From 678f7887489cdc10cb44c1cf35ab1fb0ef9fe8f2 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 21 Nov 2018 10:40:27 +0100
Subject: [PATCH] mol-plugin: multi-source obtain structure, param definition
tweaks
---
src/mol-plugin/index.ts | 4 +-
src/mol-plugin/state.ts | 1 -
src/mol-plugin/state/actions/basic.ts | 51 ++++++++++++++++++++---
src/mol-plugin/ui/controls/parameters.tsx | 13 +++---
src/mol-util/param-definition.ts | 2 +-
5 files changed, 53 insertions(+), 18 deletions(-)
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 7a87cb504..d746789f4 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -10,7 +10,7 @@ import * as React from 'react';
import * as ReactDOM from 'react-dom';
import { PluginCommands } from './command';
import { PluginSpec } from './spec';
-import { CreateStructureFromPDBe } from './state/actions/basic';
+import { ObtainAtomicStructure } from './state/actions/basic';
import { StateTransforms } from './state/transforms';
import { PluginBehaviors } from './behavior';
import { LogEntry } from 'mol-util/log-entry';
@@ -22,7 +22,7 @@ function getParam(name: string, regex: string): string {
const DefaultSpec: PluginSpec = {
actions: [
- PluginSpec.Action(CreateStructureFromPDBe),
+ PluginSpec.Action(ObtainAtomicStructure),
PluginSpec.Action(StateTransforms.Data.Download),
PluginSpec.Action(StateTransforms.Data.ParseCif),
PluginSpec.Action(StateTransforms.Model.StructureAssemblyFromModel),
diff --git a/src/mol-plugin/state.ts b/src/mol-plugin/state.ts
index db6cf78e9..e120f86bc 100644
--- a/src/mol-plugin/state.ts
+++ b/src/mol-plugin/state.ts
@@ -12,7 +12,6 @@ import { CameraSnapshotManager } from './state/camera';
import { PluginStateSnapshotManager } from './state/snapshots';
import { RxEventHelper } from 'mol-util/rx-event-helper';
import { Canvas3DParams } from 'mol-canvas3d/canvas3d';
-import { ParamDefinition } from 'mol-util/param-definition';
import { PluginCommands } from './command';
export { PluginState }
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index 002ca7f8a..0d49c8d14 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -11,16 +11,53 @@ import { ParamDefinition as PD } from 'mol-util/param-definition';
import { StateSelection } from 'mol-state/state/selection';
import { CartoonParams } from 'mol-repr/structure/representation/cartoon';
import { BallAndStickParams } from 'mol-repr/structure/representation/ball-and-stick';
+import { Download } from '../transforms/data';
-export const CreateStructureFromPDBe = StateAction.create<PluginStateObject.Root, void, { id: string }>({
+export { ObtainAtomicStructure }
+namespace ObtainAtomicStructure {
+ export type Sources = 'pdbe-updated' | 'rcsb' | 'bcif-static' | 'url' | 'file'
+ export type Source = ObtainStructureHelpers.MapParams<Sources, typeof ObtainStructureHelpers.ControlMap>
+ export interface Params {
+ source: Source
+ }
+}
+namespace ObtainStructureHelpers {
+ export const SourceOptions: [ObtainAtomicStructure.Sources, string][] = [
+ ['pdbe-updated', 'PDBe Updated'],
+ ['rcsb', 'RCSB'],
+ ['bcif-static', 'BinaryCIF (static PDBe Updated)'],
+ ['url', 'URL'],
+ // ['file', 'File']
+ ];
+ export const ControlMap = {
+ 'pdbe-updated': PD.Text('1cbs', { label: 'Id' }),
+ 'rcsb': PD.Text('1tqn', { label: 'Id' }),
+ 'bcif-static': PD.Text('1tqn', { label: 'Id' }),
+ 'url': PD.Group({ url: PD.Text(''), isBinary: PD.Boolean(false) }),
+ 'file': PD.Group({ })
+ }
+ export function getControls(key: string) { return (ControlMap as any)[key]; }
+
+ export type MapParams<P extends ObtainAtomicStructure.Sources, Map extends { [K in P]: PD.Any }> = P extends ObtainAtomicStructure.Sources ? PD.NamedParams<Map[P]['defaultValue'], P> : never
+
+ export function getUrl(src: ObtainAtomicStructure.Source): Download.Params {
+ switch (src.name) {
+ case 'url': return src.params;
+ case 'pdbe-updated': return { url: `https://www.ebi.ac.uk/pdbe/static/entry/${src.params.toLowerCase()}_updated.cif`, isBinary: false, label: `PDBe: ${src.params}` };
+ case 'rcsb': return { url: `https://files.rcsb.org/download/${src.params.toUpperCase()}.cif`, isBinary: false, label: `RCSB: ${src.params}` };
+ case 'bcif-static': return { url: `https://webchem.ncbr.muni.cz/ModelServer/static/bcif/${src.params.toLowerCase()}`, isBinary: true, label: `BinaryCIF: ${src.params}` };
+ default: throw new Error(`${src.name} not supported.`);
+ }
+ }
+}
