, 6, 3, 6, 6, 8, 3, 8, 8, 9, 4, 5, 2, 11, 6, 10, 7, 8, 1, 9
 ];
 
 let icosahedron: Primitive;

src/mol-geo/primitive/octahedron.ts

@@ -8,27 +8,27 @@ import { createPrimitive, Primitive } from './primitive';
 import { createCage, Cage } from './cage';
 
 export const octahedronVertices: ReadonlyArray<number> = [
-    0.5, 0, 0,   -0.5, 0, 0,    0, 0.5, 0,
-    0, -0.5, 0,   0, 0, 0.5,    0, 0, -0.5
+    0.5, 0, 0, -0.5, 0, 0, 0, 0.5, 0,
+    0, -0.5, 0, 0, 0, 0.5, 0, 0, -0.5
 ];
 
 export const octahedronIndices: ReadonlyArray<number> = [
-    0, 2, 4,  0, 4, 3,  0, 3, 5,
-    0, 5, 2,  1, 2, 5,  1, 5, 3,
-    1, 3, 4,  1, 4, 2
+    0, 2, 4, 0, 4, 3, 0, 3, 5,
+    0, 5, 2, 1, 2, 5, 1, 5, 3,
+    1, 3, 4, 1, 4, 2
 ];
 
 export const perforatedOctahedronIndices: ReadonlyArray<number> = [
-    0, 2, 4,   0, 4, 3,
+    0, 2, 4, 0, 4, 3,
     // 0, 3, 5,   0, 5, 2,
-    1, 2, 5,   1, 5, 3,
+    1, 2, 5, 1, 5, 3,
     // 1, 3, 4,   1, 4, 2
 ];
 
 const octahedronEdges: ReadonlyArray<number> = [
-    0, 2,  1, 3,  2, 1,  3, 0,
-    0, 4,  1, 4,  2, 4,  3, 4,
-    0, 5,  1, 5,  2, 5,  3, 5,
+    0, 2, 1, 3, 2, 1, 3, 0,
+    0, 4, 1, 4, 2, 4, 3, 4,
+    0, 5, 1, 5, 2, 5, 3, 5,
 ];
 
 let octahedron: Primitive;

src/mol-geo/primitive/plane.ts

@@ -28,7 +28,7 @@ const plane: Primitive = {
 
 const planeCage: Cage = {
     vertices: plane.vertices,
-    edges: new Uint32Array([0, 1,  2, 3,  3, 1,  2, 0])
+    edges: new Uint32Array([0, 1, 2, 3, 3, 1, 2, 0])
 };
 
 export function Plane(): Primitive {

src/mol-geo/primitive/pyramid.ts

@@ -83,8 +83,8 @@ export function PerforatedOctagonalPyramid() {
         vertices[8 * 3 + 4] = 0;
         vertices[8 * 3 + 5] = 0.5;
         const indices: ReadonlyArray<number> = [
-            0, 1, 8,  1, 2, 8,  4, 5, 8,  5, 6, 8,
-            2, 3, 9,  3, 4, 9,  6, 7, 9,  7, 0, 9
+            0, 1, 8, 1, 2, 8, 4, 5, 8, 5, 6, 8,
+            2, 3, 9, 3, 4, 9, 6, 7, 9, 7, 0, 9
         ];
         perforatedOctagonalPyramid = createPrimitive(vertices, indices);
     }

src/mol-geo/primitive/sphere.ts

@@ -5,7 +5,7 @@
  */
 
 import { Polyhedron } from './polyhedron';
-import { Icosahedron } from  './icosahedron';
+import { Icosahedron } from './icosahedron';
 import { Primitive } from './primitive';
 
 const { vertices, indices } = Icosahedron();

src/mol-geo/primitive/tetrahedron.ts

@@ -8,16 +8,16 @@ import { createPrimitive, Primitive } from './primitive';
 import { createCage, Cage } from './cage';
 
 export const tetrahedronVertices: ReadonlyArray<number> = [
-    0.5, 0.5, 0.5,  -0.5, -0.5, 0.5,  -0.5, 0.5, -0.5,  0.5, -0.5, -0.5
+    0.5, 0.5, 0.5, -0.5, -0.5, 0.5, -0.5, 0.5, -0.5, 0.5, -0.5, -0.5
 ];
 
 export const tetrahedronIndices: ReadonlyArray<number> = [
-    2, 1, 0,  0, 3, 2,  1, 3, 0,  2, 3, 1
+    2, 1, 0, 0, 3, 2, 1, 3, 0, 2, 3, 1
 ];
 
 const tetrahedronEdges: ReadonlyArray<number> = [
-    0, 1,  1, 2,  2, 0,
-    0, 3,  1, 3,  2, 3,
+    0, 1, 1, 2, 2, 0,
+    0, 3, 1, 3, 2, 3,
 ];
 
 let tetrahedron: Primitive;

src/mol-gl/compute/marching-cubes/tables.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { TriTable,  } from '../../../mol-geo/util/marching-cubes/tables';
+import { TriTable, } from '../../../mol-geo/util/marching-cubes/tables';
 import { TextureImage, createTextureImage } from '../../../mol-gl/renderable/util';
 
 let TriCount: TextureImage<Uint8Array> | undefined;

src/mol-gl/compute/util.ts

@@ -14,8 +14,8 @@ import { GLRenderingContext } from '../../mol-gl/webgl/compat';
 import { PixelData } from '../../mol-util/image';
 
 export const QuadPositions = new Float32Array([
-    1.0,  1.0,  -1.0,  1.0,  -1.0, -1.0, // First triangle
-    -1.0, -1.0,   1.0, -1.0,   1.0,  1.0  // Second triangle
+    1.0, 1.0, -1.0, 1.0, -1.0, -1.0, // First triangle
+    -1.0, -1.0, 1.0, -1.0, 1.0, 1.0 // Second triangle
 ]);
 
 export const QuadSchema = {

src/mol-gl/webgl/compat.ts

@@ -339,7 +339,7 @@ void main() {
 }`;
 
 const TextureTestTexCoords = new Float32Array([
-    -1.0, -1.0, 1.0, -1.0, -1.0,  1.0, -1.0,  1.0, 1.0, -1.0, 1.0,  1.0
+    -1.0, -1.0, 1.0, -1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0
 ]);
 
 // adapted from https://stackoverflow.com/questions/28827511/

src/mol-io/common/binary-cif/decoder.ts

@@ -104,8 +104,8 @@ function runLength(data: Int32Array, encoding: Encoding.RunLength) {
     const output = getIntArray(encoding.srcType, encoding.srcSize);
     let dataOffset = 0;
     for (let i = 0, il = data.length; i < il; i += 2) {
-        const value = data[i];  // value to be repeated
-        const length = data[i + 1];  // number of repeats
+        const value = data[i]; // value to be repeated
+        const length = data[i + 1]; // number of repeats
         for (let j = 0; j < length; ++j) {
             output[dataOffset++] = value;
         }

src/mol-io/reader/_spec/mol.spec.ts

@@ -51,7 +51,7 @@ M  END`;
 
 describe('mol reader', () => {
     it('basic', async () => {
-        const parsed =  await parseMol(MolString).run();
+        const parsed = await parseMol(MolString).run();
         if (parsed.isError) {
             throw new Error(parsed.message);
         }

src/mol-io/reader/_spec/mol2.spec.ts

@@ -246,7 +246,7 @@ GASTEIGER
 
 describe('mol2 reader', () => {
     it('basic', async () => {
-        const parsed =  await parseMol2(Mol2String, '').run();
+        const parsed = await parseMol2(Mol2String, '').run();
         if (parsed.isError) {
             throw new Error(parsed.message);
         }
@@ -297,7 +297,7 @@ describe('mol2 reader', () => {
     });
 
     it('multiblocks', async () => {
-        const parsed =  await parseMol2(Mol2StringMultiBlocks, '').run();
+        const parsed = await parseMol2(Mol2StringMultiBlocks, '').run();
         if (parsed.isError) {
             throw new Error(parsed.message);
         }
@@ -348,7 +348,7 @@ describe('mol2 reader', () => {
     });
 
     it('minimal', async () => {
-        const parsed =  await parseMol2(Mol2StringMinimal, '').run();
+        const parsed = await parseMol2(Mol2StringMinimal, '').run();
         if (parsed.isError) {
             throw new Error(parsed.message);
         }

src/mol-io/reader/_spec/sdf.spec.ts

@@ -334,7 +334,7 @@ $$$$
 
 describe('sdf reader', () => {
     it('basic', async () => {
-        const parsed =  await parseSdf(SdfString).run();
+        const parsed = await parseSdf(SdfString).run();
         if (parsed.isError) {
             throw new Error(parsed.message);
         }

src/mol-io/reader/cif/schema.ts

@@ -166,7 +166,7 @@ function flattenFrame(frame: Data.CifFrame): FlatFrame {
     const flatFrame = Object.create(null);
     for (const c of Object.keys(frame.categories)) {
         for (const f of frame.categories[c].fieldNames) {
-            const p =  FieldPath.create(c, f, true);
+            const p = FieldPath.create(c, f, true);
             flatFrame[p] = frame.categories[c].getField(f);
         }
     }

src/mol-io/reader/cif/text/parser.ts

@@ -64,7 +64,7 @@ interface TokenizerState {
 function eatValue(state: TokenizerState) {
     while (state.position < state.length) {
         switch (state.data.charCodeAt(state.position)) {
-            case 9:  // \t
+            case 9: // \t
             case 10: // \n
             case 13: // \r
             case 32: // ' '
@@ -96,7 +96,7 @@ function eatEscaped(state: TokenizerState, esc: number) {
         if (c === esc) {
             next = state.data.charCodeAt(state.position + 1);
             switch (next) {
-                case 9:  // \t
+                case 9: // \t
                 case 10: // \n
                 case 13: // \r
                 case 32: // ' '
@@ -198,7 +198,7 @@ function eatImportGet(state: TokenizerState) {
     // skipWhitespace(state)
     while (state.position < state.length) {
         switch (state.data.charCodeAt(state.position)) {
-            case 93:  // ]
+            case 93: // ]
                 ++state.position;
                 state.tokenEnd = state.position;
                 state.isImportGet = false;

