diff --git a/.eslintrc.json b/.eslintrc.json
index dde918ed0226c3a2429bdb240ed923a367819a23..61b024262d1acc3c4f46d61e99fcaa8952d80f84 100644
--- a/.eslintrc.json
+++ b/.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": [
{
diff --git a/src/cli/chem-comp-dict/create-table.ts b/src/cli/chem-comp-dict/create-table.ts
index 03da1a3ee772f5e1a890329456f77bea9ca4c76b..7cf2aeade71d069980e6d809bdb903ed74fa48ac 100644
--- a/src/cli/chem-comp-dict/create-table.ts
+++ b/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 }
diff --git a/src/cli/cifschema/util/cif-dic.ts b/src/cli/cifschema/util/cif-dic.ts
index a4ad9ee2820c57ab99ae7c77ca85bcc3cfecd044..b9ef007414f31d1c9b6989b6ca0344a531f93167 100644
--- a/src/cli/cifschema/util/cif-dic.ts
+++ b/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;
diff --git a/src/examples/domain-annotation-server/mapping.ts b/src/examples/domain-annotation-server/mapping.ts
index df5945dd94c6139ee0bdfe55377ca37a68567106..df7107b9431c2fd8730902f9d5cde0d4789035d0 100644
--- a/src/examples/domain-annotation-server/mapping.ts
+++ b/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) });
}
diff --git a/src/examples/proteopedia-wrapper/index.ts b/src/examples/proteopedia-wrapper/index.ts
index a322fc8aa1699dd94aa51c337ed0a5b8b1bef79a..26f6d852643fb9c220539b4bb2a38ffe6bf3f526 100644
--- a/src/examples/proteopedia-wrapper/index.ts
+++ b/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() {
diff --git a/src/extensions/anvil/algorithm.ts b/src/extensions/anvil/algorithm.ts
index 5a7fa55a6942bcb94246cc551281b6bec75e526e..08bdcadd519ddb0b6ebb80edb985f16f6a1f63f1 100644
--- a/src/extensions/anvil/algorithm.ts
+++ b/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++;
}
diff --git a/src/extensions/anvil/behavior.ts b/src/extensions/anvil/behavior.ts
index 3e20f6338429e2e03447721773a314e6e6cd6369..8339b34ac6f21c143717c1c626d9e18b90a90c87 100644
--- a/src/extensions/anvil/behavior.ts
+++ b/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) {
diff --git a/src/extensions/cellpack/curve.ts b/src/extensions/cellpack/curve.ts
index 7ede3c3f71884b69f2ef72bf02e6f057b57423bd..5b5c4fe64072a391ff56de71a730ffa9816af612 100644
--- a/src/extensions/cellpack/curve.ts
+++ b/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));
diff --git a/src/extensions/cellpack/data.ts b/src/extensions/cellpack/data.ts
index 98fd3475607a74254e7778c902abc8476eddb9ee..f7d8e469c9ed2c76d9003774aba7ee57addaff9b 100644
--- a/src/extensions/cellpack/data.ts
+++ b/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;
diff --git a/src/extensions/dnatco/confal-pyramids/behavior.ts b/src/extensions/dnatco/confal-pyramids/behavior.ts
index a8e03566a3701cc54b096fadd87f6732e6921ac0..ae89a8e2524fe7df39cc4e2b9635a18dd9fcba78 100644
--- a/src/extensions/dnatco/confal-pyramids/behavior.ts
+++ b/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 } };
}
});
diff --git a/src/extensions/dnatco/confal-pyramids/color.ts b/src/extensions/dnatco/confal-pyramids/color.ts
index 26d2b3f68959c72e8da16f769822a67f863cf28f..be76d6619798ad93d3c51f76130c46c91444fd34 100644
--- a/src/extensions/dnatco/confal-pyramids/color.ts
+++ b/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)],
diff --git a/src/extensions/dnatco/confal-pyramids/util.ts b/src/extensions/dnatco/confal-pyramids/util.ts
index 3f4c627a643f6ed9df090ce7a24c01b240e5117d..9a6e88ba79dec9a2ac0644aba6ce8cf261174d10 100644
--- a/src/extensions/dnatco/confal-pyramids/util.ts
+++ b/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}` : '';
diff --git a/src/extensions/g3d/model.ts b/src/extensions/g3d/model.ts
index cb4ed9478183c2fc29e71d9ddac9ff3c4b379fc7..892d14abd9cb3a5f708aef53f0be0bfd0bb00dd4 100644
--- a/src/extensions/g3d/model.ts
+++ b/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];
diff --git a/src/extensions/pdbe/preferred-assembly.ts b/src/extensions/pdbe/preferred-assembly.ts
index f4a11f08bdd103c1d969d8f5403653cc85b5198c..ef928692d1b225db83cbc9ae62b448016a45f59e 100644
--- a/src/extensions/pdbe/preferred-assembly.ts
+++ b/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);
diff --git a/src/extensions/pdbe/structure-quality-report/color.ts b/src/extensions/pdbe/structure-quality-report/color.ts
index 2ee57e131af487e02977dda52282156cb239d8c6..49f69d79e54a17162faa727a1f78d82393d1b6f2 100644
--- a/src/extensions/pdbe/structure-quality-report/color.ts
+++ b/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,
diff --git a/src/extensions/rcsb/assembly-symmetry/ui.tsx b/src/extensions/rcsb/assembly-symmetry/ui.tsx
index bcb4a1b9a1ed1a02f1aeb6e6880aae52da21ed1d..bafaa1575ed018d7ea2b842a08f0ade1dbea881f 100644
--- a/src/extensions/rcsb/assembly-symmetry/ui.tsx
+++ b/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';
diff --git a/src/extensions/rcsb/validation-report/representation.ts b/src/extensions/rcsb/validation-report/representation.ts
index 208aa6bfbfaaf107b3d78bf7c712005eb1f30821..c9a6eba02c8136e7e95cdc04b3ee5fd552fa72a5 100644
--- a/src/extensions/rcsb/validation-report/representation.ts
+++ b/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));
}
diff --git a/src/mol-canvas3d/passes/draw.ts b/src/mol-canvas3d/passes/draw.ts
index 90373c0dfb3e0589544eec4b8d777f632a895f98..63db5db451b33d91c3d9c299763a0f424acc7743 100644
--- a/src/mol-canvas3d/passes/draw.ts
+++ b/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> = {
diff --git a/src/mol-data/int/impl/sorted-array.ts b/src/mol-data/int/impl/sorted-array.ts
index 1e857f27bddfd75d354fe5c7874901e1c889fd8b..6127961d77f47af3b72cac945658be801024e62f 100644
--- a/src/mol-data/int/impl/sorted-array.ts
+++ b/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; }
diff --git a/src/mol-data/util/_spec/chunked-array.spec.ts b/src/mol-data/util/_spec/chunked-array.spec.ts
index d3c065271484f8bf087b8fdf63b4fbf2f9e03931..eb8df5e06da0c63f7dbcf9f1aa0fab09ead02f1d 100644
--- a/src/mol-data/util/_spec/chunked-array.spec.ts
+++ b/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);
diff --git a/src/mol-geo/geometry/mesh/mesh-builder.ts b/src/mol-geo/geometry/mesh/mesh-builder.ts
index 145aa1fd5a8e6875e40bd37f3224bd13d6bbeb3b..f373fe93fc4e80d78b12d5dc96f58527752accda 100644
--- a/src/mol-geo/geometry/mesh/mesh-builder.ts
+++ b/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);
}
diff --git a/src/mol-geo/geometry/text/text-builder.ts b/src/mol-geo/geometry/text/text-builder.ts
index 6ff71cf3bae101cadb80b5b39121e97c1849a86f..83e0ba64792bfaaf70bff753ae20c2c70441be6a 100644
--- a/src/mol-geo/geometry/text/text-builder.ts
+++ b/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) {
diff --git a/src/mol-geo/primitive/box.ts b/src/mol-geo/primitive/box.ts
index a0b20b245e424f45d92631646adcbe5732152b40..3fa2be2e9d296addc420ee7ae785746aecdcf0e5 100644
--- a/src/mol-geo/primitive/box.ts
