diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index d746789f47017bf8c49d336bfb8b51dc960e0115..eefc0064172ec38a4f5543f43d55c65cdeec891a 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 { ObtainAtomicStructure } from './state/actions/basic';
+import { DownloadAtomicStructure, CreateComplexRepresentation } from './state/actions/basic';
import { StateTransforms } from './state/transforms';
import { PluginBehaviors } from './behavior';
import { LogEntry } from 'mol-util/log-entry';
@@ -22,7 +22,8 @@ function getParam(name: string, regex: string): string {
const DefaultSpec: PluginSpec = {
actions: [
- PluginSpec.Action(ObtainAtomicStructure),
+ PluginSpec.Action(DownloadAtomicStructure),
+ PluginSpec.Action(CreateComplexRepresentation),
PluginSpec.Action(StateTransforms.Data.Download),
PluginSpec.Action(StateTransforms.Data.ParseCif),
PluginSpec.Action(StateTransforms.Model.StructureAssemblyFromModel),
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index 0d49c8d145196a87c06ec3a7f7e5f89ff8fbac25..9fd7a10df2ba4d41cc933089d04cdfd418ba1734 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -13,8 +13,8 @@ import { CartoonParams } from 'mol-repr/structure/representation/cartoon';
import { BallAndStickParams } from 'mol-repr/structure/representation/ball-and-stick';
import { Download } from '../transforms/data';
-export { ObtainAtomicStructure }
-namespace ObtainAtomicStructure {
+export { DownloadAtomicStructure }
+namespace DownloadAtomicStructure {
export type Sources = 'pdbe-updated' | 'rcsb' | 'bcif-static' | 'url' | 'file'
export type Source = ObtainStructureHelpers.MapParams<Sources, typeof ObtainStructureHelpers.ControlMap>
export interface Params {
@@ -22,25 +22,26 @@ namespace ObtainAtomicStructure {
}
}
namespace ObtainStructureHelpers {
- export const SourceOptions: [ObtainAtomicStructure.Sources, string][] = [
+ export const SourceOptions: [DownloadAtomicStructure.Sources, string][] = [
['pdbe-updated', 'PDBe Updated'],
['rcsb', 'RCSB'],
['bcif-static', 'BinaryCIF (static PDBe Updated)'],
['url', 'URL'],
+ // TODO
// ['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) }),
+ 'url': PD.Group({ url: PD.Text(''), isBinary: PD.Boolean(false) }, { isExpanded: true }),
'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 type MapParams<P extends DownloadAtomicStructure.Sources, Map extends { [K in P]: PD.Any }> = P extends DownloadAtomicStructure.Sources ? PD.NamedParams<Map[P]['defaultValue'], P> : never
- export function getUrl(src: ObtainAtomicStructure.Source): Download.Params {
+ export function getUrl(src: DownloadAtomicStructure.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}` };
@@ -50,10 +51,10 @@ namespace ObtainStructureHelpers {
}
}
}
-const ObtainAtomicStructure = StateAction.create<PluginStateObject.Root, void, ObtainAtomicStructure.Params>({
+const DownloadAtomicStructure = StateAction.create<PluginStateObject.Root, void, DownloadAtomicStructure.Params>({
from: [PluginStateObject.Root],
display: {
- name: 'Obtain Structure',
+ name: 'Download Structure',
description: 'Load a structure from PDBe and create its default Assembly and visual'
},
params: () => ({ source: PD.Mapped('bcif-static', ObtainStructureHelpers.SourceOptions, ObtainStructureHelpers.getControls) }),
@@ -91,6 +92,25 @@ const ObtainAtomicStructure = StateAction.create<PluginStateObject.Root, void, O
}
});
+export const CreateComplexRepresentation = StateAction.create<PluginStateObject.Molecule.Structure, void, {}>({
+ from: [PluginStateObject.Molecule.Structure],
+ display: {
+ name: 'Create Complex',
+ description: 'Split the structure into Sequence/Water/Ligands/... '
+ },
+ apply({ ref, state }) {
+ const root = state.build().to(ref);
+ 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 state.update(root.getTree());
+ }
+});
+
export const UpdateTrajectory = StateAction.create<PluginStateObject.Root, void, { action: 'advance' | 'reset', by?: number }>({
from: [],
display: {
diff --git a/src/mol-plugin/ui/controls/parameters.tsx b/src/mol-plugin/ui/controls/parameters.tsx
index e3e79de81cdcce1cb2a511a8c2c22c111fd0778b..98bbfa53f5212ae0e126d1e444ddbec81accf1ed 100644
--- a/src/mol-plugin/ui/controls/parameters.tsx
+++ b/src/mol-plugin/ui/controls/parameters.tsx
@@ -224,7 +224,7 @@ export class MultiSelectControl extends React.PureComponent<ParamProps<PD.MultiS
