diff --git a/README.md b/README.md
index 29881c843b2f5e4d025d67af3d1129c341940fa1..bea25cde6c5ecf65b2286159027280754b09413c 100644
--- a/README.md
+++ b/README.md
@@ -9,6 +9,8 @@ The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that will
This particular project is the implementation of this technology (still under development).
+*If you are looking for the "MOLeculAR structure annoTator", that package is now available on NPM as [MolArt](https://www.npmjs.com/package/molart).*
+
## Project Overview
The core of Mol* currently consists of these modules (see under `src/`):
@@ -61,8 +63,7 @@ This project builds on experience from previous solutions:
DEBUG=molstar npm run watch
### Build for production:
- npm run build
- NODE_ENV=production npm run build-webpack
+ NODE_ENV=production npm run build
**Run**
@@ -94,7 +95,7 @@ Install CIFTools `npm install ciftools -g`
### Other scripts
**Create chem comp bond table**
- export NODE_PATH="lib"; node --max-old-space-size=8192 build/src/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
+ export NODE_PATH="lib"; node --max-old-space-size=4096 lib/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
**Test model server**
@@ -132,14 +133,17 @@ To get syntax highlighting for shader and graphql files add the following to Vis
## Publish
-## Prerelease
+### Prerelease
npm version prerelease # asumes the current version ends with '-dev.X'
npm publish --tag next
-## Release
+### Release
npm version 0.X.0 # provide valid semver string
npm publish
+## Deploy
+ node ./scripts/deploy.js # currently updates the viewer on molstar.org/viewer
+
## Contributing
Just open an issue or make a pull request. All contributions are welcome.
diff --git a/package.json b/package.json
index d1f18d63a1792e98a6fdf73ab0824c7585e8d719..3c72052a1fe35f1638fae0ee923a33acdda51e80 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "molstar",
- "version": "0.2.1",
+ "version": "0.2.2",
"description": "A comprehensive macromolecular library.",
"homepage": "https://github.com/molstar/molstar#readme",
"repository": {
@@ -23,7 +23,6 @@
"watch-webpack": "webpack -w --mode development --display minimal",
"model-server": "node lib/servers/model/server.js",
"model-server-watch": "nodemon --watch lib lib/servers/model/server.js",
- "postinstall": "npm run build",
"preversion": "npm run test",
"postversion": "git push && git push --tags",
"prepublishOnly": "npm run test && npm run build"
@@ -66,9 +65,10 @@
"circular-dependency-plugin": "^5.0.2",
"concurrently": "^4.1.0",
"cpx": "^1.5.0",
- "css-loader": "^2.1.1",
+ "css-loader": "^3.0.0",
"extra-watch-webpack-plugin": "^1.0.3",
- "file-loader": "^3.0.1",
+ "file-loader": "^4.0.0",
+ "fs-extra": "^8.0.1",
"graphql-code-generator": "^0.18.2",
"graphql-codegen-time": "^0.18.2",
"graphql-codegen-typescript-template": "^0.18.2",
@@ -76,26 +76,25 @@
"jest-raw-loader": "^1.0.1",
"mini-css-extract-plugin": "^0.7.0",
"node-sass": "^4.12.0",
- "raw-loader": "^2.0.0",
+ "raw-loader": "^3.0.0",
"resolve-url-loader": "^3.1.0",
"sass-loader": "^7.1.0",
+ "simple-git": "^1.113.0",
"style-loader": "^0.23.1",
"ts-jest": "^24.0.2",
"tslint": "^5.17.0",
"typescript": "^3.5.1",
- "uglify-js": "^3.6.0",
- "util.promisify": "^1.0.0",
- "webpack": "^4.32.2",
- "webpack-cli": "^3.3.2"
+ "webpack": "^4.33.0",
+ "webpack-cli": "^3.3.4"
},
"dependencies": {
"@types/argparse": "^1.0.36",
"@types/benchmark": "^1.0.31",
"@types/compression": "0.0.36",
- "@types/express": "^4.16.1",
+ "@types/express": "^4.17.0",
"@types/jest": "^24.0.13",
- "@types/node": "^12.0.4",
- "@types/node-fetch": "^2.3.4",
+ "@types/node": "^12.0.8",
+ "@types/node-fetch": "^2.3.5",
"@types/react": "^16.8.19",
"@types/react-dom": "^16.8.4",
"@types/swagger-ui-dist": "3.0.0",
@@ -109,7 +108,8 @@
"react": "^16.8.6",
"react-dom": "^16.8.6",
"rxjs": "^6.5.2",
- "swagger-ui-dist": "^3.22.2",
+ "swagger-ui-dist": "^3.22.3",
+ "util.promisify": "^1.0.0",
"xhr2": "^0.2.0"
}
}
diff --git a/scripts/deploy.js b/scripts/deploy.js
new file mode 100644
index 0000000000000000000000000000000000000000..c1d4fc30fdb5d60f0b9161ff7294b7926e975029
--- /dev/null
+++ b/scripts/deploy.js
@@ -0,0 +1,59 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+const git = require('simple-git')
+const path = require('path')
+const fs = require("fs")
+const fse = require("fs-extra")
+
+const remoteUrl = "https://github.com/molstar/molstar.github.io.git"
+const buildDir = path.resolve(__dirname, '../build/')
+const deployDir = path.resolve(buildDir, 'deploy/')
+const localPath = path.resolve(deployDir, 'molstar.github.io/')
+
+function log(command, stdout, stderr) {
+ if (command) {
+ console.log('\n###', command)
+ stdout.pipe(process.stdout)
+ stderr.pipe(process.stderr)
+ }
+}
+
+function copyViewer() {
+ console.log('\n###', 'copy viewer files')
+ const viewerBuildPath = path.resolve(buildDir, '../build/viewer/')
+ const viewerDeployPath = path.resolve(localPath, 'viewer/')
+ fse.copySync(viewerBuildPath, viewerDeployPath, { overwrite: true })
+}
+
+if (!fs.existsSync(localPath)) {
+ console.log('\n###', 'create localPath')
+ fs.mkdirSync(localPath, { recursive: true })
+}
+
+process.chdir(localPath);
+
+if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
+ console.log('\n###', 'clone repository')
+ git()
+ .outputHandler(log)
+ .clone(remoteUrl, localPath)
+ .fetch(['--all'])
+ .exec(copyViewer)
+ .add(['-A'])
+ .commit('updated viewer')
+ .push()
+} else {
+ console.log('\n###', 'update repository')
+ git()
+ .outputHandler(log)
+ .fetch(['--all'])
+ .reset(['--hard', 'origin/master'])
+ .exec(copyViewer)
+ .add(['-A'])
+ .commit('updated viewer')
+ .push()
+}
