diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index eefc0064172ec38a4f5543f43d55c65cdeec891a..d7e521824c97734cdc7ac07a1bb8c2d4c6ef73b8 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 { DownloadAtomicStructure, CreateComplexRepresentation } from './state/actions/basic';
+import { DownloadAtomicStructure, CreateComplexRepresentation, OpenAtomicStructure } from './state/actions/basic';
import { StateTransforms } from './state/transforms';
import { PluginBehaviors } from './behavior';
import { LogEntry } from 'mol-util/log-entry';
@@ -23,6 +23,7 @@ function getParam(name: string, regex: string): string {
const DefaultSpec: PluginSpec = {
actions: [
PluginSpec.Action(DownloadAtomicStructure),
+ PluginSpec.Action(OpenAtomicStructure),
PluginSpec.Action(CreateComplexRepresentation),
PluginSpec.Action(StateTransforms.Data.Download),
PluginSpec.Action(StateTransforms.Data.ParseCif),
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index 77f5f4c4cb4e528aebefcea449bfbf80bfe8512a..f10374d3193f8bec997197dbbcd6b12cc8db12ca 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -12,10 +12,14 @@ 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';
+import { StateTree } from 'mol-state';
+import { StateTreeBuilder } from 'mol-state/tree/builder';
+
+// TODO: "structure parser provider"
export { DownloadAtomicStructure }
namespace DownloadAtomicStructure {
- export type Sources = 'pdbe-updated' | 'rcsb' | 'bcif-static' | 'url' | 'file'
+ export type Sources = 'pdbe-updated' | 'rcsb' | 'bcif-static' | 'url'
export type Source = ObtainStructureHelpers.MapParams<Sources, typeof ObtainStructureHelpers.ControlMap>
export interface Params {
source: Source
@@ -26,15 +30,13 @@ namespace ObtainStructureHelpers {
['pdbe-updated', 'PDBe Updated'],
['rcsb', 'RCSB'],
['bcif-static', 'BinaryCIF (static PDBe Updated)'],
- ['url', 'URL'],
- ['file', 'File']
+ ['url', 'URL']
];
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) }, { isExpanded: true }),
- 'file': PD.File({ accept: '.cif,.bcif' })
+ 'url': PD.Group({ url: PD.Text(''), isBinary: PD.Boolean(false) }, { isExpanded: true })
}
export function getControls(key: string) { return (ControlMap as any)[key]; }
@@ -46,7 +48,7 @@ namespace ObtainStructureHelpers {
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.`);
+ default: throw new Error(`${(src as any).name} not supported.`);
}
}
}
@@ -73,24 +75,42 @@ const DownloadAtomicStructure = StateAction.create<PluginStateObject.Root, void,
const url = ObtainStructureHelpers.getUrl(params.source);
- const root = b.toRoot()
- .apply(StateTransforms.Data.Download, url)
- .apply(StateTransforms.Data.ParseCif)
- .apply(StateTransforms.Model.TrajectoryFromMmCif, {})
- .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
- .apply(StateTransforms.Model.StructureAssemblyFromModel);
-
- root.apply(StateTransforms.Model.StructureComplexElement, { type: 'sequence' })
- .apply(StateTransforms.Representation.StructureRepresentation3D, { type: { name: 'cartoon', params: PD.getDefaultValues(CartoonParams) } });
- root.apply(StateTransforms.Model.StructureComplexElement, { type: 'ligands' })
- .apply(StateTransforms.Representation.StructureRepresentation3D, { type: { name: 'ball-and-stick', params: PD.getDefaultValues(BallAndStickParams) } });
- root.apply(StateTransforms.Model.StructureComplexElement, { type: 'water' })
- .apply(StateTransforms.Representation.StructureRepresentation3D, { type: { name: 'ball-and-stick', params: { ...PD.getDefaultValues(BallAndStickParams), alpha: 0.51 } } });
+ const data = b.toRoot().apply(StateTransforms.Data.Download, url);
+ return state.update(atomicStructureTree(data));
+ }
+});
- return state.update(root.getTree());
+export const OpenAtomicStructure = StateAction.create<PluginStateObject.Root, void, { file: File }>({
+ from: [PluginStateObject.Root],
+ display: {
+ name: 'Open Structure',