src/mol-io/reader/common/text/column/token.ts

@@ -42,7 +42,7 @@ export function areValuesEqualProvider(tokens: Tokens) {
     return function (rowA: number, rowB: number) {
         const aS = indices[2 * rowA], bS = indices[2 * rowB];
         const len = indices[2 * rowA + 1] - aS;
-        if (len !== indices[2 *  rowB + 1] - bS) return false;
+        if (len !== indices[2 * rowB + 1] - bS) return false;
         for (let i = 0; i < len; i++) {
             if (data.charCodeAt(i + aS) !== data.charCodeAt(i + bS)) {
                 return false;

src/mol-io/reader/common/text/tokenizer.ts

@@ -185,7 +185,7 @@ namespace Tokenizer {
     export function eatValue(state: Tokenizer) {
         while (state.position < state.length) {
             switch (state.data.charCodeAt(state.position)) {
-                case 9:  // \t
+                case 9: // \t
                 case 10: // \n
                 case 13: // \r
                 case 32: // ' '

src/mol-io/reader/csv/parser.ts

@@ -72,13 +72,13 @@ function eatValue(state: Tokenizer, delimiterCharCode: number) {
         const c = state.data.charCodeAt(state.position);
         ++state.position;
         switch (c) {
-            case 10:  // \n
-            case 13:  // \r
+            case 10: // \n
+            case 13: // \r
                 return true;
             case delimiterCharCode:
                 return;
-            case 9:  // \t
-            case 32:  // ' '
+            case 9: // \t
+            case 32: // ' '
                 break;
             default:
                 ++state.tokenEnd;
@@ -120,8 +120,8 @@ function eatQuoted(state: Tokenizer, quoteCharCode: number, delimiterCharCode: n
 function skipEmpty(state: Tokenizer, delimiterCharCode: number) {
     while (state.position < state.length) {
         const c = state.data.charCodeAt(state.position);
-        if (c !== 9 && c !== 32 && c !== delimiterCharCode) {  // \t or ' '
-            return c === 10 || c === 13;  // \n or \r
+        if (c !== 9 && c !== 32 && c !== delimiterCharCode) { // \t or ' '
+            return c === 10 || c === 13; // \n or \r
         }
         ++state.position;
     }
@@ -132,12 +132,12 @@ function skipWhitespace(state: Tokenizer) {
     while (state.position < state.length) {
         const c = state.data.charCodeAt(state.position);
         switch (c) {
-            case 9:  // '\t'
-            case 32:  // ' '
+            case 9: // '\t'
+            case 32: // ' '
                 prev = c;
                 ++state.position;
                 break;
-            case 10:  // \n
+            case 10: // \n
                 // handle \r\n
                 if (prev !== 13) {
                     ++state.lineNumber;
@@ -145,7 +145,7 @@ function skipWhitespace(state: Tokenizer) {
                 prev = c;
                 ++state.position;
                 break;
-            case 13:  // \r
+            case 13: // \r
                 prev = c;
                 ++state.position;
                 ++state.lineNumber;
@@ -159,7 +159,7 @@ function skipWhitespace(state: Tokenizer) {
 function skipLine(state: Tokenizer) {
     while (state.position < state.length) {
         const c = state.data.charCodeAt(state.position);
-        if (c === 10 || c === 13) return;  // \n or \r
+        if (c === 10 || c === 13) return; // \n or \r
         ++state.position;
     }
 }

src/mol-io/reader/psf/parser.ts

@@ -169,8 +169,8 @@ async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<
     const state = State(tokenizer, ctx);
 
     let title = undefined as string[] | undefined;
-    let atoms = undefined  as PsfFile['atoms'] | undefined;
-    let bonds = undefined  as PsfFile['bonds'] | undefined;
+    let atoms = undefined as PsfFile['atoms'] | undefined;
+    let bonds = undefined as PsfFile['bonds'] | undefined;
 
     const id = readLine(state.tokenizer).trim();
 

src/mol-io/writer/cif/encoder.ts

@@ -47,7 +47,7 @@ export namespace Field {
         return { name, type: Type.Str, value, valueKind: params && params.valueKind, defaultFormat: params && params.encoder ? { encoder: params.encoder } : void 0, shouldInclude: params && params.shouldInclude };
     }
 
-    export function int<K, D = any>(name: string, value: (k: K, d: D, index: number) => number, params?:  ParamsBase<K, D> & { typedArray?: ArrayEncoding.TypedArrayCtor }): Field<K, D> {
+    export function int<K, D = any>(name: string, value: (k: K, d: D, index: number) => number, params?: ParamsBase<K, D> & { typedArray?: ArrayEncoding.TypedArrayCtor }): Field<K, D> {
         return {
             name,
             type: Type.Int,
@@ -86,7 +86,7 @@ export namespace Field {
             return this;
         }
 
-        int(name: N, value: (k: K, d: D, index: number) => number, params?:  ParamsBase<K, D> & { typedArray?: ArrayEncoding.TypedArrayCtor }) {
+        int(name: N, value: (k: K, d: D, index: number) => number, params?: ParamsBase<K, D> & { typedArray?: ArrayEncoding.TypedArrayCtor }) {
             this.fields.push(Field.int(name, value, params));
             return this;
         }
@@ -116,7 +116,7 @@ export namespace Field {
         getFields() { return this.fields; }
     }
 
-    export function build<K = number, D = any, N extends string  = string>() {
+    export function build<K = number, D = any, N extends string = string>() {
         return new Builder<K, D, N>();
     }
 }

src/mol-io/writer/cif/encoder/text.ts

@@ -161,7 +161,7 @@ function writeCifLoop(category: Category, instance: Category.Instance, source: C
         if (src.rowCount === 0) continue;
 
         const it = src.keys();
-        while (it.hasNext)  {
+        while (it.hasNext) {
             const key = it.move();
 
             let multiline = false;

src/mol-io/writer/ligand-encoder.ts

@@ -105,7 +105,7 @@ export abstract class LigandEncoder implements Encoder<string> {
             if (src.rowCount === 0) continue;
 
             const it = src.keys();
-            while (it.hasNext)  {
+            while (it.hasNext) {
                 const key = it.move();
 
                 const lai = label_atom_id.value(key, data, index) as string;

src/mol-math/geometry/gaussian-density.ts

@@ -29,7 +29,7 @@ export type GaussianDensityTextureData = {
     resolution: number
 } & DensityTextureData
 
-export function computeGaussianDensity(position: PositionData, box: Box3D, radius: (index: number) => number,  props: GaussianDensityProps) {
+export function computeGaussianDensity(position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps) {
     return Task.create('Gaussian Density', async ctx => {
         return await GaussianDensityCPU(ctx, position, box, radius, props);
     });

src/mol-math/geometry/gaussian-density/cpu.ts

@@ -12,7 +12,7 @@ import { OrderedSet } from '../../../mol-data/int';
 import { GaussianDensityProps, GaussianDensityData } from '../gaussian-density';
 import { fasterExp } from '../../approx';
 
-export async function GaussianDensityCPU(ctx: RuntimeContext, position: PositionData, box: Box3D, radius: (index: number) => number,  props: GaussianDensityProps): Promise<GaussianDensityData> {
+export async function GaussianDensityCPU(ctx: RuntimeContext, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps): Promise<GaussianDensityData> {
     const { resolution, radiusOffset, smoothness } = props;
     const scaleFactor = 1 / resolution;
 

src/mol-math/geometry/gaussian-density/gpu.ts

@@ -361,7 +361,7 @@ function createGaussianDensityRenderable(webgl: WebGLContext, drawCount: number,
 
     const schema = { ...GaussianDensitySchema };
     const shaderCode = ShaderCode(GaussianDensityName, gaussianDensity_vert, gaussianDensity_frag);
-    const renderItem =  createComputeRenderItem(webgl, 'points', shaderCode, schema, values);
+    const renderItem = createComputeRenderItem(webgl, 'points', shaderCode, schema, values);
 
     return createComputeRenderable(renderItem, values);
 }
@@ -461,7 +461,7 @@ function fieldFromTexture2d(ctx: WebGLContext, texture: Texture, dim: Vec3, texD
         for (let iy = 0; iy < dy; ++iy) {
             for (let ix = 0; ix < dx; ++ix) {
                 const idx = 4 * (tmpCol * dx + (iy + tmpRow) * width + ix);
-                data[j] = image[idx + 3]  / 255;
+                data[j] = image[idx + 3] / 255;
                 idData[j] = decodeFloatRGB(image[idx], image[idx + 1], image[idx + 2]);
                 j++;
             }

src/mol-math/geometry/spacegroup/construction.ts

@@ -120,7 +120,7 @@ namespace Spacegroup {
      */
     export function getSymmetryOperatorRef(spacegroup: Spacegroup, spgrOp: number, i: number, j: number, k: number, ref: Vec3) {
 
-        const operator =  Mat4.zero();
+        const operator = Mat4.zero();
 
         Vec3.set(_ijkVec, i, j, k);
         Vec3.floor(_translationRef, ref);

src/mol-math/geometry/spacegroup/tables.ts

@@ -971,12 +971,12 @@ export const GroupData = [
     [0, 52, 16, 1, 26, 59, 20, 65],
     [0, 31, 1, 63],
     [0, 1, 24, 62],
-    [0, 15, 1, 9],  // 'P 1 21/n 1'
+    [0, 15, 1, 9], // 'P 1 21/n 1'
     // X,Y,Z
     // -X+1/2,Y+1/2,-Z+1/2
     // -X,-Y,-Z
     // X+1/2,-Y+1/2,Z+1/2
-    [0, 5, 1, 8],  // 'P 1 21/a 1'
+    [0, 5, 1, 8], // 'P 1 21/a 1'
     // X,Y,Z
     // -X+1/2,Y+1/2,-Z
     // -X,-Y,-Z
@@ -1357,37 +1357,37 @@ export function getSpacegroupIndexFromNumber(num: number) {
         case 1166: return 171;
         case 1167: return 173;
 