\ No newline at end of file
diff --git a/src/apps/chem-comp-bond/create-table.ts b/src/apps/chem-comp-bond/create-table.ts
index cc29af24a60f6490751d22ec1b4101d68cb3665e..ba541008609cb3c9c61c6dd09ff192f8e3535ad9 100644
--- a/src/apps/chem-comp-bond/create-table.ts
+++ b/src/apps/chem-comp-bond/create-table.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -15,12 +15,13 @@ 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 { Database, Table, DatabaseCollection } 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 { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
export async function ensureAvailable(path: string, url: string) {
if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
@@ -74,16 +75,6 @@ export function getEncodedCif(name: string, database: Database<Database.Schema>,
type CCB = Table<CCD_Schema['chem_comp_bond']>
type CCA = Table<CCD_Schema['chem_comp_atom']>
-const ChemCompBond_Schema = {
- comp_id: CCD_Schema['chem_comp_bond'].comp_id,
- atom_id_1: CCD_Schema['chem_comp_bond'].atom_id_1,
- atom_id_2: CCD_Schema['chem_comp_bond'].atom_id_2,
- value_order: CCD_Schema['chem_comp_bond'].value_order,
- pdbx_aromatic_flag: CCD_Schema['chem_comp_bond'].pdbx_aromatic_flag,
- pdbx_stereo_config: CCD_Schema['chem_comp_bond'].pdbx_stereo_config,
- molstar_protonation_variant: Column.Schema.Str()
-}
-
function ccbKey(compId: string, atomId1: string, atomId2: string) {
return atomId1 < atomId2 ? `${compId}:${atomId1}-${atomId2}` : `${compId}:${atomId2}-${atomId1}`
}
@@ -202,14 +193,14 @@ async function createBonds() {
}
}
- const bondTable = Table.ofArrays(ChemCompBond_Schema, {
+ const bondTable = Table.ofArrays(mmCIF_chemCompBond_schema, {
comp_id, atom_id_1, atom_id_2, value_order,
pdbx_aromatic_flag, pdbx_stereo_config, molstar_protonation_variant
})
const bondDatabase = Database.ofTables(
TABLE_NAME,
- { chem_comp_bond: ChemCompBond_Schema },
+ { chem_comp_bond: mmCIF_chemCompBond_schema },
{ chem_comp_bond: bondTable }
)
@@ -220,12 +211,15 @@ async function run(out: string, binary = false) {
const bonds = await createBonds()
const cif = getEncodedCif(TABLE_NAME, bonds, binary)
+ if (!fs.existsSync(path.dirname(out))) {
+ fs.mkdirSync(path.dirname(out));
+ }
writeFile(out, cif)
}
const TABLE_NAME = 'CHEM_COMP_BONDS'
-const DATA_DIR = path.join(__dirname, '..', '..', '..', 'data')
+const DATA_DIR = path.join(__dirname, '..', '..', '..', 'build/data')
const CCD_PATH = path.join(DATA_DIR, 'components.cif')
const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif')
const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif'
diff --git a/src/examples/proteopedia-wrapper/helpers.ts b/src/examples/proteopedia-wrapper/helpers.ts
index a15bcca86c8d9c3d20d16417680c583f3cc5f4a1..7d1360c3e31e095ea745b9afb91d16e54cb21131 100644
--- a/src/examples/proteopedia-wrapper/helpers.ts
+++ b/src/examples/proteopedia-wrapper/helpers.ts
@@ -105,6 +105,8 @@ export enum StateElements {
ModelProps = 'model-props',
Assembly = 'assembly',
+ VolumeStreaming = 'volume-streaming',
+
Sequence = 'sequence',
SequenceVisual = 'sequence-visual',
Het = 'het',
diff --git a/src/examples/proteopedia-wrapper/index.html b/src/examples/proteopedia-wrapper/index.html
index 288db037a5d4f2406c2a3b486fd2417dde62e592..5fd7d7bbc083c8f9e1637603fd524e2021e13a8d 100644
--- a/src/examples/proteopedia-wrapper/index.html
+++ b/src/examples/proteopedia-wrapper/index.html
@@ -40,6 +40,13 @@
width: 100%;
display: block;
}
+
+ #volume-streaming-wrapper {
+ position: absolute;
+ top: 100px;
+ left: 780px;
+ width: 300px;
+ }
</style>
<link rel="stylesheet" type="text/css" href="app.css" />
<script type="text/javascript" src="./index.js"></script>
@@ -55,6 +62,7 @@
</select>
</div>
<div id="app"></div>
+ <div id="volume-streaming-wrapper"></div>
<script>
// it might be a good idea to define these colors in a separate script file
var CustomColors = [0x00ff00, 0x0000ff];
@@ -66,7 +74,7 @@
function $(id) { return document.getElementById(id); }
- var pdbId = '1eve', assemblyId= 'preferred';
+ var pdbId = '1cbs', assemblyId= 'preferred';
var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
var format = 'cif';
@@ -151,6 +159,11 @@
addHetGroupsContainer();
addSeparator();
+ addHeader('Exp. Data');
+ addControl('Init', () => PluginWrapper.experimentalData.init($('volume-streaming-wrapper')));
+ addControl('Remove', () => PluginWrapper.experimentalData.remove());
+
+ addSeparator();
addHeader('State');
var snapshot;
diff --git a/src/examples/proteopedia-wrapper/index.ts b/src/examples/proteopedia-wrapper/index.ts
index bd9d4447f5a85563525caff904748792d1fdaa98..d444fed9d4c138a0488ff63cb1d0a8cd19dc1b15 100644
--- a/src/examples/proteopedia-wrapper/index.ts
+++ b/src/examples/proteopedia-wrapper/index.ts
@@ -4,6 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
+import * as ReactDOM from 'react-dom';
import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
import './index.html'
import { PluginContext } from '../../mol-plugin/context';
@@ -13,11 +14,11 @@ import { StructureRepresentation3DHelpers } from '../../mol-plugin/state/transfo
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 { StateBuilder, StateObject, StateSelection } from '../../mol-state';
import { EvolutionaryConservation } from './annotation';
import { LoadParams, SupportedFormats, RepresentationStyle, ModelInfo, StateElements } from './helpers';
import { RxEventHelper } from '../../mol-util/rx-event-helper';
-import { ControlsWrapper } from './ui/controls';
+import { ControlsWrapper, volumeStreamingControls } from './ui/controls';
import { PluginState } from '../../mol-plugin/state';
import { Scheduler } from '../../mol-task';