+++ b/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;
diff --git a/src/mol-geo/primitive/dodecahedron.ts b/src/mol-geo/primitive/dodecahedron.ts
index 7b826ffc4a8bfc1cdb24433133947fff4e2a8fc6..51314feeab74bf23996f49c2cfeec5e392bc489e 100644
--- a/src/mol-geo/primitive/dodecahedron.ts
+++ b/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;
diff --git a/src/mol-geo/primitive/icosahedron.ts b/src/mol-geo/primitive/icosahedron.ts
index 14742232e79d32f6dba61c251a6f716d958f9fe3..225f73660b0d570fb43bd401d7a071fa0e512e44 100644
--- a/src/mol-geo/primitive/icosahedron.ts
+++ b/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;
diff --git a/src/mol-geo/primitive/octahedron.ts b/src/mol-geo/primitive/octahedron.ts
index e01bb778e52277198ec284602128f4c436d1a008..37045d5452d02e38dc280361213e71190a422904 100644
--- a/src/mol-geo/primitive/octahedron.ts
+++ b/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;
diff --git a/src/mol-geo/primitive/plane.ts b/src/mol-geo/primitive/plane.ts
index 3216aca11fe179fe23e8cf013b771390a00e941f..f1fa9370f92df4e9c8ab8a560681b3057d3d7266 100644
--- a/src/mol-geo/primitive/plane.ts
+++ b/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 {
diff --git a/src/mol-geo/primitive/pyramid.ts b/src/mol-geo/primitive/pyramid.ts
index 07f6f1d344e7bb6986e42dbb66a910ac351b9666..6ec531968d9b98d06268f98f496a124b22b0fc04 100644
--- a/src/mol-geo/primitive/pyramid.ts
+++ b/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);
}
diff --git a/src/mol-geo/primitive/sphere.ts b/src/mol-geo/primitive/sphere.ts
index 392802a49bbaf8a62683d94df5e9dd5f3b18e102..775308b8599751556a19ad8c754a46e6f552be8d 100644
--- a/src/mol-geo/primitive/sphere.ts
+++ b/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();
diff --git a/src/mol-geo/primitive/tetrahedron.ts b/src/mol-geo/primitive/tetrahedron.ts
index 940fe624f90afd1136ce9bcc8305cff97f5176e1..1d96451f45eb4e5920cb93c75e69f9a475267bc4 100644
--- a/src/mol-geo/primitive/tetrahedron.ts
+++ b/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;
diff --git a/src/mol-gl/compute/marching-cubes/tables.ts b/src/mol-gl/compute/marching-cubes/tables.ts
index 0383e6a06fa7064d99139e8c9587cbf4c7290f4d..ad354fe6a7c3f0a5144cb732acb47096babe4b14 100644
--- a/src/mol-gl/compute/marching-cubes/tables.ts
+++ b/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;
diff --git a/src/mol-gl/compute/util.ts b/src/mol-gl/compute/util.ts
index b641a03889cafc0e90f283c5fa8035cd97aed44c..3dfa9e2673611766d243ce024f4624f01dd9dee6 100644
--- a/src/mol-gl/compute/util.ts
+++ b/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 = {
diff --git a/src/mol-gl/webgl/compat.ts b/src/mol-gl/webgl/compat.ts
index 95b1ef04ab2bb17113b61fa86b29ce69b448641d..242fe0e40abd661e60e0641159e3bf885bdac741 100644
--- a/src/mol-gl/webgl/compat.ts
+++ b/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/
diff --git a/src/mol-io/common/binary-cif/decoder.ts b/src/mol-io/common/binary-cif/decoder.ts
index 1c32c2a8b9c3031b07d4591dad2b3c3137ee17b4..fe6ca9ebf8b679d1fb73becbc421774bb6a21232 100644
--- a/src/mol-io/common/binary-cif/decoder.ts
+++ b/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;
}
diff --git a/src/mol-io/reader/_spec/mol.spec.ts b/src/mol-io/reader/_spec/mol.spec.ts
index 64015df72de92c43698ee86b3aab9013545e1174..923db651eebcd8e5725ab9cf69f4c278bb55f5af 100644
--- a/src/mol-io/reader/_spec/mol.spec.ts
+++ b/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);
}
diff --git a/src/mol-io/reader/_spec/mol2.spec.ts b/src/mol-io/reader/_spec/mol2.spec.ts
index d9ded86cf42f06a2f7b556428aa13d0ab20652cf..aa3a9503957b3f98c37db1d1d6b1205a8d52f710 100644
--- a/src/mol-io/reader/_spec/mol2.spec.ts
+++ b/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);
}
diff --git a/src/mol-io/reader/_spec/sdf.spec.ts b/src/mol-io/reader/_spec/sdf.spec.ts
index d7e47781990de7b517baa9c2c8c9d402d2499a53..c125d6edd2b532f4f4ef34e9aef7e84339b914ad 100644
--- a/src/mol-io/reader/_spec/sdf.spec.ts
+++ b/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);
}
diff --git a/src/mol-io/reader/cif/schema.ts b/src/mol-io/reader/cif/schema.ts
index 8a0aaaf2f7dabb730acb2fa79b1509277806661e..e9e6f1f251188d088376c6ddc1f8e24c4b355275 100644
--- a/src/mol-io/reader/cif/schema.ts
+++ b/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);
}
}
diff --git a/src/mol-io/reader/cif/text/parser.ts b/src/mol-io/reader/cif/text/parser.ts
index 9142c9075d944b10dac2e7439c36b87f265e4e8e..5c56d1c7518c7aaf2d6d1620b30036f37c12a47f 100644
--- a/src/mol-io/reader/cif/text/parser.ts
+++ b/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;
diff --git a/src/mol-io/reader/common/text/column/token.ts b/src/mol-io/reader/common/text/column/token.ts
index 8f13c8a1ee92a0f4ea511ff5b370d24c4b0a3722..b07d20a881152e2566a3e3c7469cb0f50b5dd660 100644
--- a/src/mol-io/reader/common/text/column/token.ts
+++ b/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;
diff --git a/src/mol-io/reader/common/text/tokenizer.ts b/src/mol-io/reader/common/text/tokenizer.ts
index b64e8138d70a8124763d4c63f941fc5e78efbaca..251cced322c6d3b2c2c189173b96da68c7d5661d 100644
--- a/src/mol-io/reader/common/text/tokenizer.ts
+++ b/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: // ' '
diff --git a/src/mol-io/reader/csv/parser.ts b/src/mol-io/reader/csv/parser.ts
index 3e6dd115abb8bfe4b0ad6c1fdc2648ae28be47be..ff98fedbbec7e9ed07224ff94f51a2931e1dbd12 100644
--- a/src/mol-io/reader/csv/parser.ts
+++ b/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;
}
}
diff --git a/src/mol-io/reader/psf/parser.ts b/src/mol-io/reader/psf/parser.ts
index 7884184e9fd5fb17cd09eb5878c7d34757f3eea8..7acca9aaff5f8bb112c1a40bc528a5ba077074da 100644
--- a/src/mol-io/reader/psf/parser.ts
+++ b/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();
diff --git a/src/mol-io/writer/cif/encoder.ts b/src/mol-io/writer/cif/encoder.ts
index d606cc1d3ac0d1c36e3afa4010b458a074bd5158..819ad351bcfd6ca8cdc50ad989e4d0b456de02fa 100644
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/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>();
}
}
diff --git a/src/mol-io/writer/cif/encoder/text.ts b/src/mol-io/writer/cif/encoder/text.ts
index 404b7857e0d8de5c8c518b2a1c4599258b161fa4..8603bb10afdf1db777443df58ddf163468ea1698 100644
--- a/src/mol-io/writer/cif/encoder/text.ts
+++ b/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;
diff --git a/src/mol-io/writer/ligand-encoder.ts b/src/mol-io/writer/ligand-encoder.ts
index 2e1dbe7344d23dffa4eca27da38ea72731818812..8386e15aeecfc2f830199dc9ac176534aeb5aa4e 100644
--- a/src/mol-io/writer/ligand-encoder.ts
+++ b/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;
diff --git a/src/mol-math/geometry/gaussian-density.ts b/src/mol-math/geometry/gaussian-density.ts
index 7914af1530324368134ce93fc9ba68bb285b978a..44d36fa44b966396e708eb7a50feef74faa42f96 100644