-        case 1003: return 237;  // 'P 1 1 2'  !(dyad along z)
-        case 1004: return 238;  // 'P 1 1 21'  !(unique axis c)
-        case 1005: return 239;  // 'B 1 1 2' 'B 2'
-        case 2005: return 240;  // 'A 1 2 1'
-        case 3005: return 241;  // 'C 1 21 1' ! (Origin on screw at 1/4X)
-        case 4005: return 242;  // 'I 1 2 1' 'I 2' !!! GJK @ 2003-06-02
-        case 5005: return 243;  // 'I 1 21 1'
-        case 1006: return 244;  // 'P 1 1 m'
-        case 1007: return 245;  // 'P 1 1 b'
-        case 1008: return 246;  // 'B 1 1 m'
-        case 1009: return 247;  // 'B 1 1 b'
-        case 1010: return 248;  // 'P 1 1 2/m'
-        case 1011: return 249;  // 'P 1 1 21/m'
-        case 1012: return 250;  // 'B 1 1 2/m'
-        case 1013: return 251;  // 'P 1 1 2/b'
-        case 1014: return 252;  // 'P 1 1 21/b'
-        case 2014: return 253;  // 'P 1 21/n 1'
-        case 3014: return 254;  // 'P 1 21/a 1'
-        case 1015: return 255;  // 'B 1 1 2/b'
-        case 1017: return 256;  // 'P 21 2 2' !(unique axis a)
-        case 2017: return 257;  // 'P 2 21 2' !(unique axis b)
-        case 1018: return 258;  // 'P 21 21 2 (a)' ! origin on 21 21, shift (1/4,1/4,0)
-        case 2018: return 259;  // 'P 21 2 21'  !(unique axis b)
-        case 3018: return 260;  // 'P 2 21 21'  !(unique axis a)
-        case 1020: return 261;  // 'C 2 2 21a)' ! P212121 with C centring, shift(1/4,0,0)
-        case 1021: return 262;  // 'C 2 2 2a'  ! C21212a origin on 21 21
-        case 1022: return 263;  // 'F 2 2 2a' ! same as 1018 with face centring  shift (1/4,0,0)
-        case 1023: return 264;  // 'I 2 2 2a'  ! as 1018 with origin shift (1/4,1/4,1/4)
-        case 1059: return 265;  // 'P 21/m 21/m 2/n a'
-        case 1094: return 266;  // 'P 42 21 2a' ! (as P21212a) origin on 21 21 ie Shift 1/4,1/4,1/4
-        case 1197: return 267;  // 'I 2 3a' ! Expansion of 1023 which is an expansion of 1018
+        case 1003: return 237; // 'P 1 1 2'  !(dyad along z)
+        case 1004: return 238; // 'P 1 1 21'  !(unique axis c)
+        case 1005: return 239; // 'B 1 1 2' 'B 2'
+        case 2005: return 240; // 'A 1 2 1'
+        case 3005: return 241; // 'C 1 21 1' ! (Origin on screw at 1/4X)
+        case 4005: return 242; // 'I 1 2 1' 'I 2' !!! GJK @ 2003-06-02
+        case 5005: return 243; // 'I 1 21 1'
+        case 1006: return 244; // 'P 1 1 m'
+        case 1007: return 245; // 'P 1 1 b'
+        case 1008: return 246; // 'B 1 1 m'
+        case 1009: return 247; // 'B 1 1 b'
+        case 1010: return 248; // 'P 1 1 2/m'
+        case 1011: return 249; // 'P 1 1 21/m'
+        case 1012: return 250; // 'B 1 1 2/m'
+        case 1013: return 251; // 'P 1 1 2/b'
+        case 1014: return 252; // 'P 1 1 21/b'
+        case 2014: return 253; // 'P 1 21/n 1'
+        case 3014: return 254; // 'P 1 21/a 1'
+        case 1015: return 255; // 'B 1 1 2/b'
+        case 1017: return 256; // 'P 21 2 2' !(unique axis a)
+        case 2017: return 257; // 'P 2 21 2' !(unique axis b)
+        case 1018: return 258; // 'P 21 21 2 (a)' ! origin on 21 21, shift (1/4,1/4,0)
+        case 2018: return 259; // 'P 21 2 21'  !(unique axis b)
+        case 3018: return 260; // 'P 2 21 21'  !(unique axis a)
+        case 1020: return 261; // 'C 2 2 21a)' ! P212121 with C centring, shift(1/4,0,0)
+        case 1021: return 262; // 'C 2 2 2a'  ! C21212a origin on 21 21
+        case 1022: return 263; // 'F 2 2 2a' ! same as 1018 with face centring  shift (1/4,0,0)
+        case 1023: return 264; // 'I 2 2 2a'  ! as 1018 with origin shift (1/4,1/4,1/4)
+        case 1059: return 265; // 'P 21/m 21/m 2/n a'
+        case 1094: return 266; // 'P 42 21 2a' ! (as P21212a) origin on 21 21 ie Shift 1/4,1/4,1/4
+        case 1197: return 267; // 'I 2 3a' ! Expansion of 1023 which is an expansion of 1018
     }
 
     let offset = 0;

src/mol-math/linear-algebra/3d/quat.ts

@@ -193,8 +193,8 @@ namespace Quat {
         // calculate coefficients
         if ((1.0 - cosom) > 0.000001) {
             // standard case (slerp)
-            omega  = Math.acos(cosom);
-            sinom  = Math.sin(omega);
+            omega = Math.acos(cosom);
+            sinom = Math.sin(omega);
             scale0 = Math.sin((1.0 - t) * omega) / sinom;
             scale1 = Math.sin(t * omega) / sinom;
         } else {
@@ -252,9 +252,9 @@ namespace Quat {
 
         if (fTrace > 0.0) {
             // |w| > 1/2, may as well choose w > 1/2
-            fRoot = Math.sqrt(fTrace + 1.0);  // 2w
+            fRoot = Math.sqrt(fTrace + 1.0); // 2w
             out[3] = 0.5 * fRoot;
-            fRoot = 0.5 / fRoot;  // 1/(4w)
+            fRoot = 0.5 / fRoot; // 1/(4w)
             out[0] = (m[5] - m[7]) * fRoot;
             out[1] = (m[6] - m[2]) * fRoot;
             out[2] = (m[1] - m[3]) * fRoot;

src/mol-math/misc.ts

@@ -8,11 +8,11 @@ export const halfPI = Math.PI / 2;
 export const PiDiv180 = Math.PI / 180;
 
 export function degToRad(deg: number) {
-    return deg * PiDiv180;  // deg * Math.PI / 180
+    return deg * PiDiv180; // deg * Math.PI / 180
 }
 
 export function radToDeg(rad: number) {
-    return rad / PiDiv180;  // rad * 180 / Math.PI
+    return rad / PiDiv180; // rad * 180 / Math.PI
 }
 
 export function isPowerOfTwo(x: number) {

src/mol-model-formats/shape/ply.ts

@@ -186,7 +186,7 @@ function getGrouping(vertex: PlyTable, props: PD.Values<PlyShapeParams>): Groupi
     const maxId = column ? arrayMax(ids) : rowCount - 1; // assumes uint ids
     const map = new Uint32Array(maxId + 1);
     for (let i = 0, il = ids.length; i < il; ++i) map[ids[i]] = i;
-    return { ids, map, label  };
+    return { ids, map, label };
 }
 
 type Coloring = { kind: 'vertex' | 'material' | 'uniform', red: Column<number>, green: Column<number>, blue: Column<number> }

src/mol-model-formats/structure/basic/properties.ts

@@ -77,7 +77,7 @@ function getSaccharideComponentMap(data: BasicData): SaccharideComponentMap {
     }
 
     if (data.chem_comp._rowCount > 0) {
-        const { id, type  } = data.chem_comp;
+        const { id, type } = data.chem_comp;
         for (let i = 0, il = id.rowCount; i < il; ++i) {
             const _id = id.value(i);
             if (map.has(_id)) continue;

src/mol-model-formats/structure/util.ts

@@ -25,22 +25,22 @@ export function guessElementSymbolTokens(tokens: Tokens, str: string, start: num
     if (s + 2 === e) { // two chars
         const c2 = str.charCodeAt(s + 1);
         if (
-            ((c === 78 || c === 110) && (c2 === 65 || c2 ===  97)) || // NA na Na nA
-            ((c === 67 || c ===  99) && (c2 === 76 || c2 === 108)) || // CL
+            ((c === 78 || c === 110) && (c2 === 65 || c2 === 97)) || // NA na Na nA
+            ((c === 67 || c === 99) && (c2 === 76 || c2 === 108)) || // CL
             ((c === 70 || c === 102) && (c2 === 69 || c2 === 101)) || // FE
             ((c === 83 || c === 115) && (c2 === 73 || c2 === 105)) || // SI
-            ((c === 66 || c === 98) && (c2 === 82 || c2 === 114)) ||  // BR
-            ((c === 65 || c === 97) && (c2 === 83 || c2 === 115))     // AS
+            ((c === 66 || c === 98) && (c2 === 82 || c2 === 114)) || // BR
+            ((c === 65 || c === 97) && (c2 === 83 || c2 === 115)) // AS
         ) return TokenBuilder.add(tokens, s, s + 2);
     }
 
     if (
-        c === 67 || c ===  99 || // C c
+        c === 67 || c === 99 || // C c
         c === 72 || c === 104 || // H h
         c === 78 || c === 110 || // N n
         c === 79 || c === 111 || // O o
         c === 80 || c === 112 || // P p
-        c === 83 || c === 115    // S s
+        c === 83 || c === 115 // S s
     ) return TokenBuilder.add(tokens, s, s + 1);
 
     TokenBuilder.add(tokens, s, s); // no reasonable guess, add empty token

src/mol-model-props/computed/accessible-surface-area/shrake-rupley/common.ts

@@ -32,7 +32,7 @@ export const VdWLookup = [
     1.85, // 6: S
     1.80, // 7: C (nucleic)
     1.60, // 8: N (nucleic)
-    1.40  // 9: P (nucleic)
+    1.40 // 9: P (nucleic)
 ]; // can still be appended on-the-fly for rare elements like selenium
 