import { createProteopediaCustomTheme } from './coloring';
@@ -26,6 +27,8 @@ import { BuiltInStructureRepresentations } from '../../mol-repr/structure/regist
import { BuiltInColorThemes } from '../../mol-theme/color';
import { BuiltInSizeThemes } from '../../mol-theme/size';
import { ColorNames } from '../../mol-util/color/tables';
+import { InitVolumeStreaming, CreateVolumeStreamingInfo } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
+import { ParamDefinition } from '../../mol-util/param-definition';
// import { Vec3 } from 'mol-math/linear-algebra';
// import { ParamDefinition } from 'mol-util/param-definition';
// import { Text } from 'mol-geo/geometry/text/text';
@@ -264,6 +267,28 @@ class MolStarProteopediaWrapper {
}
}
+ private experimentalDataElement?: Element = void 0;
+ experimentalData = {
+ init: async (parent: Element) => {
+ const asm = this.state.select(StateElements.Assembly)[0].obj!;
+ const params = ParamDefinition.getDefaultValues(InitVolumeStreaming.definition.params!(asm, this.plugin));
+ params.behaviorRef = StateElements.VolumeStreaming;
+ params.defaultView = 'box';
+ await this.plugin.runTask(this.state.applyAction(InitVolumeStreaming, params, StateElements.Assembly));
+ this.experimentalDataElement = parent;
+ volumeStreamingControls(this.plugin, parent);
+ },
+ remove: () => {
+ const r = this.state.select(StateSelection.Generators.ofTransformer(CreateVolumeStreamingInfo))[0];
+ if (!r) return;
+ PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.state, ref: r.transform.ref });
+ if (this.experimentalDataElement) {
+ ReactDOM.unmountComponentAtNode(this.experimentalDataElement);
+ this.experimentalDataElement = void 0;
+ }
+ }
+ }
+
hetGroups = {
reset: () => {
const update = this.state.build().delete(StateElements.HetGroupFocus);
diff --git a/src/examples/proteopedia-wrapper/ui/controls.tsx b/src/examples/proteopedia-wrapper/ui/controls.tsx
index 3de24ed90c969ad5902bea4443149ef48901e9a2..df7938cc3c9b1fa92fc1b9ddf2bc4d74c769fe79 100644
--- a/src/examples/proteopedia-wrapper/ui/controls.tsx
+++ b/src/examples/proteopedia-wrapper/ui/controls.tsx
@@ -5,10 +5,14 @@
*/
import * as React from 'react';
+import * as ReactDOM from 'react-dom';
import { PluginUIComponent } from '../../../mol-plugin/ui/base';
-import { CurrentObject } from '../../../mol-plugin/ui/plugin';
+import { CurrentObject, PluginContextContainer } from '../../../mol-plugin/ui/plugin';
import { AnimationControls } from '../../../mol-plugin/ui/state/animation';
import { CameraSnapshots } from '../../../mol-plugin/ui/camera';
+import { PluginContext } from '../../../mol-plugin/context';
+import { TransformUpdaterControl } from '../../../mol-plugin/ui/state/update-transform';
+import { StateElements } from '../helpers';
export class ControlsWrapper extends PluginUIComponent {
render() {
@@ -18,4 +22,11 @@ export class ControlsWrapper extends PluginUIComponent {
<CameraSnapshots />
</div>;
}
+}
+
+export function volumeStreamingControls(plugin: PluginContext, parent: Element) {
+ ReactDOM.render(<PluginContextContainer plugin={plugin}>
+ <TransformUpdaterControl nodeRef={StateElements.VolumeStreaming} />
+ </PluginContextContainer>,
+ parent);
}
\ No newline at end of file
diff --git a/src/mol-app/component/parameter/boolean.tsx b/src/mol-app/component/parameter/boolean.tsx
index d5ec7529ed8a225b07904a37d7cbf54c64856b68..bb93409e4f24b135c5de0efe6db297d6e92bfdd7 100644
--- a/src/mol-app/component/parameter/boolean.tsx
+++ b/src/mol-app/component/parameter/boolean.tsx
@@ -9,7 +9,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
export interface BooleanParamComponentProps {
label: string
- param: PD.Boolean
+ param: PD.BooleanParam
value: boolean
onChange(v: boolean): void
}
diff --git a/src/mol-geo/geometry/overpaint-data.ts b/src/mol-geo/geometry/overpaint-data.ts
index c256cc8dc9feae640093a59f1945af66c79634aa..b97e19a4abfcc6f8f09cb8c9df01cf58b8082781 100644
--- a/src/mol-geo/geometry/overpaint-data.ts
+++ b/src/mol-geo/geometry/overpaint-data.ts
@@ -24,7 +24,7 @@ export function applyOverpaintColor(array: Uint8Array, start: number, end: numbe
}
export function clearOverpaint(array: Uint8Array, start: number, end: number) {
- array.fill(0, start, end)
+ array.fill(0, start * 4, end * 4)
}
export function createOverpaint(count: number, overpaintData?: OverpaintData): OverpaintData {
diff --git a/src/mol-io/reader/cif/schema/mmcif-extras.ts b/src/mol-io/reader/cif/schema/mmcif-extras.ts
index 10b5e32f74df25b17eaf76414e89f7cd9d98b74b..cb35f4879008bbffd1cc4fbd6c4f577aae29a53a 100644
--- a/src/mol-io/reader/cif/schema/mmcif-extras.ts
+++ b/src/mol-io/reader/cif/schema/mmcif-extras.ts
@@ -1,10 +1,12 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
- import { mmCIF_Schema } from './mmcif';
+import { mmCIF_Schema } from './mmcif';
+import { Column } from '../../../../mol-data/db';
export const mmCIF_residueId_schema = {
label_comp_id: mmCIF_Schema.atom_site.label_comp_id,
@@ -15,4 +17,10 @@ export const mmCIF_residueId_schema = {
auth_comp_id: mmCIF_Schema.atom_site.auth_atom_id,
auth_seq_id: mmCIF_Schema.atom_site.auth_seq_id,
auth_asym_id: mmCIF_Schema.atom_site.auth_asym_id
+}
+
+export const mmCIF_chemCompBond_schema = {
+ ...mmCIF_Schema.chem_comp_bond,
+ /** Indicates if the bond entry was taken from the protonation variant dictionary */
+ molstar_protonation_variant: Column.Schema.Str()
}
\ No newline at end of file
diff --git a/src/mol-io/reader/mol2/parser.ts b/src/mol-io/reader/mol2/parser.ts
index 1f727b61fc3982636874e200ac44297234ebf8b0..4e9429f31c8937bb4b4ffa0cafa5d87027aca480 100644
--- a/src/mol-io/reader/mol2/parser.ts