+ description: 'Load a structure from file and create its default Assembly and visual'
+ },
+ params: () => ({ file: PD.File({ accept: '.cif,.bcif' }) }),
+ apply({ params, state }) {
+ const b = state.build();
+ const data = b.toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: /\.bcif$/i.test(params.file.name) });
+ return state.update(atomicStructureTree(data));
}
});
+function atomicStructureTree(b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>): StateTree {
+ const root = b
+ .apply(StateTransforms.Data.ParseCif)
+ .apply(StateTransforms.Model.TrajectoryFromMmCif, {})
+ .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
+ .apply(StateTransforms.Model.StructureAssemblyFromModel);
+
+ root.apply(StateTransforms.Model.StructureComplexElement, { type: 'sequence' })
+ .apply(StateTransforms.Representation.StructureRepresentation3D, { type: { name: 'cartoon', params: PD.getDefaultValues(CartoonParams) } });
+ root.apply(StateTransforms.Model.StructureComplexElement, { type: 'ligands' })
+ .apply(StateTransforms.Representation.StructureRepresentation3D, { type: { name: 'ball-and-stick', params: PD.getDefaultValues(BallAndStickParams) } });
+ root.apply(StateTransforms.Model.StructureComplexElement, { type: 'water' })
+ .apply(StateTransforms.Representation.StructureRepresentation3D, { type: { name: 'ball-and-stick', params: { ...PD.getDefaultValues(BallAndStickParams), alpha: 0.51 } } });
+
+ return root.getTree();
+}
+
export const CreateComplexRepresentation = StateAction.create<PluginStateObject.Molecule.Structure, void, {}>({
from: [PluginStateObject.Molecule.Structure],
display: {
diff --git a/src/mol-plugin/state/transforms/data.ts b/src/mol-plugin/state/transforms/data.ts
index d663997c5f6be5ebaac944e2f23bfc051059b150..cb7169b557f979fe3aa53493077f454ec2611104 100644
--- a/src/mol-plugin/state/transforms/data.ts
+++ b/src/mol-plugin/state/transforms/data.ts
@@ -11,6 +11,7 @@ import CIF from 'mol-io/reader/cif'
import { PluginContext } from 'mol-plugin/context';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { Transformer } from 'mol-state';
+import { readFromFile } from 'mol-util/data-source';
export { Download }
namespace Download { export interface Params { url: string, isBinary?: boolean, label?: string } }
@@ -45,6 +46,39 @@ const Download = PluginStateTransform.Create<SO.Root, SO.Data.String | SO.Data.B
}
});
+export { ReadFile }
+namespace ReadFile { export interface Params { file: File, isBinary?: boolean, label?: string } }
+const ReadFile = PluginStateTransform.Create<SO.Root, SO.Data.String | SO.Data.Binary, ReadFile.Params>({
+ name: 'read-file',
+ display: {
+ name: 'Read File',
+ description: 'Read string or binary data from the specified file'
+ },
+ from: [SO.Root],
+ to: [SO.Data.String, SO.Data.Binary],
+ params: () => ({
+ file: PD.File(),
+ label: PD.Text('', { isOptional: true }),
+ isBinary: PD.Boolean(false, { description: 'If true, open file as as binary (string otherwise)', isOptional: true })
+ }),
+ apply({ params: p }, globalCtx: PluginContext) {
+ return Task.create('Open File', async ctx => {
+ const data = await readFromFile(p.file, p.isBinary ? 'binary' : 'string').runInContext(ctx);
+ return p.isBinary
+ ? new SO.Data.Binary(data as Uint8Array, { label: p.label ? p.label : p.file.name })
+ : new SO.Data.String(data as string, { label: p.label ? p.label : p.file.name });
+ });
+ },
+ update({ oldParams, newParams, b }) {
+ if (oldParams.label !== newParams.label) {
+ (b.label as string) = newParams.label || oldParams.file.name;
+ return Transformer.UpdateResult.Updated;
+ }
+ return Transformer.UpdateResult.Unchanged;
+ },
+ isSerializable: () => ({ isSerializable: false, reason: 'Cannot serialize user loaded files.' })
+});
+
export { ParseCif }
namespace ParseCif { export interface Params { } }
const ParseCif = PluginStateTransform.Create<SO.Data.String | SO.Data.Binary, SO.Data.Cif, ParseCif.Params>({