--- a/src/mol-math/geometry/gaussian-density.ts
+++ b/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);
});
diff --git a/src/mol-math/geometry/gaussian-density/cpu.ts b/src/mol-math/geometry/gaussian-density/cpu.ts
index eb42d99a1f8eb1d27cdc0fa0d9fd8d0210f18230..50a33fbeb4ac7ad26f71a868fdfbf7f6e7ea6cae 100644
--- a/src/mol-math/geometry/gaussian-density/cpu.ts
+++ b/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;
diff --git a/src/mol-math/geometry/gaussian-density/gpu.ts b/src/mol-math/geometry/gaussian-density/gpu.ts
index 264c3fed054061a46c473e93149304e680b7a962..8aee512e1779177b38db90196a84ce633556dada 100644
--- a/src/mol-math/geometry/gaussian-density/gpu.ts
+++ b/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++;
}
diff --git a/src/mol-math/geometry/spacegroup/construction.ts b/src/mol-math/geometry/spacegroup/construction.ts
index fa3a23665a12fca070b42f50e58d4050b94ea760..26b83a3b223110273fd14a4b2d79edd19f8c99b6 100644
--- a/src/mol-math/geometry/spacegroup/construction.ts
+++ b/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);
diff --git a/src/mol-math/geometry/spacegroup/tables.ts b/src/mol-math/geometry/spacegroup/tables.ts
index 925249a87d31bb1a9000b52d2b6cbff2f1be34f3..af006653792d4016ce24b1e4757427f7b6a13ea1 100644
--- a/src/mol-math/geometry/spacegroup/tables.ts
+++ b/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;
diff --git a/src/mol-math/linear-algebra/3d/quat.ts b/src/mol-math/linear-algebra/3d/quat.ts
index a3d754d540863df4d8d6f0d0a6de0983fc91c057..f56b76dacd93c30091fbfe8714bc5dc3a79c6705 100644
--- a/src/mol-math/linear-algebra/3d/quat.ts
+++ b/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;
diff --git a/src/mol-math/misc.ts b/src/mol-math/misc.ts
index c275e02b65370cc3a5dc7fd576f16e62d2c7f788..235baa8a53d672a2136e76df813193000b64c1e0 100644
--- a/src/mol-math/misc.ts
+++ b/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) {
diff --git a/src/mol-model-formats/shape/ply.ts b/src/mol-model-formats/shape/ply.ts
index 7eabead7f08a6b43cc07b3e5e88733993c295adb..d94a8047f4b8777bcbca1fadb303206cd0da0863 100644
--- a/src/mol-model-formats/shape/ply.ts
+++ b/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> }
diff --git a/src/mol-model-formats/structure/basic/properties.ts b/src/mol-model-formats/structure/basic/properties.ts
index 8515a6722cde23cd835daeb5a5498ab43a30f651..dd6fdaf92b66639bfce5dab64cf97ad5cb936dd1 100644
--- a/src/mol-model-formats/structure/basic/properties.ts
+++ b/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;
diff --git a/src/mol-model-formats/structure/util.ts b/src/mol-model-formats/structure/util.ts
index faec9eaf0bc4982d1e8c89776803276c798bad14..f75908b0599dd7487d8f75df84d62476a6fe5bfc 100644
--- a/src/mol-model-formats/structure/util.ts
+++ b/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
diff --git a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/common.ts b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/common.ts
index 6c8c53661706cad50c71c26bf79ea2bdce579b6e..72936c707bf431ac34f69db4d6d87fc6ce94d948 100644
--- a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/common.ts
+++ b/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 */
diff --git a/src/mol-model-props/computed/interactions/charged.ts b/src/mol-model-props/computed/interactions/charged.ts
index e4c0359b994392e4d6aade1e318ae94ce23cb4c0..4dfc61b76c7121e180b8193210632d963c66a7e1 100644
--- a/src/mol-model-props/computed/interactions/charged.ts
+++ b/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
}
}
}
diff --git a/src/mol-model-props/computed/interactions/halogen-bonds.ts b/src/mol-model-props/computed/interactions/halogen-bonds.ts
index 52f5b494176e6fe2d80e3f02ca5319d45b0091a9..210067f126bbcf19852cb112a0955a9381d2452b 100644
--- a/src/mol-model-props/computed/interactions/halogen-bonds.ts
+++ b/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) {
diff --git a/src/mol-model-props/computed/interactions/hydrogen-bonds.ts b/src/mol-model-props/computed/interactions/hydrogen-bonds.ts
index 1f0ef8c037c5a2a38405ea7bf5d46ccf54d64ff7..f88dcd2b7e06e4e26a3d3ad9a26011c16816e965 100644
--- a/src/mol-model-props/computed/interactions/hydrogen-bonds.ts
+++ b/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>
diff --git a/src/mol-model/sequence/alignment/alignment.ts b/src/mol-model/sequence/alignment/alignment.ts
index a0fb519ab095a0e3789722d2dd09e5c059d30c7e..1f319a95a8e2baa761adc71e32974c967e28cbe8 100644
--- a/src/mol-model/sequence/alignment/alignment.ts
+++ b/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
);
}
}
diff --git a/src/mol-model/sequence/alignment/substitution-matrix.ts b/src/mol-model/sequence/alignment/substitution-matrix.ts
index b81612ca95a5d886c2461bbf24f1dd7229dad049..f1badec24f66ee0daf2e8aa362ed6334587c7eef 100644
--- a/src/mol-model/sequence/alignment/substitution-matrix.ts
+++ b/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 }> }>;
diff --git a/src/mol-model/sequence/constants.ts b/src/mol-model/sequence/constants.ts
index 3a6584d33174077ca54e3c7cb7214feb527d913d..7f1f9b13426d689975562f6822191798189bd34e 100644
--- a/src/mol-model/sequence/constants.ts
+++ b/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',
diff --git a/src/mol-model/structure/export/categories/atom_site.ts b/src/mol-model/structure/export/categories/atom_site.ts
index 404783aef18831e7d0de8d01bd18a5152b256824..daf85b13cc02f0699bc5e8d895b6cbee7fc08a82 100644
--- a/src/mol-model/structure/export/categories/atom_site.ts
+++ b/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)
diff --git a/src/mol-model/structure/model/properties/atomic/measures.ts b/src/mol-model/structure/model/properties/atomic/measures.ts
index 39120c2a6c2e4401b340bf48f06c9b8f2bd42f00..bfc9117cc965b8e502d3d8151d7d69f283259eac 100644
--- a/src/mol-model/structure/model/properties/atomic/measures.ts
+++ b/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 {
diff --git a/src/mol-model/structure/model/properties/utils/coarse-keys.ts b/src/mol-model/structure/model/properties/utils/coarse-keys.ts
index 3857a3519baa9cf9fc1f2283a5174dfaec82a6a5..d02b63c362ed640a4036cf037eacbdad71936788 100644
--- a/src/mol-model/structure/model/properties/utils/coarse-keys.ts
+++ b/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 };
}
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index 7ce35fbb9fdc60b8deca62a23f27c07a1d0920e4..da3f5333c7d0b284d6be524ed8fdff0270a682bf 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/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
};
}
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index f526e642fb5e55cf63039280c12b41ea95b691df..bc0e622e5b2defc62d1dae95a27c53df363b237f 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/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.