+++ b/src/mol-io/reader/mol2/parser.ts
@@ -84,7 +84,7 @@ function handleMolecule(state: State) {
molecule.mol_comment = getTokenString(tokenizer)
}
-function isStatus_bit(aString: String): Boolean {
+function isStatus_bit(aString: string): boolean {
if (aString.includes('DSPMOD') || aString.includes('TYPECOL') || aString.includes('CAP')
|| aString.includes('BACKBONE') || aString.includes('DICT') || aString.includes('ESSENTIAL')
|| aString.includes('WATER') || aString.includes('DIRECT')) {
diff --git a/src/mol-model-props/rcsb/assembly-symmetry.ts b/src/mol-model-props/rcsb/assembly-symmetry.ts
index 150a93ef4766560f6e76e3e3a2c875766e57c7a5..bdf36072cb34acacc21b0eb9a5da5ff30c894363 100644
--- a/src/mol-model-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-model-props/rcsb/assembly-symmetry.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -18,7 +18,6 @@ import { CifCategory } from '../../mol-io/reader/cif';
import { PropertyWrapper } from '../../mol-model-props/common/wrapper';
import { Task, RuntimeContext } from '../../mol-task';
import { GraphQLClient } from '../../mol-util/graphql-client';
-import { ajaxGet } from '../../mol-util/data-source';
const { str, int, float, Aliased, Vector, List } = Column.Schema;
@@ -183,13 +182,12 @@ export function AssemblySymmetry(db: AssemblySymmetry.Database): AssemblySymmetr
type SymmetryKind = 'GLOBAL' | 'LOCAL' | 'PSEUDO'
type SymmetryType = 'ASYMMETRIC' | 'CYCLIC' | 'DIHEDRAL' | 'HELICAL' | 'ICOSAHEDRAL' | 'OCTAHEDRAL' | 'TETRAHEDRAL'
-const Client = new GraphQLClient(AssemblySymmetry.GraphQLEndpointURL, ajaxGet)
-
export namespace AssemblySymmetry {
export function is(x: any): x is AssemblySymmetry {
return x['@type'] === 'rcsb_assembly_symmetry'
}
- export const GraphQLEndpointURL = '//rest-dev.rcsb.org/graphql'
+ export const GraphQLEndpointURL = '//rest-staging.rcsb.org/graphql'
+
export const Schema = {
rcsb_assembly_symmetry_info: {
updated_datetime_utc: Column.Schema.str
@@ -257,7 +255,7 @@ export namespace AssemblySymmetry {
export const Descriptor = _Descriptor;
- export async function attachFromCifOrAPI(model: Model, client: GraphQLClient = Client, ctx?: RuntimeContext) {
+ export async function attachFromCifOrAPI(model: Model, client: GraphQLClient, ctx?: RuntimeContext) {
if (model.customProperties.has(Descriptor)) return true;
let db: Database
@@ -266,8 +264,10 @@ export namespace AssemblySymmetry {
db = createDatabaseFromCif(model)
} else {
let result: AssemblySymmetryGraphQL.Query
+ console.log('model.label.toLowerCase()', model.label.toLowerCase())
const variables: AssemblySymmetryGraphQL.Variables = { pdbId: model.label.toLowerCase() };
try {
+ console.log('foo', client)
result = await client.request<AssemblySymmetryGraphQL.Query>(ctx || RuntimeContext.Synchronous, query, variables);
} catch (e) {
console.error(e)
diff --git a/src/mol-model-props/wwpdb/chem-comp-bond.ts b/src/mol-model-props/wwpdb/chem-comp-bond.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2395d4832d341d32eb8aa32d44dfbbaab79aafc5
--- /dev/null
+++ b/src/mol-model-props/wwpdb/chem-comp-bond.ts
@@ -0,0 +1,84 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Column, Table } from '../../mol-data/db';
+import { toTable } from '../../mol-io/reader/cif/schema';
+import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
+import { CifWriter } from '../../mol-io/writer/cif';
+
+export namespace ChemCompBond {
+ export type Property = Table<Schema['chem_comp_bond']>
+
+ export function getFromModel(model: Model): Property {
+ if (model.sourceData.kind !== 'mmCIF') return Table.ofUndefinedColumns(Schema.chem_comp_bond, 0);
+ const { chem_comp_bond } = model.sourceData.data
+ return Table.ofColumns(Schema.chem_comp_bond, {
+ ...chem_comp_bond,
+ molstar_protonation_variant: Column.Undefined(chem_comp_bond._rowCount, Column.Schema.Str())
+ });
+ }
+
+ export function get(model: Model): Property {
+ return model._staticPropertyData.__ChemCompBond__ || getFromModel(model);
+ }
+ function set(model: Model, prop: Property) {
+ (model._staticPropertyData.__ChemCompBond__ as Property) = prop;
+ }
+
+ export const Schema = { chem_comp_bond: mmCIF_chemCompBond_schema };
+ export type Schema = typeof Schema
+
+ export const Descriptor = CustomPropertyDescriptor({
+ isStatic: true,
+ name: 'chem_comp_bond',
+ cifExport: {
+ prefix: '',
+ context(ctx): Property { return get(ctx.firstModel); },
+ categories: [{
+ name: 'chem_comp_bond',
+ instance(ctx: Property) {
+ return CifWriter.Category.ofTable(ctx);
+ }
+ }]
+ }
+ });
+
+ function fromCifData(model: Model): Table<Schema['chem_comp_bond']> | undefined {
+ if (model.sourceData.kind !== 'mmCIF') return void 0;
+ const cat = model.sourceData.frame.categories.chem_comp_bond;
+ if (!cat) return void 0;
+ return toTable(Schema.chem_comp_bond, cat);
+ }
+
+ export async function attachFromCifOrTable(model: Model, params: {
+ // optional Table source
+ wwPDB_apiSourceTable?: (model: Model) => Promise<Table<Schema['chem_comp_bond']>>
+ }) {
+ if (model.customProperties.has(Descriptor)) return true;
+
+ let chemCompBond: Table<Schema['chem_comp_bond']> | undefined = fromCifData(model);
+ if (chemCompBond === void 0 && params.wwPDB_apiSourceTable) {
+ const data = await params.wwPDB_apiSourceTable(model);
+ if (!data) return false;
+ chemCompBond = chemCompBondFromTable(model, data);
+ } else {
+ return false;
+ }
+
+ if (!chemCompBond) return false;
+
+ model.customProperties.add(Descriptor);
+ set(model, chemCompBond);
+ return true;
+ }
+}
+
+function chemCompBondFromTable(model: Model, table: Table<ChemCompBond.Schema['chem_comp_bond']>): Table<ChemCompBond.Schema['chem_comp_bond']> {