 /** Maximum accessible surface area observed for amino acids. Taken from: http://dx.doi.org/10.1371/journal.pone.0080635 */

src/mol-model-props/computed/interactions/charged.ts

@@ -311,9 +311,9 @@ function testPiStacking(structure: Structure, infoA: Features.Info, infoB: Featu
         const offset = Math.min(getOffset(infoA, infoB, tmpNormalB), getOffset(infoB, infoA, tmpNormalA));
         if (offset <= opts.offsetMax) {
             if (angle <= opts.angleDevMax || angle >= deg180InRad - opts.angleDevMax) {
-                return InteractionType.PiStacking;  // parallel
+                return InteractionType.PiStacking; // parallel
             } else if (angle <= opts.angleDevMax + deg90InRad && angle >= deg90InRad - opts.angleDevMax) {
-                return InteractionType.PiStacking;  // t-shaped
+                return InteractionType.PiStacking; // t-shaped
             }
         }
     }

src/mol-model-props/computed/interactions/halogen-bonds.ts

@@ -76,7 +76,7 @@ function isHalogenBond(ti: FeatureType, tj: FeatureType) {
 }
 
 // http://www.pnas.org/content/101/48/16789.full
-const OptimalHalogenAngle = degToRad(180);  // adjusted from 165 to account for spherical statistics
+const OptimalHalogenAngle = degToRad(180); // adjusted from 165 to account for spherical statistics
 const OptimalAcceptorAngle = degToRad(120);
 
 function getOptions(props: HalogenBondsProps) {

src/mol-model-props/computed/interactions/hydrogen-bonds.ts

@@ -227,8 +227,8 @@ function getHydrogenBondsOptions(props: HydrogenBondsProps) {
     return {
         ...getGeometryOptions(props),
         includeWater: props.water,
-        maxSulfurDistSq: props.sulfurDistanceMax *  props.sulfurDistanceMax,
-        maxDistSq: props.distanceMax *  props.distanceMax
+        maxSulfurDistSq: props.sulfurDistanceMax * props.sulfurDistanceMax,
+        maxDistSq: props.distanceMax * props.distanceMax
     };
 }
 type HydrogenBondsOptions = ReturnType<typeof getHydrogenBondsOptions>

src/mol-model/sequence/alignment/alignment.ts

@@ -103,7 +103,7 @@ class Alignment {
                 Si[j] = Math.max(
                     Si1[j - 1] + scoreFn(i - 1, j - 1), // match
                     Vi[j], // del
-                    Hi[j]  // ins
+                    Hi[j] // ins
                 );
             }
         }

src/mol-model/sequence/alignment/substitution-matrix.ts

@@ -10,26 +10,26 @@ const aminoacidsX = 'ACDEFGHIKLMNPQRSTVWY';
 const aminoacids = 'ARNDCQEGHILKMFPSTWYVBZX';
 
 const blosum62x = [
-    [4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -1, -1, -1, 1, 0, 0, -3, -2],        // A
-    [0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -2],    // C
-    [-2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, -1, -3, -4, -3],       // D
-    [-1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, -1, -2, -3, -2],          // E
-    [-2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2, -1, 1, 3],        // F
-    [0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -2, -2, -2, 0, -2, -3, -2, -3],      // G
-    [-2, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, -2, -3, -2, 2],        // H
-    [-1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -1, 3, -3, -1],       // I
-    [-1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, -1, -2, -3, -2],        // K
-    [-1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -1, 1, -2, -1],       // L
-    [-1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1, 1, -1, -1],        // M
-    [-2, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -2],            // N
-    [-1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, -2, -1, -1, -2, -4, -3],   // P
-    [-1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, -1, -2, -2, -1],           // Q
-    [-1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3, -3, -2],        // R
-    [1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2, -3, -2],           // S
-    [0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, 0, -2, -2],       // T
-    [0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, -3, -1],        // V
-    [-3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, 2],    // W
-    [-2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, 7]       // Y
+    [4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -1, -1, -1, 1, 0, 0, -3, -2], // A
+    [0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -2], // C
+    [-2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, -1, -3, -4, -3], // D
+    [-1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, -1, -2, -3, -2], // E
+    [-2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2, -1, 1, 3], // F
+    [0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -2, -2, -2, 0, -2, -3, -2, -3], // G
+    [-2, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, -2, -3, -2, 2], // H
+    [-1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -1, 3, -3, -1], // I
+    [-1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, -1, -2, -3, -2], // K
+    [-1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -1, 1, -2, -1], // L
+    [-1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1, 1, -1, -1], // M
+    [-2, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -2], // N
+    [-1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, -2, -1, -1, -2, -4, -3], // P
+    [-1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, -1, -2, -2, -1], // Q
+    [-1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3, -3, -2], // R
+    [1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2, -3, -2], // S
+    [0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, 0, -2, -2], // T
+    [0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, -3, -1], // V
+    [-3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, 2], // W
+    [-2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, 7] // Y
 ];
 
 const blosum62 = [
@@ -56,7 +56,7 @@ const blosum62 = [
     [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1], // V
     [-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1], // B
     [-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1], // Z
-    [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1]  // X
+    [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1] // X
 ];
 
 export type SubstitutionMatrixData = Readonly<{ [k: string]: Readonly<{ [k: string]: number }> }>;

src/mol-model/sequence/constants.ts

@@ -15,7 +15,7 @@ export type NuclecicAlphabet =
     | '-' /** = Gap */
 
 // from NGL
-const ProteinOneLetterCodes: { [name: string]: AminoAlphabet }  = {
+const ProteinOneLetterCodes: { [name: string]: AminoAlphabet } = {
     'HIS': 'H',
     'ARG': 'R',
     'LYS': 'K',
@@ -37,8 +37,8 @@ const ProteinOneLetterCodes: { [name: string]: AminoAlphabet }  = {
     'GLU': 'E',
     'THR': 'T',
 
-    'SEC': 'U',  // as per IUPAC definition
-    'PYL': 'O',  // as per IUPAC definition
+    'SEC': 'U', // as per IUPAC definition
+    'PYL': 'O', // as per IUPAC definition
 
     // charmm ff
     'HSD': 'H', 'HSE': 'H', 'HSP': 'H',

src/mol-model/structure/export/categories/atom_site.ts

@@ -53,7 +53,7 @@ const atom_site_fields = () => CifWriter.fields<StructureElement.Location, Struc
     .float('B_iso_or_equiv', P.atom.B_iso_or_equiv, { digitCount: 2, encoder: E.fixedPoint2 })
     .int('pdbx_formal_charge', P.atom.pdbx_formal_charge, {
         encoder: E.deltaRLE,
-        valueKind: (k, d) =>  k.unit.model.atomicHierarchy.atoms.pdbx_formal_charge.valueKind(k.element)
+        valueKind: (k, d) => k.unit.model.atomicHierarchy.atoms.pdbx_formal_charge.valueKind(k.element)
     })
 
     .str('auth_atom_id', P.atom.auth_atom_id)

src/mol-model/structure/model/properties/atomic/measures.ts

@@ -19,8 +19,8 @@ export const ElementAtomWeights: { [e: number]: number | undefined } = {
     1: 1.008, 2: 4.0026, 3: 6.94, 4: 9.0122, 5: 10.81, 6: 10.81, 7: 14.007, 8: 15.999, 9: 18.998, 10: 20.180, 11: 22.990, 12: 24.305, 13: 26.982, 14: 28.085, 15: 30.974, 16: 32.06, 17: 35.45, 18: 39.948, 19: 39.098, 20: 40.078, 21: 44.956, 22: 47.867, 23: 50.942, 24: 51.996, 25: 54.938, 26: 55.845, 27: 58.933, 28: 58.693, 29: 63.546, 30: 65.38, 31: 69.723, 32: 72.630, 33: 74.922, 34: 78.971, 35: 79.904, 36: 83.798, 37: 85.468, 38: 87.62, 39: 88.906, 40: 91.224, 41: 92.906, 42: 95.95, 43: 96.906, 44: 101.07, 45: 102.91, 46: 106.42, 47: 107.87, 48: 112.41, 49: 114.82, 50: 118.71, 51: 121.76, 52: 127.60, 53: 127.60, 54: 131.29, 55: 132.91, 56: 137.33, 57: 138.91, 58: 140.12, 59: 140.91, 60: 144.24, 61: 144.912, 62: 150.36, 63: 151.96, 64: 157.25, 65: 158.93, 66: 162.50, 67: 164.93, 68: 167.26, 69: 168.93, 70: 173.05, 71: 174.97, 72: 178.49, 73: 180.95, 74: 183.84, 75: 186.21, 76: 190.23, 77: 192.22, 78: 195.08, 79: 196.97, 80: 200.59, 81: 204.38, 82: 207.2, 83: 208.98, 84: 1.97, 85: 2.02, 86: 2.2, 87: 3.48, 88: 2.83, 89: 2.0, 90: 232.04, 91: 231.04, 92: 238.03, 93: 237.048, 94: 244.064, 95: 243.061, 96: 247.070, 97: 247.070, 98: 251.079, 99: 252.083, 100: 257.095, 101: 258.098, 102: 259.101, 103: 262.110, 104: 267.122, 105: 270.131, 106: 271.134, 107: 270.133, 108: 270.134, 109: 278.156
 };
 
-export const DefaultVdwRadius = 1.7;  // C
-export const DefaultAtomWeight = 10.81;  // C
+export const DefaultVdwRadius = 1.7; // C
+export const DefaultAtomWeight = 10.81; // C
 export const DefaultAtomNumber = 0;
 
 export function VdwRadius(element: ElementSymbol): number {

src/mol-model/structure/model/properties/utils/coarse-keys.ts

@@ -44,7 +44,7 @@ function createLookUp(entities: Entities, chain: Map<number, Map<string, number>
         const sm = seq.get(cKey)!;
         const { elementIndices, seqRanges } = sm;
         const idx = SortedRanges.firstIntersectionIndex(seqRanges, OrderedSet.ofSingleton(s));
-        return (idx !== -1 ? elementIndices[idx] : -1)  as ElementIndex;
+        return (idx !== -1 ? elementIndices[idx] : -1) as ElementIndex;
     };
     return { findChainKey, findSequenceKey };
 }

src/mol-model/structure/model/types.ts

@@ -458,14 +458,14 @@ export namespace SecondaryStructureType {
         Turn = 0x10,
 
         // category variant
-        LeftHanded = 0x20,  // helix
+        LeftHanded = 0x20, // helix
         RightHanded = 0x40,
 