diff --git a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
index 945b253f350a68a2f8d37b81c627b7ea53cbb42e..ebb81e46a92c5fff863679de485388bf24bd17a3 100644
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/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;
}
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
index c12bce1ca5d9b0ee0631ae23b68d6a7d6d596042..427bf7378901e3e50d3b2d9aa1b05cb271263959 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/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;
diff --git a/src/mol-model/volume/volume.ts b/src/mol-model/volume/volume.ts
index db901d7fb6e8ab41f3994249ae20316647ddc251..280a32d7e26e9f2a3f455b3c77e84677b488ebf5 100644
--- a/src/mol-model/volume/volume.ts
+++ b/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;
diff --git a/src/mol-plugin-state/animation/built-in/model-index.ts b/src/mol-plugin-state/animation/built-in/model-index.ts
index 4c447db65910b3bf161b559fe863b5f359696cc1..bc969c86f6e870eb4344b8a5f77689e77d92dc71 100644
--- a/src/mol-plugin-state/animation/built-in/model-index.ts
+++ b/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);
diff --git a/src/mol-plugin-state/animation/model.ts b/src/mol-plugin-state/animation/model.ts
index d72b7114a2170a4f55ab27f32b65bf366b7fa737..5f46f7e94d56df437dc9fdb44813fe0c564a47bb 100644
--- a/src/mol-plugin-state/animation/model.ts
+++ b/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,
diff --git a/src/mol-plugin-state/builder/structure.ts b/src/mol-plugin-state/builder/structure.ts
index 5280a551f8fde4323034008d43419bfebfff536a..1c0d9db00b47815798d7386c60992b5b7aa9953f 100644
--- a/src/mol-plugin-state/builder/structure.ts
+++ b/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> {
diff --git a/src/mol-plugin-state/builder/structure/hierarchy-preset.ts b/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
index a8bcad352138520828fa074692dca2b96276c7a6..c5c68c60aeb668f8d93fb8ebacd1a54710d7a756 100644
--- a/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
+++ b/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,
diff --git a/src/mol-plugin-state/builder/structure/representation-preset.ts b/src/mol-plugin-state/builder/structure/representation-preset.ts
index 4f25df844bf8b3cac6cf965f6fe469fab7dd2c5f..119dd0f1564cbea0cd0333e0f4901016d5c0398c 100644
--- a/src/mol-plugin-state/builder/structure/representation-preset.ts
+++ b/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 { };
}
});
diff --git a/src/mol-plugin-state/helpers/structure-representation-params.ts b/src/mol-plugin-state/helpers/structure-representation-params.ts
index 621dea1713899d9ddd7cf3be2cfd91854a6447e9..07fb8c0191c59a808b0e090f8a0aa8734284271b 100644
--- a/src/mol-plugin-state/helpers/structure-representation-params.ts
+++ b/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);
diff --git a/src/mol-plugin-state/helpers/volume-representation-params.ts b/src/mol-plugin-state/helpers/volume-representation-params.ts
index 55d9ab3bd2ffe0f71b03a101e8809825337c8f1b..11189e19ef553a93de611bb0dfbb9c5c6f9b7122 100644
--- a/src/mol-plugin-state/helpers/volume-representation-params.ts
+++ b/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);
diff --git a/src/mol-plugin-state/manager/interactivity.ts b/src/mol-plugin-state/manager/interactivity.ts
index 8aae69c4b811345d56c268ec9dac8bd36f501c40..947014640573c2f8f97bec9775256822592167c3 100644
--- a/src/mol-plugin-state/manager/interactivity.ts
+++ b/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 };
}
diff --git a/src/mol-plugin-state/manager/structure/component.ts b/src/mol-plugin-state/manager/structure/component.ts
index cfc61d3d95d089de7bd2f76b590b263fcbcc1a77..5f82bb9a1a30c16928ab67013a23149b39939cf5 100644
--- a/src/mol-plugin-state/manager/structure/component.ts
+++ b/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);
}
}
diff --git a/src/mol-plugin-state/manager/structure/measurement.ts b/src/mol-plugin-state/manager/structure/measurement.ts
index 3ec049507315e44da92d2a72e947764e78519560..4907eb3e7edf84d536604126b5811b722e8265ec 100644
--- a/src/mol-plugin-state/manager/structure/measurement.ts
+++ b/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)
};
diff --git a/src/mol-plugin-state/transforms/volume.ts b/src/mol-plugin-state/transforms/volume.ts
index 16ff08e5205a3c34c55b0aff3d149a38ad4578bf..b15d79071b303e94282f3cfeb87daa9c166e37ba 100644
--- a/src/mol-plugin-state/transforms/volume.ts
+++ b/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';
diff --git a/src/mol-plugin-ui/controls/action-menu.tsx b/src/mol-plugin-ui/controls/action-menu.tsx
index b06987a49fea732911a9b3e91a5fabad5ca54f9e..5ce7e61c0fdaad308edeceba1e8ca3c7d648805e 100644
--- a/src/mol-plugin-ui/controls/action-menu.tsx
+++ b/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 }
diff --git a/src/mol-plugin-ui/controls/color.tsx b/src/mol-plugin-ui/controls/color.tsx
index 76d871353f087094a3b5c44b799411406e59e3d0..cbb04476f626a7549ac63b1150081c63ad8e3275 100644
--- a/src/mol-plugin-ui/controls/color.tsx
+++ b/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>}
diff --git a/src/mol-plugin-ui/controls/legend.tsx b/src/mol-plugin-ui/controls/legend.tsx
index 539435bb7f5fb3969903ee7591752420a89e7745..99702dc66b8b6db1485662e4842f0dc9cb2eb2e9 100644
--- a/src/mol-plugin-ui/controls/legend.tsx
+++ b/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>
diff --git a/src/mol-plugin-ui/sequence/polymer.ts b/src/mol-plugin-ui/sequence/polymer.ts
index 331f88171fbc7c89a0ff235ceeff34d01c44720f..051c49659c56ec03da0286e6dbace662c893dace 100644
--- a/src/mol-plugin-ui/sequence/polymer.ts
+++ b/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));
}
}
diff --git a/src/mol-plugin-ui/structure/measurements.tsx b/src/mol-plugin-ui/structure/measurements.tsx
index 44fab5df3a870da7f4f21ad4ebec6c86bdf4a618..b1cdfb2a33ae1bfa5b289a29e7f79959bd4b36cd 100644
--- a/src/mol-plugin-ui/structure/measurements.tsx
+++ b/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);
diff --git a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts b/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
index ad7452f0dd1719ade6ec5077436d4870054eb720..43ad81abd070d9b3d51ec70d004b6bc6ce6ff664 100644
--- a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
+++ b/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
});
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/model.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/model.ts
index 13138d154e3fbac6335004781e055d723260f434..c7f9661007b991e76cd012b7b1ea9023dc72efec 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/model.ts
+++ b/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,
