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use relative paths for module imports

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This commit is contained in:
Alexander Rose
2019-06-03 14:38:50 -07:00
parent aed60c8af6
commit 2c55165c84
527 changed files with 2499 additions and 2561 deletions
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2
.gitignore vendored
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@@ -1,8 +1,10 @@
build/
lib/
node_modules/
debug.log
npm-debug.log
tsconfig.tsbuildinfo
*.sublime-workspace
.idea

30
package.json
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@@ -13,15 +13,15 @@
"scripts": {
"lint": "tslint src/**/*.ts",
"test": "npm run lint && jest",
"build": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,gql}\" build/src/ && tsc -b",
"build": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,gql}\" lib/ && tsc -b",
"postinstall": "npm run build",
"watch": "concurrently --kill-others \"npm:watch-ts\" \"npm:watch-extra\" \"npm:watch-webpack\"",
"watch-ts": "tsc -watch",
"watch-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,gql}\" build/src/ --watch",
"watch-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,gql}\" lib/ --watch",
"build-webpack": "webpack --mode production",
"watch-webpack": "webpack -w --mode development --display minimal",
"model-server": "node build/src/servers/model/server.js",
"model-server-watch": "nodemon --watch build/src build/src/servers/model/server.js"
"model-server": "node lib/servers/model/server.js",
"model-server-watch": "nodemon --watch lib lib/servers/model/server.js"
},
"nodemonConfig": {
"ignoreRoot": [
@@ -41,29 +41,9 @@
},
"moduleDirectories": [
"node_modules",
"build/src"
"lib"
],
"testURL": "http://localhost/",
"moduleNameMapper": {
"mol-app($|/.*)": "<rootDir>/src/mol-app$1",
"mol-data($|/.*)": "<rootDir>/src/mol-data$1",
"mol-geo($|/.*)": "<rootDir>/src/mol-geo$1",
"mol-gl($|/.*)": "<rootDir>/src/mol-gl$1",
"mol-io($|/.*)": "<rootDir>/src/mol-io$1",
"mol-math($|/.*)": "<rootDir>/src/mol-math$1",
"mol-model($|/.*)": "<rootDir>/src/mol-model$1",
"mol-model-props($|/.*)": "<rootDir>/src/mol-model-props$1",
"mol-model-formats($|/.*)": "<rootDir>/src/mol-model-formats$1",
"mol-plugin($|/.*)": "<rootDir>/src/mol-plugin$1",
"mol-ql($|/.*)": "<rootDir>/src/mol-ql$1",
"mol-repr($|/.*)": "<rootDir>/src/mol-repr$1",
"mol-script($|/.*)": "<rootDir>/src/mol-script$1",
"mol-state($|/.*)": "<rootDir>/src/mol-state$1",
"mol-task($|/.*)": "<rootDir>/src/mol-task$1",
"mol-theme($|/.*)": "<rootDir>/src/mol-theme$1",
"mol-util($|/.*)": "<rootDir>/src/mol-util$1",
"mol-canvas3d($|/.*)": "<rootDir>/src/mol-canvas3d$1"
},
"testRegex": "\\.spec\\.ts$"
},
"author": "Mol* Contributors",

6
src/apps/basic-wrapper/coloring.ts
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@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { CustomElementProperty } from 'mol-model-props/common/custom-element-property';
import { Model, ElementIndex } from 'mol-model/structure';
import { Color } from 'mol-util/color';
import { CustomElementProperty } from '../../mol-model-props/common/custom-element-property';
import { Model, ElementIndex } from '../../mol-model/structure';
import { Color } from '../../mol-util/color';
export const StripedResidues = CustomElementProperty.create<number>({
isStatic: true,

4
src/apps/basic-wrapper/controls.tsx
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@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { PluginUIComponent } from 'mol-plugin/ui/base';
import { PluginUIComponent } from '../../mol-plugin/ui/base';
import * as React from 'react';
import { TransformUpdaterControl } from 'mol-plugin/ui/state/update-transform';
import { TransformUpdaterControl } from '../../mol-plugin/ui/state/update-transform';
export class BasicWrapperControls extends PluginUIComponent {

18
src/apps/basic-wrapper/helpers.ts
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@@ -4,15 +4,15 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Mat4, Vec3 } from 'mol-math/linear-algebra';
import { PluginContext } from 'mol-plugin/context';
import { PluginStateObject as PSO } from 'mol-plugin/state/objects';
import { StateTransforms } from 'mol-plugin/state/transforms';
import { StructureRepresentation3DHelpers } from 'mol-plugin/state/transforms/representation';
import { MolScriptBuilder as MS } from 'mol-script/language/builder';
import { StateBuilder } from 'mol-state';
import Expression from 'mol-script/language/expression';
import { BuiltInColorThemeName } from 'mol-theme/color';
import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
import { PluginContext } from '../../mol-plugin/context';
import { PluginStateObject as PSO } from '../../mol-plugin/state/objects';
import { StateTransforms } from '../../mol-plugin/state/transforms';
import { StructureRepresentation3DHelpers } from '../../mol-plugin/state/transforms/representation';
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { StateBuilder } from '../../mol-state';
import Expression from '../../mol-script/language/expression';
import { BuiltInColorThemeName } from '../../mol-theme/color';
type SupportedFormats = 'cif' | 'pdb'
export namespace StateHelper {

18
src/apps/basic-wrapper/index.ts
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@@ -4,16 +4,16 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { createPlugin, DefaultPluginSpec } from 'mol-plugin';
import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
import './index.html'
import { PluginContext } from 'mol-plugin/context';
import { PluginCommands } from 'mol-plugin/command';
import { StateTransforms } from 'mol-plugin/state/transforms';
import { StructureRepresentation3DHelpers } from 'mol-plugin/state/transforms/representation';
import { Color } from 'mol-util/color';
import { PluginStateObject as PSO } from 'mol-plugin/state/objects';
import { AnimateModelIndex } from 'mol-plugin/state/animation/built-in';
import { StateBuilder, StateTransform } from 'mol-state';
import { PluginContext } from '../../mol-plugin/context';
import { PluginCommands } from '../../mol-plugin/command';
import { StateTransforms } from '../../mol-plugin/state/transforms';
import { StructureRepresentation3DHelpers } from '../../mol-plugin/state/transforms/representation';
import { Color } from '../../mol-util/color';
import { PluginStateObject as PSO } from '../../mol-plugin/state/objects';
import { AnimateModelIndex } from '../../mol-plugin/state/animation/built-in';
import { StateBuilder, StateTransform } from '../../mol-state';
import { StripedResidues } from './coloring';
// import { BasicWrapperControls } from './controls';
import { StaticSuperpositionTestData, buildStaticSuperposition, dynamicSuperpositionTest } from './superposition';

20
src/apps/basic-wrapper/superposition.ts
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@@ -6,17 +6,17 @@
// TODO: move to an "example"
import { PluginContext } from 'mol-plugin/context';
import { Mat4 } from 'mol-math/linear-algebra';
import { PluginContext } from '../../mol-plugin/context';
import { Mat4 } from '../../mol-math/linear-algebra';
import { StateHelper } from './helpers';
import { PluginCommands } from 'mol-plugin/command';
import { StateSelection, StateBuilder } from 'mol-state';
import { PluginStateObject as PSO } from 'mol-plugin/state/objects';
import { MolScriptBuilder as MS } from 'mol-script/language/builder';
import { compile } from 'mol-script/runtime/query/compiler';
import { StructureSelection, QueryContext } from 'mol-model/structure';
import { superposeStructures } from 'mol-model/structure/structure/util/superposition';
import Expression from 'mol-script/language/expression';
import { PluginCommands } from '../../mol-plugin/command';
import { StateSelection, StateBuilder } from '../../mol-state';
import { PluginStateObject as PSO } from '../../mol-plugin/state/objects';
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { compile } from '../../mol-script/runtime/query/compiler';
import { StructureSelection, QueryContext } from '../../mol-model/structure';
import { superposeStructures } from '../../mol-model/structure/structure/util/superposition';
import Expression from '../../mol-script/language/expression';
export type SuperpositionTestInput = {
pdbId: string,

14
src/apps/chem-comp-bond/create-table.ts
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@@ -14,13 +14,13 @@ require('util.promisify').shim()
const readFile = util.promisify(fs.readFile)
const writeFile = util.promisify(fs.writeFile)
import { Progress } from 'mol-task'
import { Database, Table, DatabaseCollection, Column } from 'mol-data/db'
import CIF from 'mol-io/reader/cif'
import { CifWriter } from 'mol-io/writer/cif'
import { CCD_Schema } from 'mol-io/reader/cif/schema/ccd'
import { SetUtils } from 'mol-util/set'
import { DefaultMap } from 'mol-util/map'
import { Progress } from '../../mol-task'
import { Database, Table, DatabaseCollection, Column } from '../../mol-data/db'
import { CIF } from '../../mol-io/reader/cif'
import { CifWriter } from '../../mol-io/writer/cif'
import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd'
import { SetUtils } from '../../mol-util/set'
import { DefaultMap } from '../../mol-util/map'
export async function ensureAvailable(path: string, url: string) {
if (FORCE_DOWNLOAD || !fs.existsSync(path)) {

8
src/apps/cif2bcif/converter.ts
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@@ -4,11 +4,11 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import CIF, { CifCategory, getCifFieldType, CifField } from 'mol-io/reader/cif'
import { CifWriter } from 'mol-io/writer/cif'
import { CIF, CifCategory, getCifFieldType, CifField } from '../../mol-io/reader/cif'
import { CifWriter } from '../../mol-io/writer/cif'
import * as fs from 'fs'
import { Progress, Task, RuntimeContext } from 'mol-task';
import { classifyFloatArray, classifyIntArray } from 'mol-io/common/binary-cif';
import { Progress, Task, RuntimeContext } from '../../mol-task';
import { classifyFloatArray, classifyIntArray } from '../../mol-io/common/binary-cif';
function showProgress(p: Progress) {
process.stdout.write(`\r${new Array(80).join(' ')}`);