-        ClassicTurn = 0x80,  // turn
+        ClassicTurn = 0x80, // turn
         InverseTurn = 0x100,
 
         // sub-category
-        HelixOther = 0x200,  // protein
+        HelixOther = 0x200, // protein
         Helix27 = 0x400,
         Helix3Ten = 0x800,
         HelixAlpha = 0x1000,
@@ -474,99 +474,99 @@ export namespace SecondaryStructureType {
         HelixPi = 0x8000,
         HelixPolyproline = 0x10000,
 
-        DoubleHelixOther = 0x20000,  // nucleic
+        DoubleHelixOther = 0x20000, // nucleic
         DoubleHelixZ = 0x40000,
         DoubleHelixA = 0x80000,
         DoubleHelixB = 0x100000,
 
-        BetaOther = 0x200000,  // protein
-        BetaStrand = 0x400000,  // single strand
-        BetaSheet = 0x800000,  // multiple hydrogen bonded strands
-        BetaBarell = 0x1000000,  // closed series of sheets
+        BetaOther = 0x200000, // protein
+        BetaStrand = 0x400000, // single strand
+        BetaSheet = 0x800000, // multiple hydrogen bonded strands
+        BetaBarell = 0x1000000, // closed series of sheets
 
-        TurnOther = 0x2000000,  // protein
+        TurnOther = 0x2000000, // protein
         Turn1 = 0x4000000,
         Turn2 = 0x8000000,
         Turn3 = 0x10000000,
 
-        NA = 0x20000000,  // not applicable/available
+        NA = 0x20000000, // not applicable/available
     }
 
     export const SecondaryStructureMmcif: { [value: string]: number } = {
-        HELX_LH_27_P: Flag.Helix | Flag.LeftHanded | Flag.Helix27,  // left-handed 2-7 helix (protein)
-        HELX_LH_3T_P: Flag.Helix | Flag.LeftHanded | Flag.Helix3Ten,  // left-handed 3-10 helix (protein)
-        HELX_LH_AL_P: Flag.Helix | Flag.LeftHanded | Flag.HelixAlpha,  // left-handed alpha helix (protein)
-        HELX_LH_A_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixA,  // left-handed A helix (nucleic acid)
-        HELX_LH_B_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixB,  // left-handed B helix (nucleic acid)
-        HELX_LH_GA_P: Flag.Helix | Flag.LeftHanded | Flag.HelixGamma,  // left-handed gamma helix (protein)
-        HELX_LH_N: Flag.DoubleHelix | Flag.LeftHanded,  // left-handed helix with type not specified (nucleic acid)
-        HELX_LH_OM_P: Flag.Helix | Flag.LeftHanded | Flag.HelixOmega,  // left-handed omega helix (protein)
-        HELX_LH_OT_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixOther,  // left-handed helix with type that does not conform to an accepted category (nucleic acid)
-        HELX_LH_OT_P: Flag.Helix | Flag.LeftHanded | Flag.HelixOther,  // left-handed helix with type that does not conform to an accepted category (protein)
-        HELX_LH_P: Flag.Helix | Flag.LeftHanded,  // left-handed helix with type not specified (protein)
-        HELX_LH_PI_P: Flag.Helix | Flag.LeftHanded | Flag.HelixPi,  // left-handed pi helix (protein)
-        HELX_LH_PP_P: Flag.Helix | Flag.LeftHanded | Flag.HelixPolyproline,  // left-handed polyproline helix (protein)
-        HELX_LH_Z_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixZ,  // left-handed Z helix (nucleic acid)
-        HELX_N: Flag.DoubleHelix,  // helix with handedness and type not specified (nucleic acid)
-        HELX_OT_N: Flag.DoubleHelix,  // helix with handedness and type that do not conform to an accepted category (nucleic acid)
-        HELX_OT_P: Flag.Helix,  // helix with handedness and type that do not conform to an accepted category (protein)
-        HELX_P: Flag.Helix,  // helix with handedness and type not specified (protein)
-        HELX_RH_27_P: Flag.Helix | Flag.RightHanded | Flag.Helix27,  // right-handed 2-7 helix (protein)
-        HELX_RH_3T_P: Flag.Helix | Flag.RightHanded | Flag.Helix3Ten,  // right-handed 3-10 helix (protein)
-        HELX_RH_AL_P: Flag.Helix | Flag.RightHanded | Flag.HelixAlpha,  // right-handed alpha helix (protein)
-        HELX_RH_A_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixA,  // right-handed A helix (nucleic acid)
-        HELX_RH_B_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixB,  // right-handed B helix (nucleic acid)
-        HELX_RH_GA_P: Flag.Helix | Flag.RightHanded | Flag.HelixGamma,  // right-handed gamma helix (protein)
-        HELX_RH_N: Flag.DoubleHelix | Flag.RightHanded,  // right-handed helix with type not specified (nucleic acid)
-        HELX_RH_OM_P: Flag.Helix | Flag.RightHanded | Flag.HelixOmega,  // right-handed omega helix (protein)
-        HELX_RH_OT_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixOther,  // right-handed helix with type that does not conform to an accepted category (nucleic acid)
-        HELX_RH_OT_P: Flag.Helix | Flag.RightHanded | Flag.HelixOther,  // right-handed helix with type that does not conform to an accepted category (protein)
-        HELX_RH_P: Flag.Helix | Flag.RightHanded,  // right-handed helix with type not specified (protein)
-        HELX_RH_PI_P: Flag.Helix | Flag.RightHanded | Flag.HelixPi,  // right-handed pi helix (protein)
-        HELX_RH_PP_P: Flag.Helix | Flag.RightHanded | Flag.HelixPolyproline,  // right-handed polyproline helix (protein)
-        HELX_RH_Z_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixZ,  // right-handed Z helix (nucleic acid)
-        STRN: Flag.Beta | Flag.BetaStrand,  // beta strand (protein)
-        TURN_OT_P: Flag.Turn | Flag.TurnOther,  // turn with type that does not conform to an accepted category (protein)
-        TURN_P: Flag.Turn,  // turn with type not specified (protein)
-        TURN_TY1P_P: Flag.Turn | Flag.InverseTurn | Flag.Turn1,  // type I prime turn (protein)
-        TURN_TY1_P: Flag.Turn | Flag.ClassicTurn | Flag.Turn1,  // type I turn (protein)
-        TURN_TY2P_P: Flag.Turn | Flag.InverseTurn | Flag.Turn2,  // type II prime turn (protein)
-        TURN_TY2_P: Flag.Turn | Flag.ClassicTurn | Flag.Turn2,  // type II turn (protein)
-        TURN_TY3P_P: Flag.Turn | Flag.InverseTurn | Flag.Turn3,  // type III prime turn (protein)
-        TURN_TY3_P: Flag.Turn | Flag.ClassicTurn | Flag.Turn3,  // type III turn (protein)
+        HELX_LH_27_P: Flag.Helix | Flag.LeftHanded | Flag.Helix27, // left-handed 2-7 helix (protein)
+        HELX_LH_3T_P: Flag.Helix | Flag.LeftHanded | Flag.Helix3Ten, // left-handed 3-10 helix (protein)
+        HELX_LH_AL_P: Flag.Helix | Flag.LeftHanded | Flag.HelixAlpha, // left-handed alpha helix (protein)
+        HELX_LH_A_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixA, // left-handed A helix (nucleic acid)
+        HELX_LH_B_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixB, // left-handed B helix (nucleic acid)
+        HELX_LH_GA_P: Flag.Helix | Flag.LeftHanded | Flag.HelixGamma, // left-handed gamma helix (protein)
+        HELX_LH_N: Flag.DoubleHelix | Flag.LeftHanded, // left-handed helix with type not specified (nucleic acid)
+        HELX_LH_OM_P: Flag.Helix | Flag.LeftHanded | Flag.HelixOmega, // left-handed omega helix (protein)
+        HELX_LH_OT_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixOther, // left-handed helix with type that does not conform to an accepted category (nucleic acid)
+        HELX_LH_OT_P: Flag.Helix | Flag.LeftHanded | Flag.HelixOther, // left-handed helix with type that does not conform to an accepted category (protein)
+        HELX_LH_P: Flag.Helix | Flag.LeftHanded, // left-handed helix with type not specified (protein)
+        HELX_LH_PI_P: Flag.Helix | Flag.LeftHanded | Flag.HelixPi, // left-handed pi helix (protein)
+        HELX_LH_PP_P: Flag.Helix | Flag.LeftHanded | Flag.HelixPolyproline, // left-handed polyproline helix (protein)
+        HELX_LH_Z_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixZ, // left-handed Z helix (nucleic acid)
+        HELX_N: Flag.DoubleHelix, // helix with handedness and type not specified (nucleic acid)
+        HELX_OT_N: Flag.DoubleHelix, // helix with handedness and type that do not conform to an accepted category (nucleic acid)
+        HELX_OT_P: Flag.Helix, // helix with handedness and type that do not conform to an accepted category (protein)
+        HELX_P: Flag.Helix, // helix with handedness and type not specified (protein)
+        HELX_RH_27_P: Flag.Helix | Flag.RightHanded | Flag.Helix27, // right-handed 2-7 helix (protein)
+        HELX_RH_3T_P: Flag.Helix | Flag.RightHanded | Flag.Helix3Ten, // right-handed 3-10 helix (protein)
+        HELX_RH_AL_P: Flag.Helix | Flag.RightHanded | Flag.HelixAlpha, // right-handed alpha helix (protein)
+        HELX_RH_A_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixA, // right-handed A helix (nucleic acid)
+        HELX_RH_B_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixB, // right-handed B helix (nucleic acid)
+        HELX_RH_GA_P: Flag.Helix | Flag.RightHanded | Flag.HelixGamma, // right-handed gamma helix (protein)
+        HELX_RH_N: Flag.DoubleHelix | Flag.RightHanded, // right-handed helix with type not specified (nucleic acid)
+        HELX_RH_OM_P: Flag.Helix | Flag.RightHanded | Flag.HelixOmega, // right-handed omega helix (protein)
+        HELX_RH_OT_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixOther, // right-handed helix with type that does not conform to an accepted category (nucleic acid)
+        HELX_RH_OT_P: Flag.Helix | Flag.RightHanded | Flag.HelixOther, // right-handed helix with type that does not conform to an accepted category (protein)
+        HELX_RH_P: Flag.Helix | Flag.RightHanded, // right-handed helix with type not specified (protein)
+        HELX_RH_PI_P: Flag.Helix | Flag.RightHanded | Flag.HelixPi, // right-handed pi helix (protein)
+        HELX_RH_PP_P: Flag.Helix | Flag.RightHanded | Flag.HelixPolyproline, // right-handed polyproline helix (protein)
+        HELX_RH_Z_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixZ, // right-handed Z helix (nucleic acid)
+        STRN: Flag.Beta | Flag.BetaStrand, // beta strand (protein)
+        TURN_OT_P: Flag.Turn | Flag.TurnOther, // turn with type that does not conform to an accepted category (protein)
+        TURN_P: Flag.Turn, // turn with type not specified (protein)
+        TURN_TY1P_P: Flag.Turn | Flag.InverseTurn | Flag.Turn1, // type I prime turn (protein)
+        TURN_TY1_P: Flag.Turn | Flag.ClassicTurn | Flag.Turn1, // type I turn (protein)
+        TURN_TY2P_P: Flag.Turn | Flag.InverseTurn | Flag.Turn2, // type II prime turn (protein)
+        TURN_TY2_P: Flag.Turn | Flag.ClassicTurn | Flag.Turn2, // type II turn (protein)
+        TURN_TY3P_P: Flag.Turn | Flag.InverseTurn | Flag.Turn3, // type III prime turn (protein)
+        TURN_TY3_P: Flag.Turn | Flag.ClassicTurn | Flag.Turn3, // type III turn (protein)
     };
 