diff --git a/src/mol-repr/shape/loci/dihedral.ts b/src/mol-repr/shape/loci/dihedral.ts
index fd6bac07d804b710e6f2c131343fd24f4294a02f..6a59a9ddfbc2b9a1ff0a612fc7b9d0da1588e7c0 100644
--- a/src/mol-repr/shape/loci/dihedral.ts
+++ b/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);
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index f6cdff35be3ab6b06f7d9260706259501b5e94df..37e43b8631cf4508c3fb5fa4579fc426bf87e071 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/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);
diff --git a/src/mol-repr/structure/representation/putty.ts b/src/mol-repr/structure/representation/putty.ts
index 3a0aa7dd7fafb887c8d72018366f649711c52329..826c4d78ef103aacde3d0ecedff3f9c466eed9b2 100644
--- a/src/mol-repr/structure/representation/putty.ts
+++ b/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';
diff --git a/src/mol-repr/structure/visual/util/link.ts b/src/mol-repr/structure/visual/util/link.ts
index 5d6f7d2a44ded649d6e88c702eaf52fedb3bbf0c..34752801b2bd219933552315cf5b03fedcf16933 100644
--- a/src/mol-repr/structure/visual/util/link.ts
+++ b/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);
diff --git a/src/mol-repr/volume/slice.ts b/src/mol-repr/volume/slice.ts
index 49688fe58aa025588c7b8f707dce4be64a594fb8..2aa30d19756849b05bf0a3f585d90a09cafed431 100644
--- a/src/mol-repr/volume/slice.ts
+++ b/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);
diff --git a/src/mol-repr/volume/util.ts b/src/mol-repr/volume/util.ts
index fb10ce7c773cdb8fe6daec1520a1843993fd3e5d..9e8977ce4b2631bb34a4511568f40a907a7be108 100644
--- a/src/mol-repr/volume/util.ts
+++ b/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;
diff --git a/src/mol-script/language/symbol-table/structure-query.ts b/src/mol-script/language/symbol-table/structure-query.ts
index 19a157494d7a937cccfc2758f5912ce53bb37b7f..9e765f41649288a054b01a69b4a6a7d06b1c2bf6 100644
--- a/src/mol-script/language/symbol-table/structure-query.ts
+++ b/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.'),
diff --git a/src/mol-script/language/symbol.ts b/src/mol-script/language/symbol.ts
index 3694880c9cf1419c5b6f7cfe9272a9f82dba90b0..ac8973749da27c6fe2c73acf1ebf71e9b1a3f955 100644
--- a/src/mol-script/language/symbol.ts
+++ b/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 };
}
diff --git a/src/mol-script/runtime/query/base.ts b/src/mol-script/runtime/query/base.ts
index 314d07e84749c07de54d901e620d32297bad197b..ca5fc17151e049efbf9919d4820a7071f436d6e4 100644
--- a/src/mol-script/runtime/query/base.ts
+++ b/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; } };
}
diff --git a/src/mol-state/state.ts b/src/mol-state/state.ts
index 57ddc8d9abfc2812771f2758f6819eb9f0ec0d56..ff3772b4304bb94ad183121ed956699594e43fbf 100644
--- a/src/mol-state/state.ts
+++ b/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;
}
diff --git a/src/mol-state/state/builder.ts b/src/mol-state/state/builder.ts
index 345c05f655a8712366323ba99552545ccf7d80c9..e1601fbf5cefede65bfb6adb4200b7c4732375a8 100644
--- a/src/mol-state/state/builder.ts
+++ b/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); }
diff --git a/src/mol-theme/color/residue-name.ts b/src/mol-theme/color/residue-name.ts
index 727df16a5ee9fe3e499af9312bc162d087a15e47..59412412ab864c445ca2b2e2301810bec068e3ab 100644
--- a/src/mol-theme/color/residue-name.ts
+++ b/src/mol-theme/color/residue-name.ts
@@ -38,12 +38,12 @@ export const ResidueNameColors = ColorMap({
'VAL': 0xFF8CFF,
// rna bases
- 'A': 0xDC143C, // Crimson Red
- 'G': 0x32CD32, // Lime Green
- 'I': 0x9ACD32, // Yellow Green
- 'C': 0xFFD700, // Gold Yellow
- 'T': 0x4169E1, // Royal Blue
- 'U': 0x40E0D0, // Turquoise Cyan
+ 'A': 0xDC143C, // Crimson Red
+ 'G': 0x32CD32, // Lime Green
+ 'I': 0x9ACD32, // Yellow Green
+ 'C': 0xFFD700, // Gold Yellow
+ 'T': 0x4169E1, // Royal Blue
+ 'U': 0x40E0D0, // Turquoise Cyan
// dna bases
'DA': 0xDC143C,
diff --git a/src/mol-util/color/spaces/lab.ts b/src/mol-util/color/spaces/lab.ts
index 1b97c8987aca4abc820af2d24d449101149789b5..a307b2e7c2f365b6196f88487e29ecf8f18d40e1 100644
--- a/src/mol-util/color/spaces/lab.ts
+++ b/src/mol-util/color/spaces/lab.ts
@@ -67,7 +67,7 @@ namespace Lab {
x = Xn * lab_xyz(x);
z = Zn * lab_xyz(z);
- const r = xyz_rgb(3.2404542 * x - 1.5371385 * y - 0.4985314 * z); // D65 -> sRGB
+ const r = xyz_rgb(3.2404542 * x - 1.5371385 * y - 0.4985314 * z); // D65 -> sRGB
const g = xyz_rgb(-0.9692660 * x + 1.8760108 * y + 0.0415560 * z);
const b = xyz_rgb(0.0556434 * x - 0.2040259 * y + 1.0572252 * z);
@@ -127,7 +127,7 @@ namespace Lab {
const T0 = 0.137931034; // 4 / 29
const T1 = 0.206896552; // 6 / 29
- const T2 = 0.12841855; // 3 * t1 * t1
+ const T2 = 0.12841855; // 3 * t1 * t1
const T3 = 0.008856452; // t1 * t1 * t1
/** convert component from xyz to rgb */
diff --git a/src/mol-util/float-packing.ts b/src/mol-util/float-packing.ts
index 6503bac3e2b986a7cbb3a40589e7e1559dfac431..9629cd22deca8478a41a455f541723577d24f67f 100644
--- a/src/mol-util/float-packing.ts
+++ b/src/mol-util/float-packing.ts
@@ -35,7 +35,7 @@ export function decodeFloatRGB(r: number, g: number, b: number) {
}
const UnpackDownscale = 255 / 256; // 0..1 -> fraction (excluding 1)
-const PackFactors = Vec3.create(256 * 256 * 256, 256 * 256, 256);
+const PackFactors = Vec3.create(256 * 256 * 256, 256 * 256, 256);
const UnpackFactors = Vec4.create(
UnpackDownscale / PackFactors[0],
UnpackDownscale / PackFactors[1],
diff --git a/src/mol-util/input/input-observer.ts b/src/mol-util/input/input-observer.ts
index 8579c7240ad05d16a1711776ee8a3ea6bbf5f52a..9326d9f077e07a94f2444f0e90aebdb92f73dc0a 100644
--- a/src/mol-util/input/input-observer.ts
+++ b/src/mol-util/input/input-observer.ts
@@ -16,7 +16,7 @@ export function getButtons(event: MouseEvent | Touch) {
if ('buttons' in event) {
return event.buttons;
} else if ('which' in event) {
- const b = (event as any).which; // 'any' to support older browsers
+ const b = (event as any).which; // 'any' to support older browsers
if (b === 2) {
return 4;
} else if (b === 3) {
@@ -721,7 +721,7 @@ function normalizeWheel(event: any) {
const LINE_HEIGHT = 40;
const PAGE_HEIGHT = 800;
let spinX = 0, spinY = 0,
- dx = 0, dy = 0, dz = 0; // pixelX, pixelY, pixelZ
+ dx = 0, dy = 0, dz = 0; // pixelX, pixelY, pixelZ
// Legacy
if ('detail' in event) { spinY = event.detail; }
@@ -743,11 +743,11 @@ function normalizeWheel(event: any) {
if ('deltaZ' in event) { dz = event.deltaZ; }
if ((dx || dy || dz) && event.deltaMode) {
- if (event.deltaMode === 1) { // delta in LINE units
+ if (event.deltaMode === 1) { // delta in LINE units
dx *= LINE_HEIGHT;
dy *= LINE_HEIGHT;