}
export class GroupControl extends React.PureComponent<ParamProps<PD.Group<any>>, { isExpanded: boolean }> {
- state = { isExpanded: false }
+ state = { isExpanded: !!this.props.param.isExpanded }
change(value: any ) {
this.props.onChange({ name: this.props.name, param: this.props.param, value });
diff --git a/src/mol-plugin/ui/plugin.tsx b/src/mol-plugin/ui/plugin.tsx
index 3d91ea82467227d25b02e7eb5cc93d079e0a7e50..f29ed9fb5eb5d3d431318af510bb3e805bc554d3 100644
--- a/src/mol-plugin/ui/plugin.tsx
+++ b/src/mol-plugin/ui/plugin.tsx
@@ -19,6 +19,7 @@ import { BackgroundTaskProgress } from './task';
import { ApplyActionContol } from './state/apply-action';
import { PluginState } from 'mol-plugin/state';
import { UpdateTransformContol } from './state/update-transform';
+import { StateObjectCell } from 'mol-state';
export class Plugin extends React.Component<{ plugin: PluginContext }, {}> {
@@ -141,22 +142,20 @@ export class CurrentObject extends PluginComponent {
const current = this.current;
const ref = current.ref;
- // const n = this.props.plugin.state.data.tree.nodes.get(ref)!;
- const obj = current.state.cells.get(ref)!;
+ const cell = current.state.cells.get(ref)!;
+ const parent: StateObjectCell | undefined = (cell.sourceRef && current.state.cells.get(cell.sourceRef)!) || void 0;
- const type = obj && obj.obj ? obj.obj.type : void 0;
+ const type = cell && cell.obj ? cell.obj.type : void 0;
+ const transform = cell.transform;
+ const def = transform.transformer.definition;
- const transform = current.state.transforms.get(ref);
-
- const actions = type
- ? current.state.actions.fromType(type)
- : []
+ const actions = type ? current.state.actions.fromType(type) : [];
return <>
<div className='msp-section-header'>
- {obj.obj ? obj.obj.label : ref}
+ {cell.obj ? cell.obj.label : (def.display && def.display.name) || def.name}
</div>
- <UpdateTransformContol state={current.state} transform={transform} />
- {
+ { (parent && parent.status === 'ok') && <UpdateTransformContol state={current.state} transform={transform} /> }
+ {cell.status === 'ok' &&
actions.map((act, i) => <ApplyActionContol plugin={this.plugin} key={`${act.id}`} state={current.state} action={act} nodeRef={ref} />)
}
</>;
diff --git a/src/mol-state/action.ts b/src/mol-state/action.ts
index 64826d3b64472b546082a6c8ea9e12fdff842d0a..b1e2ee0e0fd565fecd874e3676762928b78d47a4 100644
--- a/src/mol-state/action.ts
+++ b/src/mol-state/action.ts
@@ -31,6 +31,7 @@ namespace StateAction {
}
export interface ApplyParams<A extends StateObject = StateObject, P extends {} = {}> {
+ ref: string,
cell: StateObjectCell,
a: A,
state: State,
diff --git a/src/mol-state/state.ts b/src/mol-state/state.ts
index d73d707efaf5280f3f4c0e385b745b8ade465f5e..53a758b1c12aeb086f5ba5eae66d8305386dd8a9 100644
--- a/src/mol-state/state.ts
+++ b/src/mol-state/state.ts
@@ -104,7 +104,7 @@ class State {
if (!cell) throw new Error(`'${ref}' does not exist.`);
if (cell.status !== 'ok') throw new Error(`Action cannot be applied to a cell with status '${cell.status}'`);
- return runTask(action.definition.apply({ cell, a: cell.obj!, params, state: this }, this.globalContext), ctx);
+ return runTask(action.definition.apply({ ref, cell, a: cell.obj!, params, state: this }, this.globalContext), ctx);
});
}
diff --git a/src/mol-util/param-definition.ts b/src/mol-util/param-definition.ts
index cd05fcd0ff37f6bbc866b9f9b9a7d08b51f44c34..08db5aee7cbd5d453064872d5cf8779479a56fe4 100644
--- a/src/mol-util/param-definition.ts
+++ b/src/mol-util/param-definition.ts
@@ -126,10 +126,13 @@ export namespace ParamDefinition {
export interface Group<T> extends Base<T> {
type: 'group',
- params: Params
+ params: Params,
+ isExpanded?: boolean
}
- export function Group<P extends Params>(params: P, info?: Info): Group<Values<P>> {
- return setInfo<Group<Values<P>>>({ type: 'group', defaultValue: getDefaultValues(params) as any, params }, info);
+ export function Group<P extends Params>(params: P, info?: Info & { isExpanded?: boolean }): Group<Values<P>> {
+ const ret = setInfo<Group<Values<P>>>({ type: 'group', defaultValue: getDefaultValues(params) as any, params }, info);
+ if (info && info.isExpanded) ret.isExpanded = info.isExpanded;
+ return ret;
}
export interface NamedParams<T = any, K = string> { name: K, params: T }