+ return Table.pick(table, ChemCompBond.Schema.chem_comp_bond, (i: number) => {
+ return model.properties.chemicalComponentMap.has(table.comp_id.value(i))
+ })
+}
\ No newline at end of file
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
index 50a524740a6dbcf4b59baac01b946519fedada9c..5388a1c473912fb8a279a8a5f125e9a35545087e 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
@@ -43,13 +43,13 @@ export namespace VolumeStreaming {
valuesInfo: [{ mean: 0, min: -1, max: 1, sigma: 0.1 }, { mean: 0, min: -1, max: 1, sigma: 0.1 }]
};
- export function createParams(data?: VolumeServerInfo.Data) {
+ export function createParams(data?: VolumeServerInfo.Data, defaultView?: ViewTypes) {
// fake the info
const info = data || { kind: 'em', header: { sampling: [fakeSampling], availablePrecisions: [{ precision: 0, maxVoxels: 0 }] }, emDefaultContourLevel: VolumeIsoValue.relative(0) };
const box = (data && data.structure.boundary.box) || Box3D.empty();
return {
- view: PD.MappedStatic(info.kind === 'em' ? 'cell' : 'selection-box', {
+ view: PD.MappedStatic(defaultView || (info.kind === 'em' ? 'cell' : 'selection-box'), {
'box': PD.Group({
bottomLeft: PD.Vec3(box.min),
topRight: PD.Vec3(box.max),
@@ -76,6 +76,8 @@ export namespace VolumeStreaming {
};
}
+ export type ViewTypes = 'box' | 'selection-box' | 'cell'
+
export type ParamDefinition = typeof createParams extends (...args: any[]) => (infer T) ? T : never
export type Params = ParamDefinition extends PD.Params ? PD.Values<ParamDefinition> : {}
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
index 97b25f4ebc995eb8e4bea2c4aa0459019211c272..bc42398ae2ff2cc4e2137ba8442e4576b40102dc 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
@@ -26,10 +26,13 @@ export const InitVolumeStreaming = StateAction.build({
display: { name: 'Volume Streaming' },
from: SO.Molecule.Structure,
params(a) {
+ const method = getStreamingMethod(a && a.data);
return {
- method: PD.Select<VolumeServerInfo.Kind>(getStreamingMethod(a && a.data), [['em', 'EM'], ['x-ray', 'X-Ray']]),
+ method: PD.Select<VolumeServerInfo.Kind>(method, [['em', 'EM'], ['x-ray', 'X-Ray']]),
id: PD.Text((a && a.data.models.length > 0 && a.data.models[0].label) || ''),
- serverUrl: PD.Text('https://ds.litemol.org')
+ serverUrl: PD.Text('https://ds.litemol.org'),
+ defaultView: PD.Text<VolumeStreaming.ViewTypes>(method === 'em' ? 'cell' : 'selection-box'),
+ behaviorRef: PD.Text('', { isHidden: true })
};
},
isApplicable: (a) => a.data.models.length === 1
@@ -56,7 +59,8 @@ export const InitVolumeStreaming = StateAction.build({
const infoObj = await state.updateTree(infoTree).runInContext(taskCtx);
const behTree = state.build().to(infoTree.ref).apply(CreateVolumeStreamingBehavior,
- PD.getDefaultValues(VolumeStreaming.createParams(infoObj.data)));
+ PD.getDefaultValues(VolumeStreaming.createParams(infoObj.data, params.defaultView)),
+ { ref: params.behaviorRef ? params.behaviorRef : void 0 });
if (params.method === 'em') {
behTree.apply(VolumeStreamingVisual, { channel: 'em' }, { state: { isGhost: true } });
diff --git a/src/mol-plugin/ui/controls/parameters.tsx b/src/mol-plugin/ui/controls/parameters.tsx
index 19323297adbb3af4c45b2fa741d8851a590750fc..84f9b0742dbd920a11b3f12a6115d9548ffe23d5 100644
--- a/src/mol-plugin/ui/controls/parameters.tsx
+++ b/src/mol-plugin/ui/controls/parameters.tsx
@@ -15,7 +15,7 @@ import { camelCaseToWords } from '../../../mol-util/string';
import * as React from 'react';
import LineGraphComponent from './line-graph/line-graph-component';
import { Slider, Slider2 } from './slider';
-import { NumericInput, IconButton } from './common';
+import { NumericInput, IconButton, ControlGroup } from './common';
import { _Props, _State } from '../base';
export interface ParameterControlsProps<P extends PD.Params = PD.Params> {
@@ -97,7 +97,7 @@ export abstract class SimpleParam<P extends PD.Any> extends React.PureComponent<
}
}
-export class BoolControl extends SimpleParam<PD.Boolean> {
+export class BoolControl extends SimpleParam<PD.BooleanParam> {
onClick = (e: React.MouseEvent<HTMLButtonElement>) => { this.update(!this.props.value); e.currentTarget.blur(); }
renderControl() {
return <button onClick={this.onClick} disabled={this.props.isDisabled}>
@@ -461,8 +461,7 @@ export class GroupControl extends React.PureComponent<ParamProps<PD.Group<any>>,
</div>
{this.state.isExpanded && <div className='msp-control-offset' style={{ display: this.state.isExpanded ? 'block' : 'none' }}>
{controls}
- </div>
- }
+ </div>}
</div>
}
}
@@ -655,9 +654,12 @@ export class ObjectListControl extends React.PureComponent<ParamProps<PD.ObjectL
<button onClick={this.toggleExpanded}>{value}</button>
</div>
</div>
+
{this.state.isExpanded && <div className='msp-control-offset'>
{this.props.value.map((v, i) => <ObjectListItem key={i} param={this.props.param} value={v} index={i} actions={this.actions} />)}
- <ObjectListEditor params={this.props.param.element} apply={this.add} value={this.props.param.ctor()} isDisabled={this.props.isDisabled} />
+ <ControlGroup header='New Item'>
+ <ObjectListEditor params={this.props.param.element} apply={this.add} value={this.props.param.ctor()} isDisabled={this.props.isDisabled} />
+ </ControlGroup>
</div>}
</>;
}
diff --git a/src/mol-plugin/ui/plugin.tsx b/src/mol-plugin/ui/plugin.tsx
index dad27abdbb59757cf1e9fc0a89f24da62b426538..d911bd492272b30235fb3328bf2a34e9c2d5811e 100644
--- a/src/mol-plugin/ui/plugin.tsx
+++ b/src/mol-plugin/ui/plugin.tsx
@@ -37,6 +37,16 @@ export class Plugin extends React.Component<{ plugin: PluginContext }, {}> {
}
}
+export class PluginContextContainer extends React.Component<{ plugin: PluginContext }> {