dz *= LINE_HEIGHT;
- } else { // delta in PAGE units
+ } else { // delta in PAGE units
dx *= PAGE_HEIGHT;
dy *= PAGE_HEIGHT;
dz *= PAGE_HEIGHT;
diff --git a/src/mol-util/marker-action.ts b/src/mol-util/marker-action.ts
index 25b5b1671501bfeee821009f907aa79235f0ea2b..53bcd5e4fadca982ce45040684d6c0847e0d680f 100644
--- a/src/mol-util/marker-action.ts
+++ b/src/mol-util/marker-action.ts
@@ -74,7 +74,7 @@ export function applyMarkerAction(array: Uint8Array, set: OrderedSet, action: Ma
const viewEnd = viewStart + ((end - 4 * viewStart) >> 2);
const frontStart = start;
- const frontEnd = Math.min(4 * viewStart, end);
+ const frontEnd = Math.min(4 * viewStart, end);
const backStart = Math.max(start, 4 * viewEnd);
const backEnd = end;
diff --git a/src/mol-util/mask.ts b/src/mol-util/mask.ts
index 72f98724f727738a72f828d06a50c9e4662569f1..e35b68d86577b31da7b750722723f74a15a16eeb 100644
--- a/src/mol-util/mask.ts
+++ b/src/mol-util/mask.ts
@@ -55,7 +55,7 @@ namespace Mask {
this._forEach(f, ctx);
return ctx;
}
- constructor(private mask: boolean[], public size: number) { this.length = mask.length; }
+ constructor(private mask: boolean[], public size: number) { this.length = mask.length; }
}
class AllMask implements Mask {
diff --git a/src/mol-util/type-helpers.ts b/src/mol-util/type-helpers.ts
index d597aa4d29b9d4c76d5036e1dadce697328b744d..d775c4bad7d10efe3ea0435ec1683498d7ccacfe 100644
--- a/src/mol-util/type-helpers.ts
+++ b/src/mol-util/type-helpers.ts
@@ -18,7 +18,7 @@ export type UintArray = Uint8Array | Uint16Array | Uint32Array | number[]
export type ValueOf<T> = T[keyof T]
export type ArrayCtor<T> = { new(size: number): { [i: number]: T, length: number } }
/** assignable ArrayLike version */
-export type AssignableArrayLike<T> = { [i: number]: T, length: number }
+export type AssignableArrayLike<T> = { [i: number]: T, length: number }
export type NonNullableArray<T extends any[] | ReadonlyArray<any>> = T extends any[] ? NonNullable<T[0]>[] : ReadonlyArray<NonNullable<T[0]>>
diff --git a/src/mol-util/zip/bin.ts b/src/mol-util/zip/bin.ts
index 8ef3f163411dd398fe1f5e9367468087abc59745..a1a1753890c64dd2e1d9e7876b21dccdb47e8820 100644
--- a/src/mol-util/zip/bin.ts
+++ b/src/mol-util/zip/bin.ts
@@ -19,7 +19,7 @@ export function readUshort(buff: Uint8Array, p: number) {
}
export function writeUshort(buff: Uint8Array, p: number, n: number) {
- buff[p] = (n) & 255; buff[p + 1] = (n >> 8) & 255;
+ buff[p] = (n) & 255; buff[p + 1] = (n >> 8) & 255;
}
export function readUint(buff: Uint8Array, p: number) {
diff --git a/src/mol-util/zip/checksum.ts b/src/mol-util/zip/checksum.ts
index cd4d93fbd3105718632be7149ec1626e537d5bb5..2ea3851a4be187c35caaed686f31a8bcbe90ada1 100644
--- a/src/mol-util/zip/checksum.ts
+++ b/src/mol-util/zip/checksum.ts
@@ -12,8 +12,8 @@ const CrcTable = (function () {
for (let n = 0; n < 256; n++) {
let c = n;
for (let k = 0; k < 8; k++) {
- if (c & 1) c = 0xedb88320 ^ (c >>> 1);
- else c = c >>> 1;
+ if (c & 1) c = 0xedb88320 ^ (c >>> 1);
+ else c = c >>> 1;
}
tab[n] = c;
}
@@ -21,13 +21,13 @@ const CrcTable = (function () {
})();
function _crc(c: number, buf: Uint8Array, off: number, len: number) {
- for (let i = 0; i < len; i++) {
+ for (let i = 0; i < len; i++) {
c = CrcTable[(c ^ buf[off + i]) & 0xff] ^ (c >>> 8);
}
return c;
}
-export function crc(b: Uint8Array, o: number, l: number) {
+export function crc(b: Uint8Array, o: number, l: number) {
return _crc(0xffffffff, b, o, l) ^ 0xffffffff;
}
diff --git a/src/mol-util/zip/deflate.ts b/src/mol-util/zip/deflate.ts
index e514ef84259c30cdb6d72cfde799a7e012894513..498f6e463265ca16f3e94348dc691e34d21f3c50 100644
--- a/src/mol-util/zip/deflate.ts
+++ b/src/mol-util/zip/deflate.ts
@@ -45,7 +45,7 @@ function deflateChunk(ctx: DeflateContext, count: number) {
const end = Math.min(i + count, dlen);
- for(; i < end; i++) {
+ for(; i < end; i++) {
c = nc;
if(i + 1 < dlen - 2) {
@@ -74,9 +74,9 @@ function deflateChunk(ctx: DeflateContext, count: number) {
if(mch !== 0) {
const len = mch >>> 16, dst = mch & 0xffff;
- const lgi = _goodIndex(len, U.of0); U.lhst[257 + lgi]++;
- const dgi = _goodIndex(dst, U.df0); U.dhst[dgi]++; ebits += U.exb[lgi] + U.dxb[dgi];
- lits[li] = (len << 23) | (i - cvrd); lits[li + 1] = (dst << 16) | (lgi << 8) | dgi; li += 2;
+ const lgi = _goodIndex(len, U.of0); U.lhst[257 + lgi]++;
+ const dgi = _goodIndex(dst, U.df0); U.dhst[dgi]++; ebits += U.exb[lgi] + U.dxb[dgi];
+ lits[li] = (len << 23) | (i - cvrd); lits[li + 1] = (dst << 16) | (lgi << 8) | dgi; li += 2;
cvrd = i + len;
} else {
U.lhst[data[i]]++;
@@ -103,15 +103,15 @@ function deflateChunk(ctx: DeflateContext, count: number) {
*/
const Opts = [
/* good lazy nice chain */
- /* 0 */ [0, 0, 0, 0, 0], /* store only */
- /* 1 */ [4, 4, 8, 4, 0], /* max speed, no lazy matches */
- /* 2 */ [4, 5, 16, 8, 0],
- /* 3 */ [4, 6, 16, 16, 0],
-
- /* 4 */ [4, 10, 16, 32, 0], /* lazy matches */
- /* 5 */ [8, 16, 32, 32, 0],
- /* 6 */ [8, 16, 128, 128, 0],
- /* 7 */ [8, 32, 128, 256, 0],
+ /* 0 */ [0, 0, 0, 0, 0], /* store only */
+ /* 1 */ [4, 4, 8, 4, 0], /* max speed, no lazy matches */
+ /* 2 */ [4, 5, 16, 8, 0],
+ /* 3 */ [4, 6, 16, 16, 0],
+
+ /* 4 */ [4, 10, 16, 32, 0], /* lazy matches */
+ /* 5 */ [8, 16, 32, 32, 0],
+ /* 6 */ [8, 16, 128, 128, 0],
+ /* 7 */ [8, 32, 128, 256, 0],
/* 8 */ [32, 128, 258, 1024, 1],
/* 9 */ [32, 258, 258, 4096, 1] /* max compression */
] as const;
@@ -164,25 +164,25 @@ function _bestMatch(data: Uint8Array, i: number, prev: Uint16Array, c: number, n
// console.log("----", i);
let dif = ((ci - pi + (1 << 15)) & 0x7fff);
if(pi === ci || c !== _hash(data, i - dif)) return 0;
- let tl = 0, td = 0; // top length, top distance
+ let tl = 0, td = 0; // top length, top distance
const dlim = Math.min(0x7fff, i);
while(dif <= dlim && --chain !== 0 && pi !== ci /* && c==UZIP.F._hash(data,i-dif)*/) {
if(tl === 0 || (data[i + tl] === data[i + tl - dif])) {
let cl = _howLong(data, i, dif);
if(cl > tl) {
- tl = cl; td = dif; if(tl >= nice) break; //*
+ tl = cl; td = dif; if(tl >= nice) break; //*
if(dif + 2 < cl) cl = dif + 2;
let maxd = 0; // pi does not point to the start of the word
for(let j = 0; j < cl - 2; j++) {
- const ei = (i - dif + j + (1 << 15)) & 0x7fff;
+ const ei = (i - dif + j + (1 << 15)) & 0x7fff;
const li = prev[ei];
const curd = (ei - li + (1 << 15)) & 0x7fff;
- if(curd > maxd) { maxd = curd; pi = ei; }
+ if(curd > maxd) { maxd = curd; pi = ei; }
}
}
}
- ci = pi; pi = prev[ci];
+ ci = pi; pi = prev[ci];
dif += ((ci - pi + (1 << 15)) & 0x7fff);
}
return (tl << 16) | td;
@@ -233,17 +233,17 @@ function _writeBlock(BFINAL: number, lits: Uint32Array, li: number, ebits: numbe
} else {