     export const SecondaryStructurePdb: { [value: string]: number } = {
-        1: Flag.Helix | Flag.RightHanded | Flag.HelixAlpha,  // Right-handed alpha (default)
-        2: Flag.Helix | Flag.RightHanded | Flag.HelixOmega,  // Right-handed omega
-        3: Flag.Helix | Flag.RightHanded | Flag.HelixPi,  // Right-handed pi
-        4: Flag.Helix | Flag.RightHanded | Flag.HelixGamma,  // Right-handed gamma
-        5: Flag.Helix | Flag.RightHanded | Flag.Helix3Ten,  // Right-handed 310
-        6: Flag.Helix | Flag.LeftHanded | Flag.HelixAlpha,  // Left-handed alpha
-        7: Flag.Helix | Flag.LeftHanded | Flag.HelixOmega,  // Left-handed omega
-        8: Flag.Helix | Flag.LeftHanded | Flag.HelixGamma,  // Left-handed gamma
-        9: Flag.Helix | Flag.Helix27,  // 27 ribbon/helix
-        10: Flag.Helix | Flag.HelixPolyproline,  // Polyproline
+        1: Flag.Helix | Flag.RightHanded | Flag.HelixAlpha, // Right-handed alpha (default)
+        2: Flag.Helix | Flag.RightHanded | Flag.HelixOmega, // Right-handed omega
+        3: Flag.Helix | Flag.RightHanded | Flag.HelixPi, // Right-handed pi
+        4: Flag.Helix | Flag.RightHanded | Flag.HelixGamma, // Right-handed gamma
+        5: Flag.Helix | Flag.RightHanded | Flag.Helix3Ten, // Right-handed 310
+        6: Flag.Helix | Flag.LeftHanded | Flag.HelixAlpha, // Left-handed alpha
+        7: Flag.Helix | Flag.LeftHanded | Flag.HelixOmega, // Left-handed omega
+        8: Flag.Helix | Flag.LeftHanded | Flag.HelixGamma, // Left-handed gamma
+        9: Flag.Helix | Flag.Helix27, // 27 ribbon/helix
+        10: Flag.Helix | Flag.HelixPolyproline, // Polyproline
     };
 
     export const SecondaryStructureStride: { [value: string]: number } = {
-        H: Flag.Helix | Flag.HelixAlpha,  // Alpha helix
-        G: Flag.Helix | Flag.Helix3Ten,  // 3-10 helix
-        I: Flag.Helix | Flag.HelixPi,  // PI-helix
-        E: Flag.Beta | Flag.BetaSheet,  // Extended conformation
-        B: Flag.Beta | Flag.BetaStrand,  // Isolated bridge
-        T: Flag.Turn,  // Turn
-        C: Flag.NA,  // Coil (none of the above)
+        H: Flag.Helix | Flag.HelixAlpha, // Alpha helix
+        G: Flag.Helix | Flag.Helix3Ten, // 3-10 helix
+        I: Flag.Helix | Flag.HelixPi, // PI-helix
+        E: Flag.Beta | Flag.BetaSheet, // Extended conformation
+        B: Flag.Beta | Flag.BetaStrand, // Isolated bridge
+        T: Flag.Turn, // Turn
+        C: Flag.NA, // Coil (none of the above)
     };
 
     export const SecondaryStructureDssp: { [value: string]: number } = {
-        H: Flag.Helix | Flag.HelixAlpha,  // alpha-helix
-        B: Flag.Beta | Flag.BetaStrand,  // residue in isolated beta-bridge
-        E: Flag.Beta | Flag.BetaSheet,  // extended strand, participates in beta ladder
-        G: Flag.Helix | Flag.Helix3Ten,  // 3-helix (310 helix)
-        I: Flag.Helix | Flag.HelixPi,  // 5 helix (pi-helix)
-        T: Flag.Turn,  // hydrogen bonded turn
-        S: Flag.Bend,  // bend
+        H: Flag.Helix | Flag.HelixAlpha, // alpha-helix
+        B: Flag.Beta | Flag.BetaStrand, // residue in isolated beta-bridge
+        E: Flag.Beta | Flag.BetaSheet, // extended strand, participates in beta ladder
+        G: Flag.Helix | Flag.Helix3Ten, // 3-helix (310 helix)
+        I: Flag.Helix | Flag.HelixPi, // 5 helix (pi-helix)
+        T: Flag.Turn, // hydrogen bonded turn
+        S: Flag.Bend, // bend
     };
 }
 

src/mol-model/structure/structure/properties.ts

@@ -39,8 +39,8 @@ const atom = {
     y: p(l => l.unit.conformation.y(l.element)),
     z: p(l => l.unit.conformation.z(l.element)),
     id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicConformation.atomId.value(l.element)),
-    occupancy: p(l => !Unit.isAtomic(l.unit) ?  notAtomic() : l.unit.model.atomicConformation.occupancy.value(l.element)),
-    B_iso_or_equiv: p(l => !Unit.isAtomic(l.unit) ?  notAtomic() : l.unit.model.atomicConformation.B_iso_or_equiv.value(l.element)),
+    occupancy: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicConformation.occupancy.value(l.element)),
+    B_iso_or_equiv: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicConformation.B_iso_or_equiv.value(l.element)),
     sourceIndex: p(l => Unit.isAtomic(l.unit)
         ? l.unit.model.atomicHierarchy.atomSourceIndex.value(l.element)
         // TODO: when implemented, this should map to the source index.

src/mol-model/structure/structure/unit/bonds/inter-compute.ts

@@ -139,7 +139,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
             // TODO: is this condition good enough?
             // - It works for cases like 3WQJ (label_asym_id: I) which have partial occupancy.
             // - Does NOT work for cases like 1RB8 (DC 7) with full occupancy.
-            if (hasOccupancy && occupancyB.value(bI) < 1 && occA < 1)  {
+            if (hasOccupancy && occupancyB.value(bI) < 1 && occA < 1) {
                 if (auth_seq_idA.value(aI) === auth_seq_idB.value(bI)) {
                     continue;
                 }

src/mol-model/structure/structure/unit/bonds/intra-compute.ts

@@ -61,7 +61,7 @@ function findIndexPairBonds(unit: Unit.Atomic) {
     const orders: number[] = [];
 
     for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
-        const aI =  atoms[_aI];
+        const aI = atoms[_aI];
         const isHa = type_symbol.value(aI) === 'H';
 
         const srcA = sourceIndex.value(aI);
@@ -118,7 +118,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
     const structConnAdded = __structConnAdded;
 
     for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
-        const aI =  atoms[_aI];
+        const aI = atoms[_aI];
 
         const elemA = type_symbol.value(aI);
         if (isWatery && (elemA !== 'H' || elemA !== 'O')) isWatery = false;

src/mol-model/volume/volume.ts

@@ -84,7 +84,7 @@ export namespace Volume {
         }
     }
 
-    const defaultStats: Grid['stats'] = { min: -1, max: 1, mean: 0, sigma: 0.1  };
+    const defaultStats: Grid['stats'] = { min: -1, max: 1, mean: 0, sigma: 0.1 };
     export function createIsoValueParam(defaultValue: Volume.IsoValue, stats?: Grid['stats']) {
         const sts = stats || defaultStats;
         const { min, max, mean, sigma } = sts;

src/mol-plugin-state/animation/built-in/model-index.ts

@@ -120,7 +120,7 @@ export const AnimateModelIndex = PluginStateAnimation.create({
 
                     return { modelIndex };
                 } else {
-                    const durationInMs =  params.duration.name === 'fixed'
+                    const durationInMs = params.duration.name === 'fixed'
                         ? params.duration.params.durationInS * 1000
                         : Math.ceil(1000 * traj.data.frameCount / params.duration.params.targetFps);
 