+ render() {
+ return <PluginReactContext.Provider value={this.props.plugin}>
+ <div className='msp-plugin'>
+ {this.props.children}
+ </div>
+ </PluginReactContext.Provider>;
+ }
+}
+
class Layout extends PluginUIComponent {
componentDidMount() {
this.subscribe(this.plugin.layout.events.updated, () => this.forceUpdate());
diff --git a/src/mol-plugin/ui/state/update-transform.tsx b/src/mol-plugin/ui/state/update-transform.tsx
index 1e6cd3ba90a9514e94cff73e318b036bad9b6ade..7aafc25eaeffdb5b0feef2a746537fbadf263f15 100644
--- a/src/mol-plugin/ui/state/update-transform.tsx
+++ b/src/mol-plugin/ui/state/update-transform.tsx
@@ -101,7 +101,6 @@ class TransformUpdaterControl extends PluginUIComponent<{ nodeRef: string, initi
if (!cell || (cell.status !== 'ok' && cell.status !== 'error')) return null;
const transform = cell.transform;
-
return <UpdateTransformContol state={state} transform={transform} initiallyCollapsed={this.props.initiallyCollapsed} customHeader={this.props.header} />;
}
}
\ No newline at end of file
diff --git a/src/mol-util/console-logger.ts b/src/mol-util/console-logger.ts
index c09f08b9aaa412e2f8a9e155fdbb3c01cfe7c8bc..8d04c03fb835ef96ee3bd36d85e8ede19ff35b8c 100644
--- a/src/mol-util/console-logger.ts
+++ b/src/mol-util/console-logger.ts
@@ -25,7 +25,7 @@ export namespace ConsoleLogger {
console.log(`[${tag}] ${msg}`);
}
- export function logId(guid: string | String, tag: string, msg: string) {
+ export function logId(guid: string, tag: string, msg: string) {
console.log(`[${guid}][${tag}] ${msg}`);
}
@@ -38,7 +38,7 @@ export namespace ConsoleLogger {
console.error(`[Warn] (${ctx}) ${e}`);
}
- export function errorId(guid: string | String, e: any) {
+ export function errorId(guid: string, e: any) {
console.error(`[${guid}][Error] ${e}`);
if (e.stack) console.error(e.stack);
}
diff --git a/src/mol-util/param-definition.ts b/src/mol-util/param-definition.ts
index 92496fc63e303412c2ebbaada2a99df030b2cb8a..d94f32864c051da74ed8261c21b74f34cbe65ceb 100644
--- a/src/mol-util/param-definition.ts
+++ b/src/mol-util/param-definition.ts
@@ -76,11 +76,11 @@ export namespace ParamDefinition {
return setInfo<MultiSelect<E, T>>({ type: 'multi-select', defaultValue, options }, info)
}
- export interface Boolean extends Base<boolean> {
+ export interface BooleanParam extends Base<boolean> {
type: 'boolean'
}
- export function Boolean(defaultValue: boolean, info?: Info): Boolean {
- return setInfo<Boolean>({ type: 'boolean', defaultValue }, info)
+ export function Boolean(defaultValue: boolean, info?: Info): BooleanParam {
+ return setInfo<BooleanParam>({ type: 'boolean', defaultValue }, info)
}
export interface Text<T extends string = string> extends Base<T> {
@@ -237,7 +237,7 @@ export namespace ParamDefinition {
}
export type Any =
- | Value<any> | Select<any> | MultiSelect<any> | Boolean | Text | Color | Vec3 | Numeric | FileParam | Interval | LineGraph
+ | Value<any> | Select<any> | MultiSelect<any> | BooleanParam | Text | Color | Vec3 | Numeric | FileParam | Interval | LineGraph
| ColorScale<any> | Group<any> | Mapped<any> | Converted<any, any> | Conditioned<any, any, any> | ScriptExpression | ObjectList
export type Params = { [k: string]: Any }
diff --git a/src/servers/common/util.ts b/src/servers/common/util.ts
new file mode 100644
index 0000000000000000000000000000000000000000..3086ffb1f4ee0b69ec51a1a86b15e5326388444e
--- /dev/null
+++ b/src/servers/common/util.ts
@@ -0,0 +1,21 @@
+/**
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ConsoleLogger } from '../../mol-util/console-logger';
+
+export function getParam<T>(params: any, ...path: string[]): T | undefined {
+ try {
+ let current = params;
+ for (const p of path) {
+ if (typeof current === 'undefined') return;
+ current = current[p];
+ }
+ return current;
+ } catch (e) {
+ ConsoleLogger.error('Config', `Unable to retrieve property ${path.join('.')} from ${JSON.stringify(params)}`);
+ }
+}
\ No newline at end of file
diff --git a/src/servers/model/config.ts b/src/servers/model/config.ts
index ac963eadf6789115e96101880ee7e61449d655bd..860f6a0a436547e5923ffdb8d233b76b90d04e42 100644
--- a/src/servers/model/config.ts
+++ b/src/servers/model/config.ts
@@ -54,8 +54,9 @@ const config = {
*/
customProperties: <ModelPropertyProviderConfig | string>{
sources: [
- './properties/pdbe',
- './properties/rcsb'
+ 'pdbe',
+ 'rcsb',
+ 'wwpdb'
],
params: {
PDBe: {
@@ -68,6 +69,14 @@ const config = {
File: {
residuewise_outlier_summary: 'e:/test/mol-star/model/props/'
}
+ },
+ RCSB: {
+ API: {
+ assembly_symmetry: 'https://rest-staging.rcsb.org/graphql'
+ }
+ },
+ wwPDB: {
+ chemCompBondTablePath: ''
}
}
},
diff --git a/src/servers/model/preprocess/master.ts b/src/servers/model/preprocess/master.ts
index 9ff8b8e1fbb321579029f40963ae563aba7f502a..4c7068208838bd82a9e09ea9c00f9ad23255ad57 100644
--- a/src/servers/model/preprocess/master.ts
+++ b/src/servers/model/preprocess/master.ts
@@ -10,9 +10,27 @@ import * as argparse from 'argparse'
import { runMaster, PreprocessEntry } from './parallel';
import { ModelPropertyProviderConfig } from '../property-provider';
+function description() {
+ const exampleCfg = {
+ numProcesses: 1,
+ customProperties: {
+ sources: [
+ 'wwpdb'
+ ],
+ params: {
+ wwPDB: {
+ chemCompBondTablePath: './build/data/ccb.bcif'
+ }
+ }
+ }
+ }
+
+ return `Preprocess CIF files to include custom properties and convert them to BinaryCIF format.\n\nExample cfg.json: ${JSON.stringify(exampleCfg, null, 2)}`
+}
+
const cmdParser = new argparse.ArgumentParser({
addHelp: true,
- description: 'Preprocess CIF files to include custom properties and convert them to BinaryCIF format.'