let ltree: number[], dtree: number[];
if(BTYPE === 1) {
- ltree = U.fltree; dtree = U.fdtree;
+ ltree = U.fltree; dtree = U.fdtree;
} else if(BTYPE === 2) {
- makeCodes(U.ltree, ML); revCodes(U.ltree, ML);
- makeCodes(U.dtree, MD); revCodes(U.dtree, MD);
- makeCodes(U.itree, MH); revCodes(U.itree, MH);
+ makeCodes(U.ltree, ML); revCodes(U.ltree, ML);
+ makeCodes(U.dtree, MD); revCodes(U.dtree, MD);
+ makeCodes(U.itree, MH); revCodes(U.itree, MH);
- ltree = U.ltree; dtree = U.dtree;
+ ltree = U.ltree; dtree = U.dtree;
- _putsE(out, pos, numl - 257); pos += 5; // 286
- _putsE(out, pos, numd - 1); pos += 5; // 30
- _putsE(out, pos, numh - 4); pos += 4; // 19
+ _putsE(out, pos, numl - 257); pos += 5; // 286
+ _putsE(out, pos, numd - 1); pos += 5; // 30
+ _putsE(out, pos, numh - 4); pos += 4; // 19
for(let i = 0; i < numh; i++) _putsE(out, pos + i * 3, U.itree[(U.ordr[i] << 1) + 1]);
pos += 3 * numh;
@@ -261,10 +261,10 @@ function _writeBlock(BFINAL: number, lits: Uint32Array, li: number, ebits: numbe
if(len !== 0) {
const qc = lits[si + 1], dst = (qc >> 16), lgi = (qc >> 8) & 255, dgi = (qc & 255);
pos = _writeLit(257 + lgi, ltree, out, pos);
- _putsE(out, pos, len - U.of0[lgi]); pos += U.exb[lgi];
+ _putsE(out, pos, len - U.of0[lgi]); pos += U.exb[lgi];
pos = _writeLit(dgi, dtree, out, pos);
- _putsF(out, pos, dst - U.df0[dgi]); pos += U.dxb[dgi]; off += len;
+ _putsF(out, pos, dst - U.df0[dgi]); pos += U.dxb[dgi]; off += len;
}
}
pos = _writeLit(256, ltree, out, pos);
@@ -300,7 +300,7 @@ function getTrees() {
const numd = _lenCodes(U.dtree, dset);
for(let i = 0; i < lset.length; i += 2) U.ihst[lset[i]]++;
for(let i = 0; i < dset.length; i += 2) U.ihst[dset[i]]++;
- const MH = _hufTree(U.ihst, U.itree, 7);
+ const MH = _hufTree(U.ihst, U.itree, 7);
let numh = 19;
while(numh > 4 && U.itree[(U.ordr[numh - 1] << 1) + 1] === 0) numh--;
return [ML, MD, MH, numl, numd, numh, lset, dset] as const;
@@ -314,7 +314,7 @@ function contSize(tree: number[], hst: NumberArray) {
function _codeTiny(set: number[], tree: number[], out: Uint8Array, pos: number) {
for(let i = 0; i < set.length; i += 2) {
- const l = set[i], rst = set[i + 1]; // console.log(l, pos, tree[(l<<1)+1]);
+ const l = set[i], rst = set[i + 1]; // console.log(l, pos, tree[(l<<1)+1]);
pos = _writeLit(l, tree, out, pos);
const rsl = l === 16 ? 2 : (l === 17 ? 3 : 7);
if(l > 15) {
@@ -328,9 +328,9 @@ function _codeTiny(set: number[], tree: number[], out: Uint8Array, pos: number)
function _lenCodes(tree: number[], set: number[]) {
let len = tree.length;
- while(len !== 2 && tree[len - 1] === 0) len -= 2; // when no distances, keep one code with length 0
+ while(len !== 2 && tree[len - 1] === 0) len -= 2; // when no distances, keep one code with length 0
for(let i = 0; i < len; i += 2) {
- const l = tree[i + 1], nxt = (i + 3 < len ? tree[i + 3] : -1), nnxt = (i + 5 < len ? tree[i + 5] : -1), prv = (i === 0 ? -1 : tree[i - 1]);
+ const l = tree[i + 1], nxt = (i + 3 < len ? tree[i + 3] : -1), nnxt = (i + 5 < len ? tree[i + 5] : -1), prv = (i === 0 ? -1 : tree[i - 1]);
if(l === 0 && nxt === l && nnxt === l) {
let lz = i + 5;
while(lz + 2 < len && tree[lz + 2] === l) lz += 2;
diff --git a/src/mol-util/zip/huffman.ts b/src/mol-util/zip/huffman.ts
index 0ee6964e623173f81a35e004e7c43955d4cae2b0..e3ce56cf80aa33e8c0b6e81b30d087d0ce63c160 100644
--- a/src/mol-util/zip/huffman.ts
+++ b/src/mol-util/zip/huffman.ts
@@ -25,7 +25,7 @@ export function _hufTree(hst: NumberArray, tree: number[], MAXL: number) {
}
for(let i = 0; i < hl; i++) if(hst[i] !== 0) list.push({ lit: i, f: hst[i], d: undefined as any });
const end = list.length, l2 = list.slice(0);
- if(end === 0) return 0; // empty histogram (usually for dist)
+ if(end === 0) return 0; // empty histogram (usually for dist)
if(end === 1) {
const lit = list[0].lit, l2 = lit === 0 ? 1 : 0;
tree[(lit << 1) + 1] = 1;
diff --git a/src/mol-util/zip/inflate.ts b/src/mol-util/zip/inflate.ts
index d4159eebf6d6a5fe812f57d271d763ecd4cb26f9..0428a24f6905e7a12de29960372b9b273d63ee0f 100644
--- a/src/mol-util/zip/inflate.ts
+++ b/src/mol-util/zip/inflate.ts
@@ -82,10 +82,10 @@ function inflateBlocks(ctx: InflateContext, count: number) {
makeCodes(U.itree, tl);
codes2map(U.itree, tl, U.imap);
- lmap = U.lmap; dmap = U.dmap;
+ lmap = U.lmap; dmap = U.dmap;
pos = _decodeTiny(U.imap, (1 << tl) - 1, HLIT + HDIST, data, pos, U.ttree);
- const mx0 = _copyOut(U.ttree, 0, HLIT, U.ltree);
+ const mx0 = _copyOut(U.ttree, 0, HLIT, U.ltree);
ML = (1 << mx0) - 1;
const mx1 = _copyOut(U.ttree, HLIT, HDIST, U.dtree);
MD = (1 << mx1) - 1;
@@ -174,11 +174,11 @@ function _decodeTiny(lmap: NumberArray, LL: number, len: number, data: Uint8Arra
} else {
let ll = 0, n = 0;
if(lit === 16) {
- n = (3 + _bitsE(data, pos, 2));
+ n = (3 + _bitsE(data, pos, 2));
pos += 2;
ll = tree[i - 1];
} else if(lit === 17) {
- n = (3 + _bitsE(data, pos, 3));
+ n = (3 + _bitsE(data, pos, 3));
pos += 3;
} else if(lit === 18) {
n = (11 + _bitsE(data, pos, 7));
diff --git a/src/mol-util/zip/util.ts b/src/mol-util/zip/util.ts
index 0cb19cc589403ae2a1bdb790f283e774e957367c..f9b4eb7329548199cd39bd5c4424c4bc7fd854d7 100644
--- a/src/mol-util/zip/util.ts
+++ b/src/mol-util/zip/util.ts
@@ -14,16 +14,16 @@ export const U = (function (){
bl_count: new u16(16),
ordr: [16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15],
of0: [3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31, 35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258, 999, 999, 999],
- exb: [0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 0, 0, 0, 0],
+ exb: [0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 0, 0, 0, 0],
ldef: new u16(32),
df0: [1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193, 257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145, 8193, 12289, 16385, 24577, 65535, 65535],
- dxb: [0, 0, 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 13, 13, 0, 0],
+ dxb: [0, 0, 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 13, 13, 0, 0],
ddef: new u32(32),
- flmap: new u16(512), fltree: [] as number[],
- fdmap: new u16(32), fdtree: [] as number[],
- lmap: new u16(32768), ltree: [] as number[], ttree: [] as number[],
- dmap: new u16(32768), dtree: [] as number[],
- imap: new u16(512), itree: [] as number[],
+ flmap: new u16(512), fltree: [] as number[],
+ fdmap: new u16(32), fdtree: [] as number[],
+ lmap: new u16(32768), ltree: [] as number[], ttree: [] as number[],
+ dmap: new u16(32768), dtree: [] as number[],
+ imap: new u16(512), itree: [] as number[],
// rev9 : new u16( 512)
rev15: new u16(1 << 15),
lhst: new u32(286), dhst: new u32(30), ihst: new u32(19),
@@ -74,7 +74,7 @@ export const U = (function (){