@@ -131,7 +131,7 @@ export const AnimateModelIndex = PluginStateAnimation.create({
                         }
                     } if (params.mode.name === 'palindrome') {
                         phase = 2 * phase;
-                        if (phase > 1) phase =  2 - phase;
+                        if (phase > 1) phase = 2 - phase;
                     }
 
                     const modelIndex = Math.min(Math.floor(traj.data.frameCount * phase), traj.data.frameCount - 1);

src/mol-plugin-state/animation/model.ts

@@ -41,7 +41,7 @@ interface PluginStateAnimation<P = any, S = any> {
 
 namespace PluginStateAnimation {
     export type CanApply = { canApply: true } | { canApply: false, reason?: string }
-    export type Duration = { kind: 'unknown' } | { kind: 'infinite' } | { kind: 'fixed', durationMs: number  }
+    export type Duration = { kind: 'unknown' } | { kind: 'infinite' } | { kind: 'fixed', durationMs: number }
 
     export interface Instance<A extends PluginStateAnimation> {
         definition: PluginStateAnimation,

src/mol-plugin-state/builder/structure.ts

@@ -147,7 +147,7 @@ export class StructureBuilder {
             type: { name: 'static', params: type },
             nullIfEmpty: true,
             label: (params?.label || '').trim()
-        },  `static-${type}`, params?.tags);
+        }, `static-${type}`, params?.tags);
     }
 
     tryCreateComponentFromSelection(structure: StateObjectRef<SO.Molecule.Structure>, selection: StructureSelectionQuery, key: string, params?: { label?: string, tags?: string[] }): Promise<StateObjectSelector<SO.Molecule.Structure> | undefined> {

src/mol-plugin-state/builder/structure/hierarchy-preset.ts

@@ -33,7 +33,7 @@ export namespace TrajectoryHierarchyPresetProvider {
 
 const CommonParams = TrajectoryHierarchyPresetProvider.CommonParams;
 
-const DefaultParams = (a: PluginStateObject.Molecule.Trajectory | undefined, plugin: PluginContext) =>  ({
+const DefaultParams = (a: PluginStateObject.Molecule.Trajectory | undefined, plugin: PluginContext) => ({
     model: PD.Optional(PD.Group(StateTransformer.getParamDefinition(StateTransforms.Model.ModelFromTrajectory, a, plugin))),
     showUnitcell: PD.Optional(PD.Boolean(false)),
     structure: PD.Optional(RootStructureDefinition.getParams(void 0, 'assembly').type),
@@ -137,7 +137,7 @@ async function applyCrystalSymmetry(props: { ijkMin: Vec3, ijkMax: Vec3, theme?:
     const structureProperties = await builder.insertStructureProperties(structure, params.structureProperties);
 
     const unitcell = await builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: false });
-    const representation =  await plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: props.theme } });
+    const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: props.theme } });
 
     return {
         model,
@@ -207,7 +207,7 @@ const crystalContacts = TrajectoryHierarchyPresetProvider({
         const structureProperties = await builder.insertStructureProperties(structure, params.structureProperties);
 
         const unitcell = await builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: true });
-        const representation =  await plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: 'operator-name', carbonColor: 'operator-name', focus: { name: 'element-symbol', params: { carbonColor: { name: 'operator-name', params: OperatorNameColorThemeProvider.defaultValues } } } } });
+        const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: 'operator-name', carbonColor: 'operator-name', focus: { name: 'element-symbol', params: { carbonColor: { name: 'operator-name', params: OperatorNameColorThemeProvider.defaultValues } } } } });
 
         return {
             model,

src/mol-plugin-state/builder/structure/representation-preset.ts

@@ -137,7 +137,7 @@ const empty = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-empty',
     display: { name: 'Empty', description: 'Removes all existing representations.' },
     async apply(ref, params, plugin) {
-        return {  };
+        return { };
     }
 });
 

src/mol-plugin-state/helpers/structure-representation-params.ts

@@ -43,7 +43,7 @@ export interface StructureRepresentationProps<
 
 export function createStructureRepresentationParams<R extends StructureRepresentationRegistry.BuiltIn, C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(ctx: PluginContext, structure?: Structure, props?: StructureRepresentationBuiltInProps<R, C, S>): StateTransformer.Params<StructureRepresentation3D>
 export function createStructureRepresentationParams<R extends RepresentationProvider<Structure>, C extends ColorTheme.Provider, S extends SizeTheme.Provider>(ctx: PluginContext, structure?: Structure, props?: StructureRepresentationProps<R, C, S>): StateTransformer.Params<StructureRepresentation3D>
-export function createStructureRepresentationParams(ctx: PluginContext, structure?: Structure, props: any = {}): StateTransformer.Params<StructureRepresentation3D>  {
+export function createStructureRepresentationParams(ctx: PluginContext, structure?: Structure, props: any = {}): StateTransformer.Params<StructureRepresentation3D> {
     const p = props as StructureRepresentationBuiltInProps;
     if (typeof p.type === 'string' || typeof p.color === 'string' || typeof p.size === 'string') return createParamsByName(ctx, structure || Structure.Empty, props);
     return createParamsProvider(ctx, structure || Structure.Empty, props);

src/mol-plugin-state/helpers/volume-representation-params.ts

@@ -43,7 +43,7 @@ export interface VolumeRepresentationProps<
 
 export function createVolumeRepresentationParams<R extends VolumeRepresentationRegistry.BuiltIn, C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(ctx: PluginContext, volume?: Volume, props?: VolumeRepresentationBuiltInProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
 export function createVolumeRepresentationParams<R extends RepresentationProvider<Volume>, C extends ColorTheme.Provider, S extends SizeTheme.Provider>(ctx: PluginContext, volume?: Volume, props?: VolumeRepresentationProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
-export function createVolumeRepresentationParams(ctx: PluginContext, volume?: Volume, props: any = {}): StateTransformer.Params<VolumeRepresentation3D>  {
+export function createVolumeRepresentationParams(ctx: PluginContext, volume?: Volume, props: any = {}): StateTransformer.Params<VolumeRepresentation3D> {
     const p = props as VolumeRepresentationBuiltInProps;
     if (typeof p.type === 'string' || typeof p.color === 'string' || typeof p.size === 'string') return createParamsByName(ctx, volume || Volume.One, props);
     return createParamsProvider(ctx, volume || Volume.One, props);

src/mol-plugin-state/manager/interactivity.ts

@@ -103,7 +103,7 @@ namespace InteractivityManager {
 
         protected normalizedLoci(reprLoci: Representation.Loci, applyGranularity = true) {
             const { loci, repr } = reprLoci;
-            const granularity =  applyGranularity ? this.props.granularity : undefined;
+            const granularity = applyGranularity ? this.props.granularity : undefined;
             return { loci: Loci.normalize(loci, granularity), repr };
         }
 

src/mol-plugin-state/manager/structure/component.ts

@@ -111,7 +111,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
         }
     }
 
-    applyPreset<P extends StructureRepresentationPresetProvider>(structures: ReadonlyArray<StructureRef>, provider: P, params?: StructureRepresentationPresetProvider.Params<P>): Promise<any>  {
+    applyPreset<P extends StructureRepresentationPresetProvider>(structures: ReadonlyArray<StructureRef>, provider: P, params?: StructureRepresentationPresetProvider.Params<P>): Promise<any> {
         return this.plugin.dataTransaction(async () => {
             for (const s of structures) {
                 const preset = await this.plugin.builders.structure.representation.applyPreset(s.cell, provider, params);
@@ -171,7 +171,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
         const mng = this.plugin.managers.structure.selection;
         mng.clear();
         for (const c of components) {
-            const loci =  Structure.toSubStructureElementLoci(c.structure.cell.obj!.data, c.cell.obj?.data!);
+            const loci = Structure.toSubStructureElementLoci(c.structure.cell.obj!.data, c.cell.obj?.data!);
             mng.fromLoci('set', loci);
         }
     }

src/mol-plugin-state/manager/structure/measurement.ts

@@ -46,7 +46,7 @@ type StructureMeasurementManagerAddOptions = {
     labelParams?: Partial<PD.Values<LociLabelTextParams>>
 }
 
-class StructureMeasurementManager extends StatefulPluginComponent<StructureMeasurementManagerState>  {
+class StructureMeasurementManager extends StatefulPluginComponent<StructureMeasurementManagerState> {
     readonly behaviors = {
         state: this.ev.behavior(this.state)
     };

src/mol-plugin-state/transforms/volume.ts

@@ -15,7 +15,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject as SO, PluginStateTransform } from '../objects';
 import { volumeFromCube } from '../../mol-model-formats/volume/cube';
 import { volumeFromDx } from '../../mol-model-formats/volume/dx';
-import {  Volume } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
 import { PluginContext } from '../../mol-plugin/context';
 import { StateSelection } from '../../mol-state';
 

src/mol-plugin-ui/controls/action-menu.tsx

@@ -40,7 +40,7 @@ export namespace ActionMenu {
     export type OnSelect = (item: Item | undefined, e?: React.MouseEvent<HTMLButtonElement>) => void
     export type OnSelectMany = (itemOrItems: Item[] | undefined, e?: React.MouseEvent<HTMLButtonElement>) => void
 
-    export type Items =  Header | Item | Items[]
+    export type Items = Header | Item | Items[]
     export type Header = { kind: 'header', label: string, isIndependent?: boolean, initiallyExpanded?: boolean, description?: string }
     export type Item = { kind: 'item', label: string, icon?: React.FC, disabled?: boolean, selected?: boolean, value: unknown, addOn?: JSX.Element, description?: string }
 

src/mol-plugin-ui/controls/color.tsx

@@ -84,7 +84,7 @@ export class CombinedColorControl extends React.PureComponent<ParamProps<PD.Colo
                     <TextInput onChange={this.onB} numeric value={b} delayMs={250} style={{ order: 3, flex: '1 1 auto', minWidth: 0 }} className='msp-form-control' onEnter={this.props.onEnter} blurOnEnter={true} blurOnEscape={true} />
                 </div>}/>
                 <div style={{ display: 'flex', textAlignLast: 'center' }}>
-                    <Button  onClick={this.onLighten} style={{ order: 1, flex: '1 1 auto', minWidth: 0 }} className='msp-form-control'>Lighten</Button>
+                    <Button onClick={this.onLighten} style={{ order: 1, flex: '1 1 auto', minWidth: 0 }} className='msp-form-control'>Lighten</Button>
                     <Button onClick={this.onDarken} style={{ order: 1, flex: '1 1 auto', minWidth: 0 }} className='msp-form-control'>Darken</Button>
                 </div>
             </div>}

src/mol-plugin-ui/controls/legend.tsx

@@ -27,7 +27,7 @@ export class ScaleLegend extends React.PureComponent<LegendProps<ScaleLegendData
     render() {
         const { legend } = this.props;
         const colors = legend.colors.map(c => Array.isArray(c) ? `${Color.toStyle(c[0])} ${100 * c[1]}%` : Color.toStyle(c)).join(', ');
-        return  <div className='msp-scale-legend'>
+        return <div className='msp-scale-legend'>
             <div style={{ background: `linear-gradient(to right, ${colors})` }}>
                 <span style={{ float: 'left' }}>{legend.minLabel}</span>
                 <span style={{ float: 'right' }}>{legend.maxLabel}</span>