+ description: description()
});
cmdParser.addArgument(['--input', '-i'], { help: 'Input filename', required: false });
cmdParser.addArgument(['--outCIF', '-oc'], { help: 'Output CIF filename', required: false });
diff --git a/src/servers/model/preprocess/preprocess.ts b/src/servers/model/preprocess/preprocess.ts
index 727da1d02398ccfab086b9db97bca3d221fdeeb8..3976748265ff4517f9fbc52df0a4b5e9faf0be56 100644
--- a/src/servers/model/preprocess/preprocess.ts
+++ b/src/servers/model/preprocess/preprocess.ts
@@ -21,7 +21,6 @@ export function preprocessFile(filename: string, propertyProvider?: ModelPropert
: convert(filename, outputCif, outputBcif);
}
-
async function preprocess(filename: string, propertyProvider?: ModelPropertiesProvider, outputCif?: string, outputBcif?: string) {
const input = await readStructureWrapper('entry', '_local_', filename, propertyProvider);
const categories = await classifyCif(input.cifFrame);
diff --git a/src/servers/model/properties/providers/pdbe.ts b/src/servers/model/properties/providers/pdbe.ts
index f0b254dd0aa98000cb0d7aeb84865f0359fe9664..7935d4a49bd1f971f84240e778d32459e61b7fd4 100644
--- a/src/servers/model/properties/providers/pdbe.ts
+++ b/src/servers/model/properties/providers/pdbe.ts
@@ -14,6 +14,7 @@ import { PDBePreferredAssembly } from '../../../../mol-model-props/pdbe/preferre
import { PDBeStructRefDomain } from '../../../../mol-model-props/pdbe/struct-ref-domain';
import { AttachModelProperty } from '../../property-provider';
import { ConsoleLogger } from '../../../../mol-util/console-logger';
+import { getParam } from '../../../common/util';
export const PDBe_structureQualityReport: AttachModelProperty = ({ model, params, cache }) => {
const PDBe_apiSourceJson = useFileSource(params)
@@ -68,20 +69,6 @@ function useFileSource(params: any) {
return !!getParam<boolean>(params, 'PDBe', 'UseFileSource')
}
-function getParam<T>(params: any, ...path: string[]): T | undefined {
- try {
- let current = params;
- for (const p of path) {
- if (typeof current === 'undefined') return;
- current = current[p];
- }
- return current;
- } catch (e) {
- ConsoleLogger.error('Config', `Unable to retrieve property ${path.join('.')} from ${JSON.stringify(params)}`);
- }
-}
-
-
function apiQueryProvider(urlPrefix: string, cache: any) {
const cacheKey = UUID.create22();
return async (model: Model) => {
diff --git a/src/servers/model/properties/providers/rcsb.ts b/src/servers/model/properties/providers/rcsb.ts
index e2ae21e66dd80fe2487b687600a708524b7fcf7d..011ad4b3cb367457b2c749e723628be487509c76 100644
--- a/src/servers/model/properties/providers/rcsb.ts
+++ b/src/servers/model/properties/providers/rcsb.ts
@@ -1,12 +1,23 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { AssemblySymmetry } from '../../../../mol-model-props/rcsb/assembly-symmetry';
import { AttachModelProperty } from '../../property-provider';
+import { ajaxGet } from '../../../../mol-util/data-source';
+import { GraphQLClient } from '../../../../mol-util/graphql-client';
+import { getParam } from '../../../common/util';
-export const RCSB_assemblySymmetry: AttachModelProperty = ({ model }) => {
- return AssemblySymmetry.attachFromCifOrAPI(model)
+export const RCSB_assemblySymmetry: AttachModelProperty = ({ model, params }) => {
+ const url = getApiUrl(params, 'assembly_symmetry', `https:${AssemblySymmetry.GraphQLEndpointURL}`)
+ const client = new GraphQLClient(url, ajaxGet)
+ return AssemblySymmetry.attachFromCifOrAPI(model, client)
+}
+
+function getApiUrl(params: any, name: string, fallback: string) {
+ const path = getParam<string>(params, 'RCSB', 'API', name);
+ if (!path) return fallback;
+ return path;
}
\ No newline at end of file
diff --git a/src/servers/model/properties/providers/wwpdb.ts b/src/servers/model/properties/providers/wwpdb.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d5ea7136e5a082ff8b7140f74fd9e7a2d21e6b62
--- /dev/null
+++ b/src/servers/model/properties/providers/wwpdb.ts
@@ -0,0 +1,44 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as fs from 'fs'
+import * as util from 'util'
+import { AttachModelProperty } from '../../property-provider';
+import { ChemCompBond } from '../../../../mol-model-props/wwpdb/chem-comp-bond';
+import { Table } from '../../../../mol-data/db';
+import { CIF } from '../../../../mol-io/reader/cif';
+import { getParam } from '../../../common/util';
+
+require('util.promisify').shim()
+const readFile = util.promisify(fs.readFile)
+
+export const wwPDB_chemCompBond: AttachModelProperty = ({ model, params }) => {
+ const wwPDB_apiSourceTable = getChemCompBondTableProvider(getTablePath(params))
+ return ChemCompBond.attachFromCifOrTable(model, { wwPDB_apiSourceTable });
+}
+
+async function read(path: string) {
+ return path.endsWith('.bcif') ? new Uint8Array(await readFile(path)) : readFile(path, 'utf8');
+}
+
+function getChemCompBondTableProvider(path: string): () => Promise<Table<ChemCompBond.Schema['chem_comp_bond']>> {
+ let chemCompBondTable: Table<ChemCompBond.Schema['chem_comp_bond']>
+ return async function() {
+ if (chemCompBondTable === undefined) {
+ const parsed = await CIF.parse(await read(path)).run()
+ if (parsed.isError) throw new Error(parsed.toString())
+ const table = CIF.toDatabase(ChemCompBond.Schema, parsed.result.blocks[0])
+ chemCompBondTable = table.chem_comp_bond
+ }
+ return chemCompBondTable
+ }
+}
+
+function getTablePath(params: any) {
+ const path = getParam<string>(params, 'wwPDB', 'chemCompBondTablePath');
+ if (!path) throw new Error(`wwPDB 'chemCompBondTablePath' not set!`);
+ return path;
+}
\ No newline at end of file
diff --git a/src/servers/model/properties/wwpdb.ts b/src/servers/model/properties/wwpdb.ts
new file mode 100644
index 0000000000000000000000000000000000000000..cb4040db1f7ac0ac78899f42d472e24113019bd9
--- /dev/null
+++ b/src/servers/model/properties/wwpdb.ts
@@ -0,0 +1,16 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { AttachModelProperties } from '../property-provider';
+import { wwPDB_chemCompBond } from './providers/wwpdb';
+
+export const attachModelProperties: AttachModelProperties = (args) => {
+ // return a list of promises that start attaching the props in parallel
+ // (if there are downloads etc.)