6
src/apps/domain-annotation-server/mapping.ts
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@@ -4,10 +4,10 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Table } from 'mol-data/db'
import { CifWriter } from 'mol-io/writer/cif'
import { Table } from '../../mol-data/db'
import { CifWriter } from '../../mol-io/writer/cif'
import * as S from './schemas'
//import { getCategoryInstanceProvider } from './utils'
// import { getCategoryInstanceProvider } from './utils'
export default function create(allData: any) {
const mols = Object.keys(allData);

2
src/apps/domain-annotation-server/schemas.ts
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@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Column } from 'mol-data/db'
import { Column } from '../../mol-data/db'
import Type = Column.Schema

20
src/apps/image-generator/index.ts
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@@ -8,16 +8,16 @@ import * as argparse from 'argparse'
import createContext = require('gl')
import fs = require('fs')
import { PNG } from 'pngjs'
import { Canvas3D, Canvas3DParams } from 'mol-canvas3d/canvas3d';
import InputObserver from 'mol-util/input/input-observer';
import { ColorTheme } from 'mol-theme/color';
import { SizeTheme } from 'mol-theme/size';
import { CartoonRepresentationProvider } from 'mol-repr/structure/representation/cartoon';
import CIF, { CifFrame } from 'mol-io/reader/cif'
import { trajectoryFromMmCIF } from 'mol-model-formats/structure/mmcif';
import { Model, Structure } from 'mol-model/structure';
import { ajaxGet } from 'mol-util/data-source';
import { ColorNames } from 'mol-util/color/tables';
import { Canvas3D, Canvas3DParams } from '../../mol-canvas3d/canvas3d';
import InputObserver from '../../mol-util/input/input-observer';
import { ColorTheme } from '../../mol-theme/color';
import { SizeTheme } from '../../mol-theme/size';
import { CartoonRepresentationProvider } from '../../mol-repr/structure/representation/cartoon';
import { CIF, CifFrame } from '../../mol-io/reader/cif'
import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
import { Model, Structure } from '../../mol-model/structure';
import { ajaxGet } from '../../mol-util/data-source';
import { ColorNames } from '../../mol-util/color/tables';
const width = 2048
const height = 1536

6
src/apps/schema-generator/schema-from-cif-dic.ts
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@@ -9,8 +9,8 @@ import * as argparse from 'argparse'
import * as fs from 'fs'
import fetch from 'node-fetch'
import Csv from 'mol-io/reader/csv/parser'
import CIF, { CifFrame } from 'mol-io/reader/cif'
import { parseCsv } from '../../mol-io/reader/csv/parser'
import { CIF, CifFrame } from '../../mol-io/reader/cif'
import { generateSchema } from './util/cif-dic'
import { generate } from './util/generate'
import { Filter } from './util/schema'
@@ -52,7 +52,7 @@ async function runGenerateSchema(name: string, fieldNamesPath?: string, typescri
async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
const fieldNamesStr = fs.readFileSync(fieldNamesPath, 'utf8')
const parsed = await Csv(fieldNamesStr, { noColumnNames: true }).run();
const parsed = await parseCsv(fieldNamesStr, { noColumnNames: true }).run();
if (parsed.isError) throw parser.error
const csvFile = parsed.result;

4
src/apps/schema-generator/util/cif-dic.ts
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@@ -5,8 +5,8 @@
*/
import { Database, Column, EnumCol, StrCol, IntCol, ListCol, FloatCol, CoordCol, MatrixCol, VectorCol } from './schema'
import * as Data from 'mol-io/reader/cif/data-model'
import { CifFrame } from 'mol-io/reader/cif/data-model';
import * as Data from '../../../mol-io/reader/cif/data-model'
import { CifFrame } from '../../../mol-io/reader/cif/data-model';
export function getFieldType (type: string, description: string, values?: string[]): Column {
switch (type) {

2
src/apps/schema-generator/util/generate.ts
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@@ -5,7 +5,7 @@
*/
import { Database, Filter, Column } from './schema'
import { indentString } from 'mol-util/string';
import { indentString } from '../../../mol-util/string';
function header (name: string, info: string, importDatabasePath = 'mol-data/db') {
return `/**

10
src/apps/state-docs/index.ts
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@@ -4,13 +4,13 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import * as _ from 'mol-plugin/state/transforms'
import { StateTransformer, StateObject } from 'mol-state';
import { StringBuilder } from 'mol-util';
import * as _ from '../../mol-plugin/state/transforms'
import { StateTransformer, StateObject } from '../../mol-state';
import { StringBuilder } from '../../mol-util';
import * as fs from 'fs';
import { paramsToMd } from './pd-to-md';
import { PluginContext } from 'mol-plugin/context';
import { ParamDefinition } from 'mol-util/param-definition';
import { PluginContext } from '../../mol-plugin/context';
import { ParamDefinition } from '../../mol-util/param-definition';
// force the transform to be evaluated
_.StateTransforms.Data.Download.id

2
src/apps/state-docs/pd-to-md.ts
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@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
export function paramsToMd(params: PD.Params) {
return getParams(params, 0);

4
src/apps/structure-info/helpers.ts
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@@ -9,8 +9,8 @@ import * as fs from 'fs'
import fetch from 'node-fetch'
require('util.promisify').shim();
import CIF from 'mol-io/reader/cif'
import { Progress } from 'mol-task'
import { CIF } from '../../mol-io/reader/cif'
import { Progress } from '../../mol-task'
const readFileAsync = util.promisify(fs.readFile);

12
src/apps/structure-info/model.ts
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@@ -8,13 +8,13 @@
import * as argparse from 'argparse'
require('util.promisify').shim();
import { CifFrame } from 'mol-io/reader/cif'
import { Model, Structure, StructureElement, Unit, StructureProperties, UnitRing } from 'mol-model/structure'
// import { Run, Progress } from 'mol-task'
import { OrderedSet } from 'mol-data/int';
import { CifFrame } from '../../mol-io/reader/cif'
import { Model, Structure, StructureElement, Unit, StructureProperties, UnitRing } from '../../mol-model/structure'
// import { Run, Progress } from '../../mol-task'
import { OrderedSet } from '../../mol-data/int';
import { openCif, downloadCif } from './helpers';
import { Vec3 } from 'mol-math/linear-algebra';
import { trajectoryFromMmCIF } from 'mol-model-formats/structure/mmcif';
import { Vec3 } from '../../mol-math/linear-algebra';
import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
async function downloadFromPdb(pdb: string) {

18
src/apps/structure-info/volume.ts
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@@ -8,16 +8,16 @@ import * as fs from 'fs'
import * as argparse from 'argparse'
import * as util from 'util'
import { VolumeData, VolumeIsoValue } from 'mol-model/volume'
import { VolumeData, VolumeIsoValue } from '../../mol-model/volume'
import { downloadCif } from './helpers'
import CIF from 'mol-io/reader/cif'
import { DensityServer_Data_Database } from 'mol-io/reader/cif/schema/density-server';
import { Table } from 'mol-data/db';
import { StringBuilder } from 'mol-util';
import { Task } from 'mol-task';
import { createVolumeIsosurfaceMesh } from 'mol-repr/volume/isosurface';
import { createEmptyTheme } from 'mol-theme/theme';
import { volumeFromDensityServerData } from 'mol-model-formats/volume/density-server';
import { CIF } from '../../mol-io/reader/cif'
import { DensityServer_Data_Database } from '../../mol-io/reader/cif/schema/density-server';
import { Table } from '../../mol-data/db';
import { StringBuilder } from '../../mol-util';
import { Task } from '../../mol-task';
import { createVolumeIsosurfaceMesh } from '../../mol-repr/volume/isosurface';
import { createEmptyTheme } from '../../mol-theme/theme';
import { volumeFromDensityServerData } from '../../mol-model-formats/volume/density-server';
require('util.promisify').shim();
const writeFileAsync = util.promisify(fs.writeFile);

30
src/apps/viewer/extensions/jolecule.ts
View File

@@ -4,21 +4,21 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { StateTree, StateBuilder, StateAction, State } from 'mol-state';
import { StateTransforms } from 'mol-plugin/state/transforms';
import { createModelTree, complexRepresentation } from 'mol-plugin/state/actions/structure';
import { PluginContext } from 'mol-plugin/context';
import { PluginStateObject } from 'mol-plugin/state/objects';
import { ParamDefinition } from 'mol-util/param-definition';
import { PluginCommands } from 'mol-plugin/command';
import { Vec3 } from 'mol-math/linear-algebra';
import { PluginStateSnapshotManager } from 'mol-plugin/state/snapshots';
import { MolScriptBuilder as MS } from 'mol-script/language/builder';
import { Text } from 'mol-geo/geometry/text/text';
import { UUID } from 'mol-util';
import { ColorNames } from 'mol-util/color/tables';
import { Camera } from 'mol-canvas3d/camera';
import { StructureRepresentation3DHelpers } from 'mol-plugin/state/transforms/representation';
import { StateTree, StateBuilder, StateAction, State } from '../../../mol-state';
import { StateTransforms } from '../../../mol-plugin/state/transforms';
import { createModelTree, complexRepresentation } from '../../../mol-plugin/state/actions/structure';
import { PluginContext } from '../../../mol-plugin/context';
import { PluginStateObject } from '../../../mol-plugin/state/objects';
import { ParamDefinition } from '../../../mol-util/param-definition';
import { PluginCommands } from '../../../mol-plugin/command';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { PluginStateSnapshotManager } from '../../../mol-plugin/state/snapshots';
import { MolScriptBuilder as MS } from '../../../mol-script/language/builder';
import { Text } from '../../../mol-geo/geometry/text/text';
import { UUID } from '../../../mol-util';
import { ColorNames } from '../../../mol-util/color/tables';
import { Camera } from '../../../mol-canvas3d/camera';
import { StructureRepresentation3DHelpers } from '../../../mol-plugin/state/transforms/representation';
export const CreateJoleculeState = StateAction.build({
display: { name: 'Jolecule State Import' },