src/mol-plugin-ui/sequence/polymer.ts

@@ -92,7 +92,7 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
         for (let i = 0; i < length; ++i) {
             if (this.missing.has(this.modelNum, this.asymId, this.seqId(i))) missing.push(i);
         }
-        this.observed = OrderedSet.subtract(Interval.ofBounds(0, length),  SortedArray.ofSortedArray(missing));
+        this.observed = OrderedSet.subtract(Interval.ofBounds(0, length), SortedArray.ofSortedArray(missing));
     }
 }
 

src/mol-plugin-ui/structure/measurements.tsx

@@ -126,7 +126,7 @@ export class MeasurementControls extends PurePluginUIComponent<{}, { isBusy: boo
     }
 
     toggleAdd = () => this.setState({ action: this.state.action === 'add' ? void 0 : 'add' });
-    toggleOptions = () => this.setState({ action: this.state.action === 'options' ? void 0 : 'options'  });
+    toggleOptions = () => this.setState({ action: this.state.action === 'options' ? void 0 : 'options' });
 
     highlight(loci: StructureElement.Loci) {
         this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci }, false);

src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts

@@ -157,7 +157,7 @@ class StructureFocusRepresentationBehavior extends PluginBehavior.WithSubscriber
         });
 
         if (this.params.excludeTargetFromSurroundings) {
-            surroundings =  MS.struct.modifier.exceptBy({
+            surroundings = MS.struct.modifier.exceptBy({
                 0: surroundings,
                 by: target
             });

src/mol-plugin/behavior/dynamic/volume-streaming/model.ts

@@ -13,7 +13,7 @@ export class VolumeServerInfo extends PluginStateObject.Create<VolumeServerInfo.
 
 export namespace VolumeServerInfo {
     export type Kind = 'x-ray' | 'em'
-    export interface EntryData  {
+    export interface EntryData {
         kind: Kind,
         // for em, the EMDB access code, for x-ray, the PDB id
         dataId: string,

src/mol-repr/shape/loci/dihedral.ts

@@ -326,7 +326,7 @@ function buildText(data: DihedralData, props: DihedralProps, text?: Text): Text
 
         let angle = radToDeg(tmpState.angle).toFixed(2);
         if (angle === '-0.00') angle = '0.00';
-        const label =  props.customText || `${angle}\u00B0`;
+        const label = props.customText || `${angle}\u00B0`;
         const radius = Math.max(2, tmpState.sphereA.radius, tmpState.sphereB.radius, tmpState.sphereC.radius, tmpState.sphereD.radius);
         const scale = radius / 2;
         builder.add(label, tmpVec[0], tmpVec[1], tmpVec[2], 0.1, scale, i);

src/mol-repr/structure/complex-visual.ts

@@ -37,7 +37,7 @@ import { TextureMesh } from '../../mol-geo/geometry/texture-mesh/texture-mesh';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { isPromiseLike } from '../../mol-util/type-helpers';
 
-export interface  ComplexVisual<P extends StructureParams> extends Visual<Structure, P> { }
+export interface ComplexVisual<P extends StructureParams> extends Visual<Structure, P> { }
 
 function createComplexRenderObject<G extends Geometry>(structure: Structure, geometry: G, locationIt: LocationIterator, theme: Theme, props: PD.Values<Geometry.Params<G>>, materialId: number) {
     const { createValues, createRenderableState } = Geometry.getUtils(geometry);

src/mol-repr/structure/representation/putty.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { PolymerTubeVisual,  PolymerTubeParams } from '../visual/polymer-tube-mesh';
+import { PolymerTubeVisual, PolymerTubeParams } from '../visual/polymer-tube-mesh';
 import { PolymerGapVisual, PolymerGapParams } from '../visual/polymer-gap-cylinder';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { UnitsRepresentation } from '../units-representation';

src/mol-repr/structure/visual/util/link.ts

@@ -49,7 +49,7 @@ export function calculateShiftDir(out: Vec3, v1: Vec3, v2: Vec3, v3: Vec3 | null
     if (v3 !== null) {
         Vec3.sub(tmpShiftV13, v1, v3);
     } else {
-        Vec3.copy(tmpShiftV13, v1);  // no reference point, use v1
+        Vec3.copy(tmpShiftV13, v1); // no reference point, use v1
     }
     Vec3.normalize(tmpShiftV13, tmpShiftV13);
 

src/mol-repr/volume/slice.ts

@@ -43,9 +43,9 @@ export async function createImage(ctx: VisualContext, volume: Volume, theme: The
     } = getSliceInfo(volume.grid, props);
 
     const corners = new Float32Array(
-        dim === 'x' ? [x, 0, 0,  x, y, 0,  x, 0, z,  x, y, z] :
-            dim === 'y' ? [0, y, 0,  x, y, 0,  0, y, z,  x, y, z] :
-                [0, 0, z,  0, y, z,  x, 0, z,  x, y, z]
+        dim === 'x' ? [x, 0, 0, x, y, 0, x, 0, z, x, y, z] :
+            dim === 'y' ? [0, y, 0, x, y, 0, 0, y, z, x, y, z] :
+                [0, 0, z, 0, y, z, x, 0, z, x, y, z]
     );
 
     const imageArray = new Uint8Array(width * height * 4);

src/mol-repr/volume/util.ts

@@ -65,7 +65,7 @@ export function getVolumeTexture2dLayout(dim: Vec3, padding = 0) {
     let rows = 1;
     let columns = width;
     if (powerOfTwoSize < width * dim[2]) {
-        columns =  Math.floor(powerOfTwoSize / width);
+        columns = Math.floor(powerOfTwoSize / width);
         rows = Math.ceil(dim[2] / columns);
         width *= columns;
         height *= rows;

src/mol-script/language/symbol-table/structure-query.ts

@@ -87,8 +87,8 @@ const generator = {
 
     atomGroups: symbol(Arguments.Dictionary({
         'entity-test': Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test for the 1st atom of every entity' }),
-        'chain-test': Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test for the 1st atom of every chain'  }),
-        'residue-test': Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test for the 1st atom every residue'  }),
+        'chain-test': Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test for the 1st atom of every chain' }),
+        'residue-test': Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test for the 1st atom every residue' }),
         'atom-test': Argument(Type.Bool, { isOptional: true, defaultValue: true }),
         'group-by': Argument(Type.Any, { isOptional: true, defaultValue: `atom-key`, description: 'Group atoms to sets based on this property. Default: each atom has its own set' }),
     }), Types.ElementSelectionQuery, 'Return all atoms for which the tests are satisfied, grouped into sets.'),

src/mol-script/language/symbol.ts

@@ -7,7 +7,7 @@
 import { Type } from './type';
 import { Expression } from './expression';
 
-export type Argument<T extends Type = Type>  = {
+export type Argument<T extends Type = Type> = {
     type: T,
     isOptional: boolean,
     isRest: boolean,
@@ -31,7 +31,7 @@ export namespace Arguments {
         map: { [P in keyof T]: Argument<T[P]> },
         '@type': T
     }
-    export type PropTypes<Map extends { [key: string]: Argument<any>  }> = { [P in keyof Map]: Map[P]['type']['@type'] }
+    export type PropTypes<Map extends { [key: string]: Argument<any> }> = { [P in keyof Map]: Map[P]['type']['@type'] }
     export function Dictionary<Map extends { [key: string]: Argument<any> }>(map: Map): Arguments<PropTypes<Map>> {
         return { kind: 'dictionary', map, '@type': 0 as any };
     }

src/mol-script/runtime/query/base.ts

@@ -63,7 +63,7 @@ export type QueryCompiledSymbolRuntime = { kind: 'const', value: any } | { kind:
 export type CompiledQueryFn<T = any> = { isConst: boolean, fn: QueryFn }
 
 export namespace QueryCompiledSymbol {
-    export function Const(value: any): QueryCompiledSymbolRuntime  {
+    export function Const(value: any): QueryCompiledSymbolRuntime {
         return { kind: 'const', value };
     }
 
@@ -73,7 +73,7 @@ export namespace QueryCompiledSymbol {
 }
 
 export namespace CompiledQueryFn {
-    export function Const(value: any): CompiledQueryFn  {
+    export function Const(value: any): CompiledQueryFn {
         return { isConst: true, fn: function CompiledQueryFn_Const(ctx) { return value; } };
     }
 

src/mol-state/state.ts

@@ -966,7 +966,7 @@ function createObject(ctx: UpdateContext, cell: StateObjectCell, transformer: St
     return runTask(transformer.definition.apply({ a, params, cache: cell.cache, spine: ctx.spine, dependencies: resolveDependencies(cell) }, ctx.parent.globalContext), ctx.taskCtx);
 }
 
-async function updateObject(ctx: UpdateContext, cell: StateObjectCell,  transformer: StateTransformer, a: StateObject, b: StateObject, oldParams: any, newParams: any) {
+async function updateObject(ctx: UpdateContext, cell: StateObjectCell, transformer: StateTransformer, a: StateObject, b: StateObject, oldParams: any, newParams: any) {
     if (!transformer.definition.update) {
         return StateTransformer.UpdateResult.Recreate;
     }

src/mol-state/state/builder.ts

@@ -253,7 +253,7 @@ namespace StateBuilder {
         to<A extends StateObject, T extends StateTransformer>(ref: StateTransform.Ref): To<A, T>
         to<C extends StateObjectCell>(cell: C): To<StateObjectCell.Obj<C>, StateObjectCell.Transformer<C>>
         to<S extends StateObjectSelector>(selector: S): To<StateObjectSelector.Obj<S>, StateObjectSelector.Transformer<S>>
-        to(ref: StateTransform.Ref | StateObjectCell | StateObjectSelector) { return  this.root.to(ref as any); }
+        to(ref: StateTransform.Ref | StateObjectCell | StateObjectSelector) { return this.root.to(ref as any); }
         toRoot<A extends StateObject>() { return this.root.toRoot<A>(); }
         delete(ref: StateObjectRef) { return this.root.delete(ref); }