+ return [
+ wwPDB_chemCompBond(args)
+ ];
+}
\ No newline at end of file
diff --git a/src/servers/model/property-provider.ts b/src/servers/model/property-provider.ts
index d3b4ad00a0d836192f02361b408ee31ad3f189a4..d929c30c7320093b85d5b4677fe889fcb7c3b81f 100644
--- a/src/servers/model/property-provider.ts
+++ b/src/servers/model/property-provider.ts
@@ -9,6 +9,17 @@ import { Model } from '../../mol-model/structure';
import Config from './config';
import { ConsoleLogger } from '../../mol-util/console-logger';
+// TODO enable dynamic imports again
+import * as pdbeProps from './properties/pdbe'
+import * as rcsbProps from './properties/rcsb'
+import * as wwpdbProps from './properties/wwpdb'
+
+const attachModelProperties: { [k: string]: AttachModelProperties } = {
+ pdbe: pdbeProps.attachModelProperties,
+ rcsb: rcsbProps.attachModelProperties,
+ wwpdb: wwpdbProps.attachModelProperties
+}
+
export interface ModelPropertyProviderConfig {
sources: string[],
params?: { [name: string]: any }
@@ -39,7 +50,11 @@ export function createModelPropertiesProvider(configOrPath: ModelPropertyProvide
const ps: AttachModelProperties[] = [];
for (const p of config.sources) {
- ps.push(require(p).attachModelProperties);
+ if (p in attachModelProperties) {
+ ps.push(attachModelProperties[p]);
+ } else {
+ ConsoleLogger.error('Config', `Could not find property provider '${p}', ignoring.`);
+ }
}
return (model, cache) => {
diff --git a/src/servers/volume/local.ts b/src/servers/volume/local.ts
index 99993cfbcfa10612463f83325ff959db7cd93f43..f2145c2badfc82440a9a4ed0ed1c2cc68bc2aa76 100644
--- a/src/servers/volume/local.ts
+++ b/src/servers/volume/local.ts
@@ -16,7 +16,7 @@ import { LimitsConfig, addLimitsArgs, setLimitsConfig } from './config';
console.log(`VolumeServer Local ${VERSION}, (c) 2018-2019, Mol* contributors`);
console.log();
-function help() {
+function description() {
const exampleJobs: LocalApi.JobEntry[] = [{
source: {
filename: `g:/test/mdb/xray-1tqn.mdb`,
@@ -55,7 +55,7 @@ function help() {
const parser = new argparse.ArgumentParser({
addHelp: true,
- description: help()
+ description: description()
});
addLimitsArgs(parser)
parser.addArgument(['jobs'], {
diff --git a/tslint.json b/tslint.json
index 1c88592ea6631a73315ede0d282296f9626b68c6..ecf0639ee5c4ae7ba5c27ed412efe60d3867995c 100644
--- a/tslint.json
+++ b/tslint.json
@@ -6,6 +6,7 @@
],
"arrow-parens": false,
"no-var-keyword": true,
+ "no-construct": true,
"ordered-imports": [false],
"trailing-comma": [false],
"class-name": false,
@@ -17,6 +18,12 @@
true,
"spaces"
],
+ "ban-types": [
+ true,
+ ["String", "Use primitive 'string' instead."],
+ ["Boolean", "Use primitive 'boolean' instead."],
+ ["Number", "Use primitive 'number' instead."]
+ ],
"no-eval": true,
"no-internal-module": true,
"no-trailing-whitespace": true,
diff --git a/webpack.config.js b/webpack.config.js
index 3de9e1565111c706a5f326ff84f7f9f143cc4e28..9c4d98c40544b636d4b16b027b416707bbaff62d 100644
--- a/webpack.config.js
+++ b/webpack.config.js
@@ -8,16 +8,19 @@ const sharedConfig = {
module: {
rules: [
{
- loader: 'file-loader',
test: /\.(woff2?|ttf|otf|eot|svg|html)$/,
- include: [path.resolve(__dirname, 'lib/')],
- options: {
- name: '[name].[ext]'
- }
+ include: [path.resolve(__dirname, 'build/src/')],
+ use: [{
+ loader: 'file-loader',
+ options: { name: '[name].[ext]' }
+ }]
},
{
test: /\.(s*)css$/,
- use: [MiniCssExtractPlugin.loader, 'css-loader', 'resolve-url-loader', 'sass-loader']
+ use: [
+ MiniCssExtractPlugin.loader,
+ 'css-loader', 'resolve-url-loader', 'sass-loader'
+ ]
}
]
},
@@ -73,6 +76,12 @@ function createNodeEntryPoint(name, dir, out) {
target: 'node',
entry: path.resolve(__dirname, `lib/${dir}/${name}.js`),
output: { filename: `${name}.js`, path: path.resolve(__dirname, `build/${out}`) },
+ externals: {
+ argparse: 'require("argparse")',
+ 'node-fetch': 'require("node-fetch")',
+ 'util.promisify': 'require("util.promisify")',
+ xhr2: 'require("xhr2")',
+ },
...sharedConfig
}
}