8
src/apps/viewer/index.ts
View File

@@ -4,11 +4,11 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { createPlugin, DefaultPluginSpec } from 'mol-plugin';
import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
import './index.html'
import { PluginContext } from 'mol-plugin/context';
import { PluginCommands } from 'mol-plugin/command';
import { PluginSpec } from 'mol-plugin/spec';
import { PluginContext } from '../../mol-plugin/context';
import { PluginCommands } from '../../mol-plugin/command';
import { PluginSpec } from '../../mol-plugin/spec';
import { CreateJoleculeState } from './extensions/jolecule';
require('mol-plugin/skin/light.scss')

6
src/examples/proteopedia-wrapper/annotation.ts
View File

@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { CustomElementProperty } from 'mol-model-props/common/custom-element-property';
import { Model, ElementIndex, ResidueIndex } from 'mol-model/structure';
import { Color } from 'mol-util/color';
import { CustomElementProperty } from '../../mol-model-props/common/custom-element-property';
import { Model, ElementIndex, ResidueIndex } from '../../mol-model/structure';
import { Color } from '../../mol-util/color';
const EvolutionaryConservationPalette: Color[] = [
[255, 255, 129], // insufficient

14
src/examples/proteopedia-wrapper/coloring.ts
View File

@@ -6,14 +6,14 @@
*/
import { Unit, StructureProperties, StructureElement, Link } from 'mol-model/structure';
import { Unit, StructureProperties, StructureElement, Link } from '../../mol-model/structure';
import { Color } from 'mol-util/color';
import { Location } from 'mol-model/location';
import { ColorTheme, LocationColor } from 'mol-theme/color';
import { ParamDefinition as PD } from 'mol-util/param-definition'
import { ThemeDataContext } from 'mol-theme/theme';
import { Column } from 'mol-data/db';
import { Color } from '../../mol-util/color';
import { Location } from '../../mol-model/location';
import { ColorTheme, LocationColor } from '../../mol-theme/color';
import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { ThemeDataContext } from '../../mol-theme/theme';
import { Column } from '../../mol-data/db';
const Description = 'Gives every chain a color from a list based on its `asym_id` value.'

10
src/examples/proteopedia-wrapper/helpers.ts
View File

@@ -4,11 +4,11 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { ResidueIndex, Model } from 'mol-model/structure';
import { BuiltInStructureRepresentationsName } from 'mol-repr/structure/registry';
import { BuiltInColorThemeName } from 'mol-theme/color';
import { AminoAcidNames } from 'mol-model/structure/model/types';
import { PluginContext } from 'mol-plugin/context';
import { ResidueIndex, Model } from '../../mol-model/structure';
import { BuiltInStructureRepresentationsName } from '../../mol-repr/structure/registry';
import { BuiltInColorThemeName } from '../../mol-theme/color';
import { AminoAcidNames } from '../../mol-model/structure/model/types';
import { PluginContext } from '../../mol-plugin/context';
export interface ModelInfo {
hetResidues: { name: string, indices: ResidueIndex[] }[],

36
src/examples/proteopedia-wrapper/index.ts
View File

@@ -4,32 +4,32 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { createPlugin, DefaultPluginSpec } from 'mol-plugin';
import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
import './index.html'
import { PluginContext } from 'mol-plugin/context';
import { PluginCommands } from 'mol-plugin/command';
import { StateTransforms } from 'mol-plugin/state/transforms';
import { StructureRepresentation3DHelpers } from 'mol-plugin/state/transforms/representation';
import { Color } from 'mol-util/color';
import { PluginStateObject as PSO, PluginStateObject } from 'mol-plugin/state/objects';
import { AnimateModelIndex } from 'mol-plugin/state/animation/built-in';
import { StateBuilder, StateObject } from 'mol-state';
import { PluginContext } from '../../mol-plugin/context';
import { PluginCommands } from '../../mol-plugin/command';
import { StateTransforms } from '../../mol-plugin/state/transforms';
import { StructureRepresentation3DHelpers } from '../../mol-plugin/state/transforms/representation';
import { Color } from '../../mol-util/color';
import { PluginStateObject as PSO, PluginStateObject } from '../../mol-plugin/state/objects';
import { AnimateModelIndex } from '../../mol-plugin/state/animation/built-in';
import { StateBuilder, StateObject } from '../../mol-state';
import { EvolutionaryConservation } from './annotation';
import { LoadParams, SupportedFormats, RepresentationStyle, ModelInfo, StateElements } from './helpers';
import { RxEventHelper } from 'mol-util/rx-event-helper';
import { RxEventHelper } from '../../mol-util/rx-event-helper';
import { ControlsWrapper } from './ui/controls';
import { PluginState } from 'mol-plugin/state';
import { Scheduler } from 'mol-task';
import { PluginState } from '../../mol-plugin/state';
import { Scheduler } from '../../mol-task';
import { createProteopediaCustomTheme } from './coloring';
import { MolScriptBuilder as MS } from 'mol-script/language/builder';
import { BuiltInStructureRepresentations } from 'mol-repr/structure/registry';
import { BuiltInColorThemes } from 'mol-theme/color';
import { BuiltInSizeThemes } from 'mol-theme/size';
import { ColorNames } from 'mol-util/color/tables';
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { BuiltInStructureRepresentations } from '../../mol-repr/structure/registry';
import { BuiltInColorThemes } from '../../mol-theme/color';
import { BuiltInSizeThemes } from '../../mol-theme/size';
import { ColorNames } from '../../mol-util/color/tables';
// import { Vec3 } from 'mol-math/linear-algebra';
// import { ParamDefinition } from 'mol-util/param-definition';
// import { Text } from 'mol-geo/geometry/text/text';
require('mol-plugin/skin/light.scss')
require('../../mol-plugin/skin/light.scss')
class MolStarProteopediaWrapper {
static VERSION_MAJOR = 3;

8
src/examples/proteopedia-wrapper/ui/controls.tsx
View File

@@ -5,10 +5,10 @@
*/
import * as React from 'react';
import { PluginUIComponent } from 'mol-plugin/ui/base';
import { CurrentObject } from 'mol-plugin/ui/plugin';
import { AnimationControls } from 'mol-plugin/ui/state/animation';
import { CameraSnapshots } from 'mol-plugin/ui/camera';
import { PluginUIComponent } from '../../../mol-plugin/ui/base';
import { CurrentObject } from '../../../mol-plugin/ui/plugin';
import { AnimationControls } from '../../../mol-plugin/ui/state/animation';
import { CameraSnapshots } from '../../../mol-plugin/ui/camera';
export class ControlsWrapper extends PluginUIComponent {
render() {

4
src/examples/task.ts
View File

@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Task, Progress, Scheduler, MultistepTask, chunkedSubtask } from 'mol-task'
import { now } from 'mol-util/now';
import { Task, Progress, Scheduler, MultistepTask, chunkedSubtask } from '../mol-task'
import { now } from '../mol-util/now';
export async function test1() {
const t = Task.create('test', async () => 1);

4
src/mol-app/component/color-theme.tsx
View File

@@ -5,8 +5,8 @@
*/
import * as React from 'react'
import { ColorTheme } from 'mol-theme/color';
import { Color } from 'mol-util/color';
import { ColorTheme } from '../../mol-theme/color';
import { Color } from '../../mol-util/color';
export interface ColorThemeComponentProps {
colorTheme: ColorTheme<any>

2
src/mol-app/component/parameter/boolean.tsx
View File

@@ -5,7 +5,7 @@
*/
import * as React from 'react'
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
export interface BooleanParamComponentProps {
label: string

6
src/mol-app/component/parameter/color.tsx
View File

@@ -5,9 +5,9 @@
*/
import * as React from 'react'
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ColorNames } from 'mol-util/color/tables';
import { Color } from 'mol-util/color';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { ColorNames } from '../../../mol-util/color/tables';
import { Color } from '../../../mol-util/color';
export interface ColorParamComponentProps {
label: string

2
src/mol-app/component/parameter/multi-select.tsx
View File

@@ -5,7 +5,7 @@
*/
import * as React from 'react'
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
export interface MultiSelectParamComponentProps<T extends string> {
label: string

2
src/mol-app/component/parameter/number.tsx
View File

@@ -5,7 +5,7 @@
*/
import * as React from 'react'
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
export interface NumberParamComponentProps {
label: string

2
src/mol-app/component/parameter/select.tsx
View File

@@ -5,7 +5,7 @@
*/
import * as React from 'react'
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
export interface SelectParamComponentProps<T extends string> {
label: string

2
src/mol-app/component/parameter/text.tsx
View File

@@ -5,7 +5,7 @@
*/
import * as React from 'react'
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
export interface TextParamComponentProps {
label: string

4
src/mol-app/component/parameters.tsx
View File

@@ -5,14 +5,14 @@
*/
import * as React from 'react'
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { BooleanParamComponent } from './parameter/boolean';
import { NumberParamComponent } from './parameter/number';
import { SelectParamComponent } from './parameter/select';
import { MultiSelectParamComponent } from './parameter/multi-select';
import { TextParamComponent } from './parameter/text';
import { ColorParamComponent } from './parameter/color';
import { camelCaseToWords } from 'mol-util/string';
import { camelCaseToWords } from '../../mol-util/string';
interface ParametersProps<P extends PD.Params> {
params: P

4
src/mol-canvas3d/camera.ts
View File

@@ -5,9 +5,9 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Mat4, Vec3, Vec4, EPSILON } from 'mol-math/linear-algebra'
import { Mat4, Vec3, Vec4, EPSILON } from '../mol-math/linear-algebra'
import { Viewport, cameraProject, cameraUnproject } from './camera/util';
import { Object3D } from 'mol-gl/object3d';
import { Object3D } from '../mol-gl/object3d';
import { BehaviorSubject } from 'rxjs';
import { CameraTransitionManager } from './camera/transition';

6
src/mol-canvas3d/camera/transition.ts
View File

@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Camera } from 'mol-canvas3d/camera';
import { Quat, Vec3 } from 'mol-math/linear-algebra';
import { lerp } from 'mol-math/interpolate';
import { Camera } from '../camera';
import { Quat, Vec3 } from '../../mol-math/linear-algebra';
import { lerp } from '../../mol-math/interpolate';
export { CameraTransitionManager }