codes2map(U.fdtree, 5, U.fdmap);
revCodes(U.fdtree, 5);
- pushV(U.itree, 19, 0); pushV(U.ltree, 286, 0); pushV(U.dtree, 30, 0); pushV(U.ttree, 320, 0);
+ pushV(U.itree, 19, 0); pushV(U.ltree, 286, 0); pushV(U.dtree, 30, 0); pushV(U.ttree, 320, 0);
/*
for(var i=0; i< 19; i++) U.itree.push(0,0);
for(var i=0; i<286; i++) U.ltree.push(0,0);
@@ -87,7 +87,7 @@ export function codes2map(tree: number[], MAX_BITS: number, map: Uint16Array) {
const max_code = tree.length;
const r15 = U.rev15;
for(let i = 0; i < max_code; i += 2) {
- if(tree[i + 1] !== 0) {
+ if(tree[i + 1] !== 0) {
const lit = i >> 1;
const cl = tree[i + 1], val = (lit << 4) | cl; // : (0x8000 | (U.of0[lit-257]<<7) | (U.exb[lit-257]<<4) | cl);
const rest = (MAX_BITS - cl);
@@ -96,13 +96,13 @@ export function codes2map(tree: number[], MAX_BITS: number, map: Uint16Array) {
// tree[i]=r15[i0]>>>(15-MAX_BITS);
while(i0 !== i1) {
const p0 = r15[i0] >>> (15 - MAX_BITS);
- map[p0] = val; i0++;
+ map[p0] = val; i0++;
}
}
}
}
-export function makeCodes(tree: number[], MAX_BITS: number) { // code, length
+export function makeCodes(tree: number[], MAX_BITS: number) { // code, length
const max_code = tree.length;
const bl_count = U.bl_count;
diff --git a/src/mol-util/zip/zip.ts b/src/mol-util/zip/zip.ts
index 2380ceb00d93d664adb2d37631635aabe73e6082..173cd9f90cbf97f1535236650dcf3d0b9aa97c2e 100644
--- a/src/mol-util/zip/zip.ts
+++ b/src/mol-util/zip/zip.ts
@@ -32,15 +32,15 @@ export async function unzip(runtime: RuntimeContext, buf: ArrayBuffer, onlyNames
// const csize = readUint(data, o);
o += 4;
- const coffs = readUint(data, o); o += 4;
+ const coffs = readUint(data, o); o += 4;
o = coffs;
for(let i = 0; i < cnu; i++) {
// const sign = readUint(data, o);
o += 4;
- o += 4; // versions;
- o += 4; // flag + compr
- o += 4; // time
+ o += 4; // versions;
+ o += 4; // flag + compr
+ o += 4; // time
// const crc32 = readUint(data, o);
o += 4;
@@ -52,10 +52,10 @@ export async function unzip(runtime: RuntimeContext, buf: ArrayBuffer, onlyNames
const nl = readUshort(data, o);
const el = readUshort(data, o + 2);
const cl = readUshort(data, o + 4);
- o += 6; // name, extra, comment
- o += 8; // disk, attribs
+ o += 6; // name, extra, comment
+ o += 8; // disk, attribs
- const roff = readUint(data, o); o += 4;
+ const roff = readUint(data, o); o += 4;
o += nl + el + cl;
await _readLocal(runtime, data, roff, out, csize, usize, onlyNames);
@@ -72,7 +72,7 @@ async function _readLocal(runtime: RuntimeContext, data: Uint8Array, o: number,
// const gpflg = readUshort(data, o);
o += 2;
// if((gpflg&8)!=0) throw "unknown sizes";
- const cmpr = readUshort(data, o);
+ const cmpr = readUshort(data, o);
o += 2;
// const time = readUint(data, o);
@@ -90,7 +90,7 @@ async function _readLocal(runtime: RuntimeContext, data: Uint8Array, o: number,
o += 2;
const name = readUTF8(data, o, nlen);
- o += nlen; // console.log(name);
+ o += nlen; // console.log(name);
o += elen;
if(onlyNames) {
@@ -178,7 +178,7 @@ export async function deflate(runtime: RuntimeContext, data: Uint8Array, opts?:
if(opts === undefined) opts = { level: 6 };
let off = 0;
const buf = new Uint8Array(50 + Math.floor(data.length * 1.1));
- buf[off] = 120; buf[off + 1] = 156; off += 2;
+ buf[off] = 120; buf[off + 1] = 156; off += 2;
off = await _deflateRaw(runtime, data, buf, off, opts.level);
const crcValue = adler(data, 0, data.length);
buf[off + 0] = ((crcValue >>> 24) & 255);
@@ -214,14 +214,14 @@ export async function zip(runtime: RuntimeContext, obj: { [k: string]: Uint8Arra
}
for(const p in zpd) tot += zpd[p].file.length + 30 + 46 + 2 * sizeUTF8(p);
- tot += 22;
+ tot += 22;
const data = new Uint8Array(tot);
let o = 0;
const fof = [];
for(const p in zpd) {
- const file = zpd[p]; fof.push(o);
+ const file = zpd[p]; fof.push(o);
o = _writeHeader(data, o, p, file, 0);
}
let i = 0;
@@ -233,12 +233,12 @@ export async function zip(runtime: RuntimeContext, obj: { [k: string]: Uint8Arra
}
const csize = o - ioff;
- writeUint(data, o, 0x06054b50); o += 4;
- o += 4; // disks
- writeUshort(data, o, i); o += 2;
- writeUshort(data, o, i); o += 2; // number of c d records
- writeUint(data, o, csize); o += 4;
- writeUint(data, o, ioff); o += 4;
+ writeUint(data, o, 0x06054b50); o += 4;
+ o += 4; // disks
+ writeUshort(data, o, i); o += 2;
+ writeUshort(data, o, i); o += 2; // number of c d records
+ writeUint(data, o, csize); o += 4;
+ writeUint(data, o, ioff); o += 4;
o += 2;
return data.buffer;
}
@@ -253,26 +253,26 @@ function _writeHeader(data: Uint8Array, o: number, p: string, obj: { cpr: boolea
const file = obj.file;
writeUint(data, o, t === 0 ? 0x04034b50 : 0x02014b50); o += 4; // sign
- if(t === 1) o += 2; // ver made by
- writeUshort(data, o, 20); o += 2; // ver
- writeUshort(data, o, 0); o += 2; // gflip
- writeUshort(data, o, obj.cpr ? 8 : 0); o += 2; // cmpr
+ if(t === 1) o += 2; // ver made by
+ writeUshort(data, o, 20); o += 2; // ver
+ writeUshort(data, o, 0); o += 2; // gflip
+ writeUshort(data, o, obj.cpr ? 8 : 0); o += 2; // cmpr
- writeUint(data, o, 0); o += 4; // time
- writeUint(data, o, obj.crc); o += 4; // crc32
- writeUint(data, o, file.length); o += 4; // csize
- writeUint(data, o, obj.usize); o += 4; // usize
+ writeUint(data, o, 0); o += 4; // time
+ writeUint(data, o, obj.crc); o += 4; // crc32
+ writeUint(data, o, file.length); o += 4; // csize
+ writeUint(data, o, obj.usize); o += 4; // usize
- writeUshort(data, o, sizeUTF8(p)); o += 2; // nlen
- writeUshort(data, o, 0); o += 2; // elen
+ writeUshort(data, o, sizeUTF8(p)); o += 2; // nlen
+ writeUshort(data, o, 0); o += 2; // elen
if(t === 1) {
- o += 2; // comment length
- o += 2; // disk number
- o += 6; // attributes
- writeUint(data, o, roff); o += 4; // usize
+ o += 2; // comment length
+ o += 2; // disk number
+ o += 6; // attributes
+ writeUint(data, o, roff); o += 4; // usize
}
- const nlen = writeUTF8(data, o, p); o += nlen;
+ const nlen = writeUTF8(data, o, p); o += nlen;
if(t === 0) {
data.set(file, o);
o += file.length;
diff --git a/webpack.config.common.js b/webpack.config.common.js
index c2032c79d6873b17463fd4f23799f1b7704aaedc..d403e707fbf7905510aba8ee0b38f277d86da2de 100644
--- a/webpack.config.common.js
+++ b/webpack.config.common.js
@@ -35,7 +35,7 @@ const sharedConfig = {
'process.env.DEBUG': JSON.stringify(process.env.DEBUG),
'__MOLSTAR_DEBUG_TIMESTAMP__': webpack.DefinePlugin.runtimeValue(() => `${new Date().valueOf()}`, true)
}),
- new MiniCssExtractPlugin({ filename: 'molstar.css', }),
+ new MiniCssExtractPlugin({ filename: 'molstar.css' }),
new VersionFile({
extras: { timestamp: `${new Date().valueOf()}` },
packageFile: path.resolve(__dirname, 'package.json'),