+const ObtainAtomicStructure = StateAction.create<PluginStateObject.Root, void, ObtainAtomicStructure.Params>({
from: [PluginStateObject.Root],
display: {
- name: 'Entry from PDBe',
- description: 'Download a structure from PDBe and create its default Assembly and visual'
+ name: 'Obtain Structure',
+ description: 'Load a structure from PDBe and create its default Assembly and visual'
},
- params: () => ({ id: PD.Text('1grm', { label: 'PDB id' }) }),
+ params: () => ({ source: PD.Mapped('bcif-static', ObtainStructureHelpers.SourceOptions, ObtainStructureHelpers.getControls) }),
apply({ params, state }) {
- const url = `http://www.ebi.ac.uk/pdbe/static/entry/${params.id.toLowerCase()}_updated.cif`;
const b = state.build();
// const query = MolScriptBuilder.struct.generator.atomGroups({
@@ -34,8 +71,10 @@ export const CreateStructureFromPDBe = StateAction.create<PluginStateObject.Root
// ])
// });
+ const url = ObtainStructureHelpers.getUrl(params.source);
+
const root = b.toRoot()
- .apply(StateTransforms.Data.Download, { url })
+ .apply(StateTransforms.Data.Download, url)
.apply(StateTransforms.Data.ParseCif)
.apply(StateTransforms.Model.TrajectoryFromMmCif, {})
.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
diff --git a/src/mol-plugin/ui/controls/parameters.tsx b/src/mol-plugin/ui/controls/parameters.tsx
index de4a6afbb..e3e79de81 100644
--- a/src/mol-plugin/ui/controls/parameters.tsx
+++ b/src/mol-plugin/ui/controls/parameters.tsx
@@ -226,19 +226,17 @@ export class MultiSelectControl extends React.PureComponent<ParamProps<PD.MultiS
export class GroupControl extends React.PureComponent<ParamProps<PD.Group<any>>, { isExpanded: boolean }> {
state = { isExpanded: false }
- change(value: PD.Mapped<any>['defaultValue'] ) {
+ change(value: any ) {
this.props.onChange({ name: this.props.name, param: this.props.param, value });
}
onChangeParam: ParamOnChange = e => {
- const value: PD.Mapped<any>['defaultValue'] = this.props.value;
- this.change({ ...value.params, [e.name]: e.value });
+ this.change({ ...this.props.value, [e.name]: e.value });
}
toggleExpanded = () => this.setState({ isExpanded: !this.state.isExpanded });
render() {
- const value: PD.Mapped<any>['defaultValue'] = this.props.value;
const params = this.props.param.params;
const label = this.props.param.label || camelCaseToWords(this.props.name);
@@ -250,7 +248,7 @@ export class GroupControl extends React.PureComponent<ParamProps<PD.Group<any>>,
</button>
</div>
{this.state.isExpanded && <div className='msp-control-offset' style={{ display: this.state.isExpanded ? 'block' : 'none' }}>
- <ParameterControls params={params} onChange={this.onChangeParam} values={value.params} onEnter={this.props.onEnter} isDisabled={this.props.isDisabled} />
+ <ParameterControls params={params} onChange={this.onChangeParam} values={this.props.value} onEnter={this.props.onEnter} isDisabled={this.props.isDisabled} />
</div>
}
</div>
@@ -268,8 +266,7 @@ export class MappedControl extends React.PureComponent<ParamProps<PD.Mapped<any>
}
onChangeParam: ParamOnChange = e => {
- const value: PD.Mapped<any>['defaultValue'] = this.props.value;
- this.change({ name: value.name, params: e.value });
+ this.change({ name: this.props.value.name, params: e.value });
}
render() {
@@ -288,7 +285,7 @@ export class MappedControl extends React.PureComponent<ParamProps<PD.Mapped<any>
return <div>
{select}
- <Mapped param={param} value={value} name={`${label} Properties`} onChange={this.onChangeParam} onEnter={this.props.onEnter} isDisabled={this.props.isDisabled} />
+ <Mapped param={param} value={value.params} name={`${label} Properties`} onChange={this.onChangeParam} onEnter={this.props.onEnter} isDisabled={this.props.isDisabled} />
</div>
}
}
diff --git a/src/mol-util/param-definition.ts b/src/mol-util/param-definition.ts
index e508a72c7..cd05fcd0f 100644
--- a/src/mol-util/param-definition.ts
+++ b/src/mol-util/param-definition.ts
@@ -132,7 +132,7 @@ export namespace ParamDefinition {
return setInfo<Group<Values<P>>>({ type: 'group', defaultValue: getDefaultValues(params) as any, params }, info);
}
- export interface NamedParams<T = any> { name: string, params: T }
+ export interface NamedParams<T = any, K = string> { name: K, params: T }
export interface Mapped<T> extends Base<NamedParams<T>> {
type: 'mapped',
select: Select<string>,
--
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