2
src/mol-canvas3d/camera/util.ts
View File

@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Mat4, Vec3, Vec4, EPSILON } from 'mol-math/linear-algebra'
import { Mat4, Vec3, Vec4, EPSILON } from '../../mol-math/linear-algebra'
export { Viewport }

34
src/mol-canvas3d/canvas3d.ts
View File

@@ -5,30 +5,30 @@
*/
import { BehaviorSubject, Subscription } from 'rxjs';
import { now } from 'mol-util/now';
import { Vec3 } from 'mol-math/linear-algebra'
import InputObserver, { ModifiersKeys, ButtonsType } from 'mol-util/input/input-observer'
import Renderer, { RendererStats, RendererParams } from 'mol-gl/renderer'
import { GraphicsRenderObject } from 'mol-gl/render-object'
import { now } from '../mol-util/now';
import { Vec3 } from '../mol-math/linear-algebra'
import InputObserver, { ModifiersKeys, ButtonsType } from '../mol-util/input/input-observer'
import Renderer, { RendererStats, RendererParams } from '../mol-gl/renderer'
import { GraphicsRenderObject } from '../mol-gl/render-object'
import { TrackballControls, TrackballControlsParams } from './controls/trackball'
import { Viewport } from './camera/util'
import { createContext, WebGLContext, getGLContext } from 'mol-gl/webgl/context';
import { Representation } from 'mol-repr/representation';
import Scene from 'mol-gl/scene';
import { GraphicsRenderVariant } from 'mol-gl/webgl/render-item';
import { PickingId } from 'mol-geo/geometry/picking';
import { MarkerAction } from 'mol-geo/geometry/marker-data';
import { Loci, EmptyLoci, isEmptyLoci } from 'mol-model/loci';
import { createContext, WebGLContext, getGLContext } from '../mol-gl/webgl/context';
import { Representation } from '../mol-repr/representation';
import Scene from '../mol-gl/scene';
import { GraphicsRenderVariant } from '../mol-gl/webgl/render-item';
import { PickingId } from '../mol-geo/geometry/picking';
import { MarkerAction } from '../mol-geo/geometry/marker-data';
import { Loci, EmptyLoci, isEmptyLoci } from '../mol-model/loci';
import { Camera } from './camera';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ParamDefinition as PD } from '../mol-util/param-definition';
import { BoundingSphereHelper, DebugHelperParams } from './helper/bounding-sphere-helper';
import { SetUtils } from 'mol-util/set';
import { SetUtils } from '../mol-util/set';
import { Canvas3dInteractionHelper } from './helper/interaction-events';
import { PostprocessingParams, PostprocessingPass } from './passes/postprocessing';
import { MultiSampleParams, MultiSamplePass } from './passes/multi-sample';
import { GLRenderingContext } from 'mol-gl/webgl/compat';
import { PixelData } from 'mol-util/image';
import { readTexture } from 'mol-gl/compute/util';
import { GLRenderingContext } from '../mol-gl/webgl/compat';
import { PixelData } from '../mol-util/image';
import { readTexture } from '../mol-gl/compute/util';
import { DrawPass } from './passes/draw';
import { PickPass } from './passes/pick';

8
src/mol-canvas3d/controls/trackball.ts
View File

@@ -8,11 +8,11 @@
* copyright (c) 2010-2018 three.js authors. MIT License
*/
import { Quat, Vec2, Vec3, EPSILON } from 'mol-math/linear-algebra';
import { Quat, Vec2, Vec3, EPSILON } from '../../mol-math/linear-algebra';
import { cameraLookAt, Viewport } from '../camera/util';
import InputObserver, { DragInput, WheelInput, ButtonsType, PinchInput } from 'mol-util/input/input-observer';
import { Object3D } from 'mol-gl/object3d';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import InputObserver, { DragInput, WheelInput, ButtonsType, PinchInput } from '../../mol-util/input/input-observer';
import { Object3D } from '../../mol-gl/object3d';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
export const TrackballControlsParams = {
noScroll: PD.Boolean(true, { isHidden: true }),

28
src/mol-canvas3d/helper/bounding-sphere-helper.ts
View File

@@ -4,20 +4,20 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { createRenderObject, GraphicsRenderObject, getNextMaterialId } from 'mol-gl/render-object'
import { MeshBuilder } from 'mol-geo/geometry/mesh/mesh-builder';
import { addSphere } from 'mol-geo/geometry/mesh/builder/sphere';
import { Mesh } from 'mol-geo/geometry/mesh/mesh';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import Scene from 'mol-gl/scene';
import { WebGLContext } from 'mol-gl/webgl/context';
import { Sphere3D } from 'mol-math/geometry';
import { Color } from 'mol-util/color';
import { ColorNames } from 'mol-util/color/tables';
import { TransformData } from 'mol-geo/geometry/transform-data';
import { sphereVertexCount } from 'mol-geo/primitive/sphere';
import { ValueCell } from 'mol-util';
import { Geometry } from 'mol-geo/geometry/geometry';
import { createRenderObject, GraphicsRenderObject, getNextMaterialId } from '../../mol-gl/render-object'
import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import Scene from '../../mol-gl/scene';
import { WebGLContext } from '../../mol-gl/webgl/context';
import { Sphere3D } from '../../mol-math/geometry';
import { Color } from '../../mol-util/color';
import { ColorNames } from '../../mol-util/color/tables';
import { TransformData } from '../../mol-geo/geometry/transform-data';
import { sphereVertexCount } from '../../mol-geo/primitive/sphere';
import { ValueCell } from '../../mol-util';
import { Geometry } from '../../mol-geo/geometry/geometry';
export const DebugHelperParams = {
sceneBoundingSpheres: PD.Boolean(false, { description: 'Show scene bounding spheres.' }),

10
src/mol-canvas3d/helper/interaction-events.ts
View File

@@ -4,11 +4,11 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { PickingId } from 'mol-geo/geometry/picking';
import { EmptyLoci } from 'mol-model/loci';
import { Representation } from 'mol-repr/representation';
import InputObserver, { ModifiersKeys, ButtonsType } from 'mol-util/input/input-observer';
import { RxEventHelper } from 'mol-util/rx-event-helper';
import { PickingId } from '../../mol-geo/geometry/picking';
import { EmptyLoci } from '../../mol-model/loci';
import { Representation } from '../../mol-repr/representation';
import InputObserver, { ModifiersKeys, ButtonsType } from '../../mol-util/input/input-observer';
import { RxEventHelper } from '../../mol-util/rx-event-helper';
type Canvas3D = import('../canvas3d').Canvas3D

10
src/mol-canvas3d/passes/draw.ts
View File

@@ -4,12 +4,12 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { WebGLContext } from 'mol-gl/webgl/context';
import { createRenderTarget, RenderTarget } from 'mol-gl/webgl/render-target';
import Renderer from 'mol-gl/renderer';
import Scene from 'mol-gl/scene';
import { WebGLContext } from '../../mol-gl/webgl/context';
import { createRenderTarget, RenderTarget } from '../../mol-gl/webgl/render-target';
import Renderer from '../../mol-gl/renderer';
import Scene from '../../mol-gl/scene';
import { BoundingSphereHelper } from '../helper/bounding-sphere-helper';
import { createTexture, Texture } from 'mol-gl/webgl/texture';
import { createTexture, Texture } from '../../mol-gl/webgl/texture';
export class DrawPass {

24
src/mol-canvas3d/passes/multi-sample.ts
View File

@@ -4,18 +4,18 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { QuadSchema, QuadValues } from 'mol-gl/compute/util';
import { TextureSpec, UniformSpec, Values } from 'mol-gl/renderable/schema';
import { Texture } from 'mol-gl/webgl/texture';
import { WebGLContext } from 'mol-gl/webgl/context';
import { ValueCell } from 'mol-util';
import { Vec2 } from 'mol-math/linear-algebra';
import { ShaderCode } from 'mol-gl/shader-code';
import { createComputeRenderItem } from 'mol-gl/webgl/render-item';
import { createComputeRenderable, ComputeRenderable } from 'mol-gl/renderable';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { RenderTarget, createRenderTarget } from 'mol-gl/webgl/render-target';
import { Camera } from 'mol-canvas3d/camera';
import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
import { TextureSpec, UniformSpec, Values } from '../../mol-gl/renderable/schema';
import { Texture } from '../../mol-gl/webgl/texture';
import { WebGLContext } from '../../mol-gl/webgl/context';
import { ValueCell } from '../../mol-util';
import { Vec2 } from '../../mol-math/linear-algebra';
import { ShaderCode } from '../../mol-gl/shader-code';
import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
import { createComputeRenderable, ComputeRenderable } from '../../mol-gl/renderable';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { RenderTarget, createRenderTarget } from '../../mol-gl/webgl/render-target';
import { Camera } from '../../mol-canvas3d/camera';
import { PostprocessingPass } from './postprocessing';
import { DrawPass } from './draw';

12
src/mol-canvas3d/passes/pick.ts
View File

@@ -4,12 +4,12 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { WebGLContext } from 'mol-gl/webgl/context';
import { createRenderTarget, RenderTarget } from 'mol-gl/webgl/render-target';
import Renderer from 'mol-gl/renderer';
import Scene from 'mol-gl/scene';
import { PickingId } from 'mol-geo/geometry/picking';
import { decodeFloatRGB } from 'mol-util/float-packing';
import { WebGLContext } from '../../mol-gl/webgl/context';
import { createRenderTarget, RenderTarget } from '../../mol-gl/webgl/render-target';
import Renderer from '../../mol-gl/renderer';
import Scene from '../../mol-gl/scene';
import { PickingId } from '../../mol-geo/geometry/picking';
import { decodeFloatRGB } from '../../mol-util/float-packing';
const readBuffer = new Uint8Array(4)

24
src/mol-canvas3d/passes/postprocessing.ts
View File

@@ -4,19 +4,19 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { QuadSchema, QuadValues } from 'mol-gl/compute/util';
import { TextureSpec, Values, UniformSpec, DefineSpec } from 'mol-gl/renderable/schema';
import { ShaderCode } from 'mol-gl/shader-code';
import { WebGLContext } from 'mol-gl/webgl/context';
import { Texture } from 'mol-gl/webgl/texture';
import { ValueCell } from 'mol-util';
import { createComputeRenderItem } from 'mol-gl/webgl/render-item';
import { createComputeRenderable, ComputeRenderable } from 'mol-gl/renderable';
import { Vec2, Vec3 } from 'mol-math/linear-algebra';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { createRenderTarget, RenderTarget } from 'mol-gl/webgl/render-target';
import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
import { TextureSpec, Values, UniformSpec, DefineSpec } from '../../mol-gl/renderable/schema';
import { ShaderCode } from '../../mol-gl/shader-code';
import { WebGLContext } from '../../mol-gl/webgl/context';
import { Texture } from '../../mol-gl/webgl/texture';
import { ValueCell } from '../../mol-util';
import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
import { createComputeRenderable, ComputeRenderable } from '../../mol-gl/renderable';
import { Vec2, Vec3 } from '../../mol-math/linear-algebra';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { createRenderTarget, RenderTarget } from '../../mol-gl/webgl/render-target';
import { DrawPass } from './draw';
import { Camera } from 'mol-canvas3d/camera';
import { Camera } from '../../mol-canvas3d/camera';
const PostprocessingSchema = {
...QuadSchema,

2
src/mol-data/db/column.ts
View File

@@ -6,7 +6,7 @@
*/
import * as ColumnHelpers from './column-helpers'
import { Tensor as Tensors } from 'mol-math/linear-algebra'
import { Tensor as Tensors } from '../../mol-math/linear-algebra'
interface Column<T> {
readonly schema: Column.Schema,

2
src/mol-data/db/table.ts
View File

@@ -6,7 +6,7 @@
import Column from './column'
import { sortArray } from '../util/sort'
import { StringBuilder } from 'mol-util';
import { StringBuilder } from '../../mol-util';
/** A collection of columns */
type Table<Schema extends Table.Schema> = {

2
src/mol-data/util/array.ts
View File

@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { ArrayCtor } from 'mol-util/type-helpers';
import { ArrayCtor } from '../../mol-util/type-helpers';
export function arrayFind<T>(array: ArrayLike<T>, f: (v: T) => boolean): T | undefined {
for (let i = 0, _i = array.length; i < _i; i++) {

2
src/mol-data/util/buckets.ts
View File

@@ -5,7 +5,7 @@
*/
import { sort, arraySwap } from './sort';
import { AssignableArrayLike } from 'mol-util/type-helpers';
import { AssignableArrayLike } from '../../mol-util/type-helpers';
type Bucket = {
key: any,

22
src/mol-geo/geometry/base.ts
View File

@@ -4,19 +4,19 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { RenderableState } from 'mol-gl/renderable';
import { ValueCell } from 'mol-util';
import { BaseValues } from 'mol-gl/renderable/schema';
import { RenderableState } from '../../mol-gl/renderable';
import { ValueCell } from '../../mol-util';
import { BaseValues } from '../../mol-gl/renderable/schema';
import { LocationIterator } from '../util/location-iterator';
import { ParamDefinition as PD } from 'mol-util/param-definition'
import { Color } from 'mol-util/color';
import { Vec3 } from 'mol-math/linear-algebra';
import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { Color } from '../../mol-util/color';
import { Vec3 } from '../../mol-math/linear-algebra';
import { TransformData, createIdentityTransform } from './transform-data';
import { Theme } from 'mol-theme/theme';
import { ColorNames } from 'mol-util/color/tables';
import { NullLocation } from 'mol-model/location';
import { UniformColorTheme } from 'mol-theme/color/uniform';
import { UniformSizeTheme } from 'mol-theme/size/uniform';
import { Theme } from '../../mol-theme/theme';
import { ColorNames } from '../../mol-util/color/tables';
import { NullLocation } from '../../mol-model/location';
import { UniformColorTheme } from '../../mol-theme/color/uniform';
import { UniformSizeTheme } from '../../mol-theme/size/uniform';
export const VisualQualityInfo = {
'custom': {},

12
src/mol-geo/geometry/color-data.ts
View File

@@ -4,13 +4,13 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util';
import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
import { Color } from 'mol-util/color';
import { Vec2, Vec3 } from 'mol-math/linear-algebra';
import { ValueCell } from '../../mol-util';
import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
import { Color } from '../../mol-util/color';
import { Vec2, Vec3 } from '../../mol-math/linear-algebra';
import { LocationIterator } from '../util/location-iterator';
import { NullLocation } from 'mol-model/location';
import { LocationColor, ColorTheme } from 'mol-theme/color';
import { NullLocation } from '../../mol-model/location';
import { LocationColor, ColorTheme } from '../../mol-theme/color';
import { Geometry } from './geometry';
export type ColorType = 'uniform' | 'instance' | 'group' | 'groupInstance'

26
src/mol-geo/geometry/direct-volume/direct-volume.ts
View File

@@ -4,25 +4,25 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util'
import { Sphere3D, Box3D } from 'mol-math/geometry'
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { DirectVolumeValues } from 'mol-gl/renderable/direct-volume';
import { Vec3, Mat4, Vec2 } from 'mol-math/linear-algebra';
import { ValueCell } from '../../../mol-util'
import { Sphere3D, Box3D } from '../../../mol-math/geometry'
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { DirectVolumeValues } from '../../../mol-gl/renderable/direct-volume';
import { Vec3, Mat4, Vec2 } from '../../../mol-math/linear-algebra';
import { Box } from '../../primitive/box';
import { createTransferFunctionTexture, getControlPointsFromVec2Array } from './transfer-function';
import { Texture } from 'mol-gl/webgl/texture';
import { LocationIterator } from 'mol-geo/util/location-iterator';
import { Texture } from '../../../mol-gl/webgl/texture';
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { TransformData } from '../transform-data';
import { createColors } from '../color-data';
import { createMarkers } from '../marker-data';
import { GeometryUtils } from '../geometry';
import { transformPositionArray } from 'mol-geo/util';
import { calculateBoundingSphere } from 'mol-gl/renderable/util';
import { Theme } from 'mol-theme/theme';
import { RenderableState } from 'mol-gl/renderable';
import { ColorListOptions, ColorListName } from 'mol-util/color/scale';
import { Color } from 'mol-util/color';
import { transformPositionArray } from '../../../mol-geo/util';
import { calculateBoundingSphere } from '../../../mol-gl/renderable/util';
import { Theme } from '../../../mol-theme/theme';
import { RenderableState } from '../../../mol-gl/renderable';
import { ColorListOptions, ColorListName } from '../../../mol-util/color/scale';
import { Color } from '../../../mol-util/color';
import { BaseGeometry } from '../base';
import { createEmptyOverpaint } from '../overpaint-data';
import { createEmptyTransparency } from '../transparency-data';

12
src/mol-geo/geometry/direct-volume/transfer-function.ts
View File

@@ -4,12 +4,12 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { TextureImage } from 'mol-gl/renderable/util';
import { spline } from 'mol-math/interpolate';
import { ColorScale, Color } from 'mol-util/color';
import { ValueCell } from 'mol-util';
import { Vec2 } from 'mol-math/linear-algebra';
import { ColorListName } from 'mol-util/color/scale';
import { TextureImage } from '../../../mol-gl/renderable/util';
import { spline } from '../../../mol-math/interpolate';
import { ColorScale, Color } from '../../../mol-util/color';
import { ValueCell } from '../../../mol-util';
import { Vec2 } from '../../../mol-math/linear-algebra';
import { ColorListName } from '../../../mol-util/color/scale';
export interface ControlPoint { x: number, alpha: number }

14
src/mol-geo/geometry/geometry.ts
View File

@@ -7,20 +7,20 @@
import { Mesh } from './mesh/mesh';
import { Points } from './points/points';
import { Text } from './text/text';
import { RenderableState } from 'mol-gl/renderable';
import { RenderableState } from '../../mol-gl/renderable';
import { LocationIterator } from '../util/location-iterator';
import { ColorType } from './color-data';
import { SizeType } from './size-data';
import { Lines } from './lines/lines';
import { ParamDefinition as PD } from 'mol-util/param-definition'
import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { DirectVolume } from './direct-volume/direct-volume';
import { Color } from 'mol-util/color';
import { Color } from '../../mol-util/color';
import { Spheres } from './spheres/spheres';
import { arrayMax } from 'mol-util/array';
import { arrayMax } from '../../mol-util/array';
import { TransformData } from './transform-data';
import { Theme } from 'mol-theme/theme';
import { RenderObjectValuesType } from 'mol-gl/render-object';
import { ValueOf } from 'mol-util/type-helpers';
import { Theme } from '../../mol-theme/theme';
import { RenderObjectValuesType } from '../../mol-gl/render-object';
import { ValueOf } from '../../mol-util/type-helpers';
import { TextureMesh } from './texture-mesh/texture-mesh';
export type GeometryKindType = {

8
src/mol-geo/geometry/lines/lines-builder.ts
View File

@@ -4,11 +4,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util/value-cell'
import { ChunkedArray } from 'mol-data/util';
import { ValueCell } from '../../../mol-util/value-cell'
import { ChunkedArray } from '../../../mol-data/util';
import { Lines } from './lines';
import { Mat4, Vec3 } from 'mol-math/linear-algebra';
import { Cage } from 'mol-geo/primitive/cage';
import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
import { Cage } from '../../../mol-geo/primitive/cage';
export interface LinesBuilder {
add(startX: number, startY: number, startZ: number, endX: number, endY: number, endZ: number, group: number): void

16
src/mol-geo/geometry/lines/lines.ts
View File

@@ -4,8 +4,8 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util'
import { Mat4 } from 'mol-math/linear-algebra'
import { ValueCell } from '../../../mol-util'
import { Mat4 } from '../../../mol-math/linear-algebra'
import { transformPositionArray/* , transformDirectionArray, getNormalMatrix */ } from '../../util';
import { GeometryUtils } from '../geometry';
import { createColors } from '../color-data';
@@ -13,14 +13,14 @@ import { createMarkers } from '../marker-data';
import { createSizes } from '../size-data';
import { TransformData } from '../transform-data';
import { LocationIterator } from '../../util/location-iterator';
import { LinesValues } from 'mol-gl/renderable/lines';
import { LinesValues } from '../../../mol-gl/renderable/lines';
import { Mesh } from '../mesh/mesh';
import { LinesBuilder } from './lines-builder';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { calculateBoundingSphere } from 'mol-gl/renderable/util';
import { Sphere3D } from 'mol-math/geometry';
import { Theme } from 'mol-theme/theme';
import { Color } from 'mol-util/color';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { calculateBoundingSphere } from '../../../mol-gl/renderable/util';
import { Sphere3D } from '../../../mol-math/geometry';
import { Theme } from '../../../mol-theme/theme';
import { Color } from '../../../mol-util/color';
import { BaseGeometry } from '../base';
import { createEmptyOverpaint } from '../overpaint-data';
import { createEmptyTransparency } from '../transparency-data';

6
src/mol-geo/geometry/marker-data.ts
View File

@@ -4,9 +4,9 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util/value-cell'
import { Vec2 } from 'mol-math/linear-algebra'
import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
import { ValueCell } from '../../mol-util/value-cell'
import { Vec2 } from '../../mol-math/linear-algebra'
import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
export type MarkerData = {
tMarker: ValueCell<TextureImage<Uint8Array>>

4
src/mol-geo/geometry/mesh/builder/bounding-box.ts
View File

@@ -4,8 +4,8 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Vec3 } from 'mol-math/linear-algebra';
import { Box3D } from 'mol-math/geometry';
import { Vec3 } from '../../../../mol-math/linear-algebra';
import { Box3D } from '../../../../mol-math/geometry';
import { MeshBuilder } from '../mesh-builder';
import { CylinderProps } from '../../../primitive/cylinder';
import { addCylinder } from './cylinder';

2
src/mol-geo/geometry/mesh/builder/cylinder.ts
View File

@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { Vec3, Mat4 } from '../../../../mol-math/linear-algebra';
import { MeshBuilder } from '../mesh-builder';
import { Primitive } from '../../../primitive/primitive';
import { Cylinder, CylinderProps } from '../../../primitive/cylinder';

4
src/mol-geo/geometry/mesh/builder/sheet.ts
View File

@@ -5,8 +5,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Vec3 } from 'mol-math/linear-algebra';
import { ChunkedArray } from 'mol-data/util';
import { Vec3 } from '../../../../mol-math/linear-algebra';
import { ChunkedArray } from '../../../../mol-data/util';
import { MeshBuilder } from '../mesh-builder';
const tA = Vec3.zero()

2
src/mol-geo/geometry/mesh/builder/sphere.ts
View File

@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { Vec3, Mat4 } from '../../../../mol-math/linear-algebra';
import { MeshBuilder } from '../mesh-builder';
import { Primitive } from '../../../primitive/primitive';
import { Sphere } from '../../../primitive/sphere';

4
src/mol-geo/geometry/mesh/builder/tube.ts
View File

@@ -5,8 +5,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Vec3 } from 'mol-math/linear-algebra';
import { ChunkedArray } from 'mol-data/util';
import { Vec3 } from '../../../../mol-math/linear-algebra';
import { ChunkedArray } from '../../../../mol-data/util';
import { MeshBuilder } from '../mesh-builder';
const normalVector = Vec3.zero()

8
src/mol-geo/geometry/mesh/mesh-builder.ts
View File

@@ -4,13 +4,13 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util/value-cell'
import { Vec3, Mat4, Mat3 } from 'mol-math/linear-algebra';
import { ChunkedArray } from 'mol-data/util';
import { ValueCell } from '../../../mol-util/value-cell'
import { Vec3, Mat4, Mat3 } from '../../../mol-math/linear-algebra';
import { ChunkedArray } from '../../../mol-data/util';
import { Mesh } from './mesh';
import { getNormalMatrix } from '../../util';
import { Primitive } from '../../primitive/primitive';
import { Cage } from 'mol-geo/primitive/cage';
import { Cage } from '../../../mol-geo/primitive/cage';
import { addSphere } from './builder/sphere';
import { addCylinder } from './builder/cylinder';

20
src/mol-geo/geometry/mesh/mesh.ts
View File

@@ -4,22 +4,22 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Task } from 'mol-task'
import { ValueCell } from 'mol-util'
import { Vec3, Mat4 } from 'mol-math/linear-algebra'
import { Sphere3D } from 'mol-math/geometry'
import { Task } from '../../../mol-task'
import { ValueCell } from '../../../mol-util'
import { Vec3, Mat4 } from '../../../mol-math/linear-algebra'
import { Sphere3D } from '../../../mol-math/geometry'
import { transformPositionArray/* , transformDirectionArray, getNormalMatrix */ } from '../../util';
import { GeometryUtils } from '../geometry';
import { createMarkers } from '../marker-data';
import { TransformData } from '../transform-data';
import { LocationIterator } from '../../util/location-iterator';
import { createColors } from '../color-data';
import { ChunkedArray } from 'mol-data/util';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { calculateBoundingSphere } from 'mol-gl/renderable/util';
import { Theme } from 'mol-theme/theme';
import { MeshValues } from 'mol-gl/renderable/mesh';
import { Color } from 'mol-util/color';
import { ChunkedArray } from '../../../mol-data/util';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { calculateBoundingSphere } from '../../../mol-gl/renderable/util';
import { Theme } from '../../../mol-theme/theme';
import { MeshValues } from '../../../mol-gl/renderable/mesh';
import { Color } from '../../../mol-util/color';
import { BaseGeometry } from '../base';
import { createEmptyOverpaint } from '../overpaint-data';
import { createEmptyTransparency } from '../transparency-data';

8
src/mol-geo/geometry/overpaint-data.ts
View File

@@ -4,10 +4,10 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util/value-cell'
import { Vec2 } from 'mol-math/linear-algebra'
import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
import { Color } from 'mol-util/color';
import { ValueCell } from '../../mol-util/value-cell'
import { Vec2 } from '../../mol-math/linear-algebra'
import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
import { Color } from '../../mol-util/color';
export type OverpaintData = {
tOverpaint: ValueCell<TextureImage<Uint8Array>>

4
src/mol-geo/geometry/points/points-builder.ts
View File

@@ -4,8 +4,8 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util/value-cell'
import { ChunkedArray } from 'mol-data/util';
import { ValueCell } from '../../../mol-util/value-cell'
import { ChunkedArray } from '../../../mol-data/util';
import { Points } from './points';
export interface PointsBuilder {

18
src/mol-geo/geometry/points/points.ts
View File

@@ -4,8 +4,8 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util'
import { Mat4 } from 'mol-math/linear-algebra'
import { ValueCell } from '../../../mol-util'
import { Mat4 } from '../../../mol-math/linear-algebra'
import { transformPositionArray/* , transformDirectionArray, getNormalMatrix */ } from '../../util';
import { GeometryUtils } from '../geometry';
import { createColors } from '../color-data';
@@ -13,13 +13,13 @@ import { createMarkers } from '../marker-data';
import { createSizes } from '../size-data';
import { TransformData } from '../transform-data';
import { LocationIterator } from '../../util/location-iterator';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { calculateBoundingSphere } from 'mol-gl/renderable/util';
import { Sphere3D } from 'mol-math/geometry';
import { Theme } from 'mol-theme/theme';
import { PointsValues } from 'mol-gl/renderable/points';
import { RenderableState } from 'mol-gl/renderable';
import { Color } from 'mol-util/color';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { calculateBoundingSphere } from '../../../mol-gl/renderable/util';
import { Sphere3D } from '../../../mol-math/geometry';
import { Theme } from '../../../mol-theme/theme';
import { PointsValues } from '../../../mol-gl/renderable/points';
import { RenderableState } from '../../../mol-gl/renderable';
import { Color } from '../../../mol-util/color';
import { BaseGeometry } from '../base';
import { createEmptyOverpaint } from '../overpaint-data';
import { createEmptyTransparency } from '../transparency-data';

12
src/mol-geo/geometry/size-data.ts
View File

@@ -4,14 +4,14 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util';
import { Vec2 } from 'mol-math/linear-algebra';
import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
import { ValueCell } from '../../mol-util';
import { Vec2 } from '../../mol-math/linear-algebra';
import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
import { LocationIterator } from '../util/location-iterator';
import { Location, NullLocation } from 'mol-model/location';
import { SizeTheme } from 'mol-theme/size';
import { Location, NullLocation } from '../../mol-model/location';
import { SizeTheme } from '../../mol-theme/size';
import { Geometry } from './geometry';
import { encodeFloatLog, decodeFloatLog } from 'mol-util/float-packing';
import { encodeFloatLog, decodeFloatLog } from '../../mol-util/float-packing';
export type SizeType = 'uniform' | 'instance' | 'group' | 'groupInstance'

4
src/mol-geo/geometry/spheres/spheres-builder.ts
View File

@@ -4,8 +4,8 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util/value-cell'
import { ChunkedArray } from 'mol-data/util';
import { ValueCell } from '../../../mol-util/value-cell'
import { ChunkedArray } from '../../../mol-data/util';
import { Spheres } from './spheres';
const quadMapping = new Float32Array([

16
src/mol-geo/geometry/spheres/spheres.ts
View File

@@ -4,19 +4,19 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util';
import { ValueCell } from '../../../mol-util';
import { GeometryUtils } from '../geometry';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { TransformData } from '../transform-data';
import { LocationIterator } from 'mol-geo/util/location-iterator';
import { Theme } from 'mol-theme/theme';
import { SpheresValues } from 'mol-gl/renderable/spheres';
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { Theme } from '../../../mol-theme/theme';
import { SpheresValues } from '../../../mol-gl/renderable/spheres';
import { createColors } from '../color-data';
import { createMarkers } from '../marker-data';
import { calculateBoundingSphere } from 'mol-gl/renderable/util';
import { Sphere3D } from 'mol-math/geometry';
import { calculateBoundingSphere } from '../../../mol-gl/renderable/util';
import { Sphere3D } from '../../../mol-math/geometry';
import { createSizes, getMaxSize } from '../size-data';
import { Color } from 'mol-util/color';
import { Color } from '../../../mol-util/color';
import { BaseGeometry } from '../base';
import { createEmptyOverpaint } from '../overpaint-data';
import { createEmptyTransparency } from '../transparency-data';

6
src/mol-geo/geometry/text/font-atlas.ts
View File

@@ -4,9 +4,9 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { edt } from 'mol-math/geometry/distance-transform';
import { createTextureImage, TextureImage } from 'mol-gl/renderable/util';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { edt } from '../../../mol-math/geometry/distance-transform';
import { createTextureImage, TextureImage } from '../../../mol-gl/renderable/util';
const TextAtlasCache: { [k: string]: FontAtlas } = {}

6
src/mol-geo/geometry/text/text-builder.ts
View File

@@ -4,9 +4,9 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ValueCell } from 'mol-util/value-cell'
import { ChunkedArray } from 'mol-data/util';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { ValueCell } from '../../../mol-util/value-cell'
import { ChunkedArray } from '../../../mol-data/util';
import { Text } from './text';
import { getFontAtlas } from './font-atlas';

26
src/mol-geo/geometry/text/text.ts
View File

@@ -4,25 +4,25 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ValueCell } from 'mol-util';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { ValueCell } from '../../../mol-util';
import { GeometryUtils } from '../geometry';
import { LocationIterator } from 'mol-geo/util/location-iterator';
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { TransformData } from '../transform-data';
import { Theme } from 'mol-theme/theme';
import { Theme } from '../../../mol-theme/theme';
import { createColors } from '../color-data';
import { createSizes, getMaxSize } from '../size-data';
import { createMarkers } from '../marker-data';
import { ColorNames } from 'mol-util/color/tables';
import { Sphere3D } from 'mol-math/geometry';
import { calculateBoundingSphere, TextureImage, createTextureImage } from 'mol-gl/renderable/util';
import { TextValues } from 'mol-gl/renderable/text';
import { Color } from 'mol-util/color';
import { Vec3 } from 'mol-math/linear-algebra';
import { ColorNames } from '../../../mol-util/color/tables';
import { Sphere3D } from '../../../mol-math/geometry';
import { calculateBoundingSphere, TextureImage, createTextureImage } from '../../../mol-gl/renderable/util';
import { TextValues } from '../../../mol-gl/renderable/text';
import { Color } from '../../../mol-util/color';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { FontAtlasParams } from './font-atlas';
import { RenderableState } from 'mol-gl/renderable';
import { clamp } from 'mol-math/interpolate';
import { createRenderObject as _createRenderObject } from 'mol-gl/render-object';
import { RenderableState } from '../../../mol-gl/renderable';
import { clamp } from '../../../mol-math/interpolate';
import { createRenderObject as _createRenderObject } from '../../../mol-gl/render-object';
import { BaseGeometry } from '../base';
import { createEmptyOverpaint } from '../overpaint-data';
import { createEmptyTransparency } from '../transparency-data';

22
src/mol-geo/geometry/texture-mesh/texture-mesh.ts
View File

@@ -4,24 +4,24 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util'
import { Sphere3D } from 'mol-math/geometry'
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { LocationIterator } from 'mol-geo/util/location-iterator';
import { ValueCell } from '../../../mol-util'
import { Sphere3D } from '../../../mol-math/geometry'
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { TransformData } from '../transform-data';
import { createColors } from '../color-data';
import { createMarkers } from '../marker-data';
import { GeometryUtils } from '../geometry';
import { Theme } from 'mol-theme/theme';
import { Color } from 'mol-util/color';
import { Theme } from '../../../mol-theme/theme';
import { Color } from '../../../mol-util/color';
import { BaseGeometry } from '../base';
import { createEmptyOverpaint } from '../overpaint-data';
import { createEmptyTransparency } from '../transparency-data';
import { TextureMeshValues } from 'mol-gl/renderable/texture-mesh';
import { calculateTransformBoundingSphere } from 'mol-gl/renderable/util';
import { Texture } from 'mol-gl/webgl/texture';
import { Vec2 } from 'mol-math/linear-algebra';
import { fillSerial } from 'mol-util/array';
import { TextureMeshValues } from '../../../mol-gl/renderable/texture-mesh';
import { calculateTransformBoundingSphere } from '../../../mol-gl/renderable/util';
import { Texture } from '../../../mol-gl/webgl/texture';
import { Vec2 } from '../../../mol-math/linear-algebra';
import { fillSerial } from '../../../mol-util/array';
export interface TextureMesh {
readonly kind: 'texture-mesh',

6
src/mol-geo/geometry/transform-data.ts
View File

@@ -4,9 +4,9 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util';
import { Mat4 } from 'mol-math/linear-algebra';
import { fillSerial } from 'mol-util/array';
import { ValueCell } from '../../mol-util';
import { Mat4 } from '../../mol-math/linear-algebra';
import { fillSerial } from '../../mol-util/array';
export type TransformData = {
/**

8
src/mol-geo/geometry/transparency-data.ts
View File

@@ -4,10 +4,10 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util/value-cell'
import { Vec2 } from 'mol-math/linear-algebra'
import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
import { Transparency } from 'mol-theme/transparency';
import { ValueCell } from '../../mol-util/value-cell'
import { Vec2 } from '../../mol-math/linear-algebra'
import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
import { Transparency } from '../../mol-theme/transparency';
export type TransparencyData = {
tTransparency: ValueCell<TextureImage<Uint8Array>>

2
src/mol-geo/primitive/box.ts
View File

@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Vec3 } from 'mol-math/linear-algebra'
import { Vec3 } from '../../mol-math/linear-algebra'
import { Primitive, PrimitiveBuilder } from './primitive';
import { polygon } from './polygon'
import { Cage, createCage } from './cage';

2
src/mol-geo/primitive/cylinder.ts
View File

@@ -6,7 +6,7 @@
// adapted from three.js, MIT License Copyright 2010-2018 three.js authors
import { Vec3 } from 'mol-math/linear-algebra'
import { Vec3 } from '../../mol-math/linear-algebra'
import { Primitive } from './primitive';
export const DefaultCylinderProps = {

6
src/mol-geo/primitive/plane.ts
View File

@@ -1,12 +1,12 @@
import { Primitive } from './primitive';
import { Cage } from './cage';
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Primitive } from './primitive';
import { Cage } from './cage';
const plane: Primitive = {
vertices: new Float32Array([
-0.5, 0.5, 0,

2
src/mol-geo/primitive/polyhedron.ts
View File

@@ -6,7 +6,7 @@
// adapted from three.js, MIT License Copyright 2010-2018 three.js authors
import { Vec3 } from 'mol-math/linear-algebra'
import { Vec3 } from '../../mol-math/linear-algebra'
import { computeIndexedVertexNormals, appplyRadius } from '../util'
import { Primitive } from './primitive';

2
src/mol-geo/primitive/primitive.ts
View File

@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Vec3 } from 'mol-math/linear-algebra';
import { Vec3 } from '../../mol-math/linear-algebra';
export interface Primitive {
vertices: ArrayLike<number>

2
src/mol-geo/primitive/prism.ts
View File

@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Vec3 } from 'mol-math/linear-algebra'
import { Vec3 } from '../../mol-math/linear-algebra'
import { Primitive, PrimitiveBuilder } from './primitive';
import { polygon } from './polygon'
import { Cage } from './cage';

2
src/mol-geo/primitive/pyramid.ts
View File

@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Vec3 } from 'mol-math/linear-algebra'
import { Vec3 } from '../../mol-math/linear-algebra'
import { Primitive, PrimitiveBuilder, createPrimitive } from './primitive';
import { polygon } from './polygon'
import { Cage } from './cage';

2
src/mol-geo/primitive/spiked-ball.ts
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@@ -6,7 +6,7 @@
import { createPrimitive, Primitive } from './primitive';
import { dodecahedronVertices, dodecahedronFaces } from './dodecahedron';
import { Vec3 } from 'mol-math/linear-algebra';
import { Vec3 } from '../../mol-math/linear-algebra';
function calcCenter(out: Vec3, ...vec3s: Vec3[]) {
Vec3.set(out, 0, 0, 0)

2
src/mol-geo/primitive/star.ts
View File

@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Vec3 } from 'mol-math/linear-algebra'
import { Vec3 } from '../../mol-math/linear-algebra'
import { Primitive, PrimitiveBuilder } from './primitive';
export const DefaultStarProps = {

2
src/mol-geo/primitive/wedge.ts
View File

@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Vec3 } from 'mol-math/linear-algebra'
import { Vec3 } from '../../mol-math/linear-algebra'
import { Primitive, PrimitiveBuilder } from './primitive';
import { polygon } from './polygon'
import { PrismCage } from './prism';

4
src/mol-geo/util.ts
View File

@@ -4,8 +4,8 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Vec3, Mat4, Mat3 } from 'mol-math/linear-algebra'
import { NumberArray } from 'mol-util/type-helpers';
import { Vec3, Mat4, Mat3 } from '../mol-math/linear-algebra'
import { NumberArray } from '../mol-util/type-helpers';
export function normalizeVec3Array<T extends NumberArray> (a: T) {
const n = a.length

4
src/mol-geo/util/location-iterator.ts
View File

@@ -4,8 +4,8 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Iterator } from 'mol-data';
import { NullLocation, Location } from 'mol-model/location';
import { Iterator } from '../../mol-data';
import { NullLocation, Location } from '../../mol-model/location';
export interface LocationValue {
location: Location

6
src/mol-geo/util/marching-cubes/algorithm.ts
View File

@@ -5,11 +5,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Task, RuntimeContext } from 'mol-task'
import { Tensor } from 'mol-math/linear-algebra'
import { Task, RuntimeContext } from '../../../mol-task'
import { Tensor } from '../../../mol-math/linear-algebra'
import { Mesh } from '../../geometry/mesh/mesh'
import { Index, EdgeIdInfo, CubeEdges, EdgeTable, TriTable } from './tables'
import { defaults } from 'mol-util'
import { defaults } from '../../../mol-util'
import { MarchinCubesBuilder, MarchinCubesMeshBuilder, MarchinCubesLinesBuilder } from './builder';
import { Lines } from '../../geometry/lines/lines';

2
src/mol-geo/util/marching-cubes/builder.ts
View File

@@ -7,7 +7,7 @@
*/
import { ChunkedArray } from '../../../mol-data/util';
import { ValueCell, noop } from 'mol-util';
import { ValueCell, noop } from '../../../mol-util';
import { Mesh } from '../../geometry/mesh/mesh';
import { AllowedContours } from './tables';
import { LinesBuilder } from '../../geometry/lines/lines-builder';

2
src/mol-gl/_spec/gl.shim.ts
View File

@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { idFactory } from 'mol-util/id-factory'
import { idFactory } from '../../mol-util/id-factory'
const c = {
ACTIVE_ATTRIBUTE_MAX_LENGTH: 35722,

22
src/mol-gl/_spec/renderer.spec.ts
View File

@@ -6,24 +6,24 @@
import { createGl } from './gl.shim';
import { Camera } from 'mol-canvas3d/camera';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { ValueCell } from 'mol-util';
import { Camera } from '../../mol-canvas3d/camera';
import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
import { ValueCell } from '../../mol-util';
import Renderer from '../renderer';
import { createValueColor } from 'mol-geo/geometry/color-data';
import { createValueSize } from 'mol-geo/geometry/size-data';
import { createValueColor } from '../../mol-geo/geometry/color-data';
import { createValueSize } from '../../mol-geo/geometry/size-data';
import { createContext } from '../webgl/context';
import { RenderableState } from '../renderable';
import { createRenderObject } from '../render-object';
import { PointsValues } from '../renderable/points';
import Scene from '../scene';
import { createEmptyMarkers } from 'mol-geo/geometry/marker-data';
import { fillSerial } from 'mol-util/array';
import { Color } from 'mol-util/color';
import { Sphere3D } from 'mol-math/geometry';
import { createEmptyOverpaint } from 'mol-geo/geometry/overpaint-data';
import { createEmptyTransparency } from 'mol-geo/geometry/transparency-data';
import { createEmptyMarkers } from '../../mol-geo/geometry/marker-data';
import { fillSerial } from '../../mol-util/array';
import { Color } from '../../mol-util/color';
import { Sphere3D } from '../../mol-math/geometry';
import { createEmptyOverpaint } from '../../mol-geo/geometry/overpaint-data';
import { createEmptyTransparency } from '../../mol-geo/geometry/transparency-data';
function createRenderer(gl: WebGLRenderingContext) {
const ctx = createContext(gl)

16
src/mol-gl/compute/histogram-pyramid/reduction.ts
View File

@@ -8,16 +8,16 @@ import { createComputeRenderable, ComputeRenderable } from '../../renderable'
import { WebGLContext } from '../../webgl/context';
import { createComputeRenderItem } from '../../webgl/render-item';
import { Values, TextureSpec, UniformSpec } from '../../renderable/schema';
import { Texture, createTexture } from 'mol-gl/webgl/texture';
import { ShaderCode } from 'mol-gl/shader-code';
import { ValueCell } from 'mol-util';
import { Texture, createTexture } from '../../../mol-gl/webgl/texture';
import { ShaderCode } from '../../../mol-gl/shader-code';
import { ValueCell } from '../../../mol-util';
import { QuadSchema, QuadValues } from '../util';
import { Vec2 } from 'mol-math/linear-algebra';
import { Vec2 } from '../../../mol-math/linear-algebra';
import { getHistopyramidSum } from './sum';
import { Framebuffer, createFramebuffer } from 'mol-gl/webgl/framebuffer';
import { isPowerOfTwo } from 'mol-math/misc';
import quad_vert from 'mol-gl/shader/quad.vert'
import reduction_frag from 'mol-gl/shader/histogram-pyramid/reduction.frag'
import { Framebuffer, createFramebuffer } from '../../../mol-gl/webgl/framebuffer';
import { isPowerOfTwo } from '../../../mol-math/misc';
import quad_vert from '../../../mol-gl/shader/quad.vert'
import reduction_frag from '../../../mol-gl/shader/histogram-pyramid/reduction.frag'
const HistopyramidReductionSchema = {
...QuadSchema,

12
src/mol-gl/compute/histogram-pyramid/sum.ts
View File

@@ -8,13 +8,13 @@ import { createComputeRenderable, ComputeRenderable } from '../../renderable'
import { WebGLContext } from '../../webgl/context';
import { createComputeRenderItem } from '../../webgl/render-item';
import { Values, TextureSpec } from '../../renderable/schema';
import { Texture, createTexture } from 'mol-gl/webgl/texture';
import { ShaderCode } from 'mol-gl/shader-code';
import { ValueCell } from 'mol-util';
import { decodeFloatRGB } from 'mol-util/float-packing';
import { Texture, createTexture } from '../../../mol-gl/webgl/texture';
import { ShaderCode } from '../../../mol-gl/shader-code';
import { ValueCell } from '../../../mol-util';
import { decodeFloatRGB } from '../../../mol-util/float-packing';
import { QuadSchema, QuadValues } from '../util';
import quad_vert from 'mol-gl/shader/quad.vert'
import sum_frag from 'mol-gl/shader/histogram-pyramid/sum.frag'
import quad_vert from '../../../mol-gl/shader/quad.vert'
import sum_frag from '../../../mol-gl/shader/histogram-pyramid/sum.frag'
const HistopyramidSumSchema = {
...QuadSchema,

12
src/mol-gl/compute/marching-cubes/active-voxels.ts
View File

@@ -8,14 +8,14 @@ import { createComputeRenderable } from '../../renderable'
import { WebGLContext } from '../../webgl/context';
import { createComputeRenderItem } from '../../webgl/render-item';
import { Values, TextureSpec, UniformSpec } from '../../renderable/schema';
import { Texture, createTexture } from 'mol-gl/webgl/texture';
import { ShaderCode } from 'mol-gl/shader-code';
import { ValueCell } from 'mol-util';
import { Vec3, Vec2 } from 'mol-math/linear-algebra';
import { Texture, createTexture } from '../../../mol-gl/webgl/texture';
import { ShaderCode } from '../../../mol-gl/shader-code';
import { ValueCell } from '../../../mol-util';
import { Vec3, Vec2 } from '../../../mol-math/linear-algebra';
import { QuadSchema, QuadValues } from '../util';
import { getTriCount } from './tables';
import quad_vert from 'mol-gl/shader/quad.vert'
import active_voxels_frag from 'mol-gl/shader/marching-cubes/active-voxels.frag'
import quad_vert from '../../../mol-gl/shader/quad.vert'
import active_voxels_frag from '../../../mol-gl/shader/marching-cubes/active-voxels.frag'
/** name for shared framebuffer used for gpu marching cubes operations */
const FramebufferName = 'marching-cubes-active-voxels'

12
src/mol-gl/compute/marching-cubes/isosurface.ts
View File

@@ -8,15 +8,15 @@ import { createComputeRenderable } from '../../renderable'
import { WebGLContext } from '../../webgl/context';
import { createComputeRenderItem } from '../../webgl/render-item';
import { Values, TextureSpec, UniformSpec } from '../../renderable/schema';
import { Texture, createTexture } from 'mol-gl/webgl/texture';
import { ShaderCode } from 'mol-gl/shader-code';
import { ValueCell } from 'mol-util';
import { Vec3, Vec2, Mat4 } from 'mol-math/linear-algebra';
import { Texture, createTexture } from '../../../mol-gl/webgl/texture';
import { ShaderCode } from '../../../mol-gl/shader-code';
import { ValueCell } from '../../../mol-util';
import { Vec3, Vec2, Mat4 } from '../../../mol-math/linear-algebra';
import { QuadSchema, QuadValues } from '../util';
import { HistogramPyramid } from '../histogram-pyramid/reduction';
import { getTriIndices } from './tables';
import quad_vert from 'mol-gl/shader/quad.vert'
import isosurface_frag from 'mol-gl/shader/marching-cubes/isosurface.frag'
import quad_vert from '../../../mol-gl/shader/quad.vert'
import isosurface_frag from '../../../mol-gl/shader/marching-cubes/isosurface.frag'
/** name for shared framebuffer used for gpu marching cubes operations */
const FramebufferName = 'marching-cubes-isosurface'

4
src/mol-gl/compute/marching-cubes/tables.ts
View File

@@ -4,8 +4,8 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { TriTable, } from 'mol-geo/util/marching-cubes/tables';
import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
import { TriTable, } from '../../../mol-geo/util/marching-cubes/tables';
import { TextureImage, createTextureImage } from '../../../mol-gl/renderable/util';
let TriCount: TextureImage<Uint8Array> | undefined
export function getTriCount(): TextureImage<Uint8Array> {

14
src/mol-gl/compute/util.ts
View File

@@ -4,13 +4,13 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { WebGLContext } from 'mol-gl/webgl/context';
import { Texture } from 'mol-gl/webgl/texture';
import { printTextureImage } from 'mol-gl/renderable/util';
import { defaults, ValueCell } from 'mol-util';
import { ValueSpec, AttributeSpec, UniformSpec, Values } from 'mol-gl/renderable/schema';
import { Vec2 } from 'mol-math/linear-algebra';
import { GLRenderingContext } from 'mol-gl/webgl/compat';
import { WebGLContext } from '../../mol-gl/webgl/context';
import { Texture } from '../../mol-gl/webgl/texture';
import { printTextureImage } from '../../mol-gl/renderable/util';
import { defaults, ValueCell } from '../../mol-util';
import { ValueSpec, AttributeSpec, UniformSpec, Values } from '../../mol-gl/renderable/schema';
import { Vec2 } from '../../mol-math/linear-algebra';
import { GLRenderingContext } from '../../mol-gl/webgl/compat';
export const QuadPositions = new Float32Array([
1.0, 1.0, -1.0, 1.0, -1.0, -1.0, // First triangle

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