diff --git a/src/apps/state-docs/pd-to-md.ts b/src/apps/state-docs/pd-to-md.ts
index b285668073b8b80f070ff20d1b201f45fcda0943..310962f40f1f96d053db19466506e87595dfc8da 100644
--- a/src/apps/state-docs/pd-to-md.ts
+++ b/src/apps/state-docs/pd-to-md.ts
@@ -28,6 +28,8 @@ function paramInfo(param: PD.Any, offset: number): string {
case 'group': return `Object with:\n${getParams(param.params, offset + 2)}`;
case 'mapped': return `Object { name: string, params: object } where name+params are:\n${getMapped(param, offset + 2)}`;
case 'line-graph': return `A list of 2d vectors [xi, yi][]`;
+ // TODO: support more languages
+ case 'script-expression': return `An expression in the specified language { language: 'mol-script', expressiong: string }`;
default:
const _: never = param;
console.warn(`${_} has no associated UI component`);
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 3fd3b6d97a0e6bf0a5419f01dcf0959a5cf0d628..95d5b9673a3fc14fd36ab38b69714d0f9d6e708a 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -40,6 +40,7 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Action(StateTransforms.Model.StructureSymmetryFromModel),
PluginSpec.Action(StateTransforms.Model.StructureFromModel),
PluginSpec.Action(StateTransforms.Model.ModelFromTrajectory),
+ PluginSpec.Action(StateTransforms.Model.UserStructureSelection),
PluginSpec.Action(StateTransforms.Volume.VolumeFromCcp4),
PluginSpec.Action(StateTransforms.Representation.StructureRepresentation3D),
PluginSpec.Action(StateTransforms.Representation.StructureLabels3D),
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index fd46f04fad369b6cb8eee92d9eb65d9b268f0069..dd52f03e21207603c8123c540b2ef209939be7f2 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -22,6 +22,8 @@ import { stringToWords } from 'mol-util/string';
import { PluginStateObject as SO, PluginStateTransform } from '../objects';
import { trajectoryFromGRO } from 'mol-model-formats/structure/gro';
import { parseGRO } from 'mol-io/reader/gro/parser';
+import { parseMolScript } from 'mol-script/language/parser';
+import { transpileMolScript } from 'mol-script/script/mol-script/symbols';
export { TrajectoryFromMmCif };
export { TrajectoryFromPDB };
@@ -31,8 +33,10 @@ export { StructureFromModel };
export { StructureAssemblyFromModel };
export { StructureSymmetryFromModel };
export { StructureSelection };
+export { UserStructureSelection };
export { StructureComplexElement };
export { CustomModelProperties };
+
type TrajectoryFromMmCif = typeof TrajectoryFromMmCif
const TrajectoryFromMmCif = PluginStateTransform.BuiltIn({
name: 'trajectory-from-mmcif',
@@ -243,6 +247,31 @@ const StructureSelection = PluginStateTransform.BuiltIn({
}
});
+type UserStructureSelection = typeof UserStructureSelection
+const UserStructureSelection = PluginStateTransform.BuiltIn({
+ name: 'user-structure-selection',
+ display: { name: 'Structure Selection', description: 'Create a molecular structure from the specified query expression.' },
+ from: SO.Molecule.Structure,
+ to: SO.Molecule.Structure,
+ params: {
+ query: PD.ScriptExpression({ language: 'mol-script', expression: '(sel.atom.atom-groups :residue-test (= atom.resname ALA))' }),
+ label: PD.makeOptional(PD.Text(''))
+ }
+})({
+ apply({ a, params }) {
+ // TODO: use cache, add "update"
+ const parsed = parseMolScript(params.query.expression);
+ if (parsed.length === 0) throw new Error('No query');
+ const query = transpileMolScript(parsed[0]);
+ const compiled = compile<Sel>(query);
+ const result = compiled(new QueryContext(a.data));
+ const s = Sel.unionStructure(result);
+ if (s.elementCount === 0) return StateObject.Null;
+ const props = { label: `${params.label || 'Selection'}`, description: structureDesc(s) };
+ return new SO.Molecule.Structure(s, props);
+ }
+});
+
namespace StructureComplexElement {
export type Types = 'atomic-sequence' | 'water' | 'atomic-het' | 'spheres'
}
diff --git a/src/mol-plugin/ui/controls/parameters.tsx b/src/mol-plugin/ui/controls/parameters.tsx
index ed0baaa35f518ad4dcf46f6b0c8f4b02d84ea619..c09203ccdf7e27ca81bbe27594b0ac10518e95cb 100644
--- a/src/mol-plugin/ui/controls/parameters.tsx
+++ b/src/mol-plugin/ui/controls/parameters.tsx
@@ -63,6 +63,7 @@ function controlFor(param: PD.Any): ParamControl | undefined {
case 'group': return GroupControl;
case 'mapped': return MappedControl;
case 'line-graph': return LineGraphControl;
+ case 'script-expression': return ScriptExpressionControl;
default:
const _: never = param;
console.warn(`${_} has no associated UI component`);
@@ -77,7 +78,7 @@ export interface ParamProps<P extends PD.Base<any> = PD.Base<any>> { name: strin
export type ParamControl = React.ComponentClass<ParamProps<any>>
export abstract class SimpleParam<P extends PD.Any> extends React.PureComponent<ParamProps<P>> {
- protected update(value: any) {
+ protected update(value: P['defaultValue']) {
this.props.onChange({ param: this.props.param, name: this.props.name, value });
}
@@ -562,3 +563,32 @@ export class ConvertedControl extends React.PureComponent<ParamProps<PD.Converte
return <Converted param={this.props.param.converted} value={value} name={this.props.name} onChange={this.onChange} onEnter={this.props.onEnter} isDisabled={this.props.isDisabled} />
}
}
+
+export class ScriptExpressionControl extends SimpleParam<PD.ScriptExpression> {
+ onChange = (e: React.ChangeEvent<HTMLInputElement>) => {
+ const value = e.target.value;
+ if (value !== this.props.value.expression) {
+ this.update({ language: this.props.value.language, expression: value });
+ }
+ }
+
+ onKeyPress = (e: React.KeyboardEvent<HTMLInputElement>) => {
+ if (!this.props.onEnter) return;
+ if ((e.keyCode === 13 || e.charCode === 13)) {
+ this.props.onEnter();
+ }
+ }
+
+ renderControl() {
+ // TODO: improve!
+
+ const placeholder = this.props.param.label || camelCaseToWords(this.props.name);
+ return <input type='text'
+ value={this.props.value.expression || ''}
+ placeholder={placeholder}
+ onChange={this.onChange}
+ onKeyPress={this.props.onEnter ? this.onKeyPress : void 0}
+ disabled={this.props.isDisabled}
+ />;
+ }
+}
\ No newline at end of file
diff --git a/src/mol-util/param-definition.ts b/src/mol-util/param-definition.ts
index 46d8abbfeb457cfbb5ae83f320374cb77cd266e2..3bb4e3ed84140937872cf12da198e9c63ed3501f 100644
--- a/src/mol-util/param-definition.ts
+++ b/src/mol-util/param-definition.ts
@@ -213,7 +213,14 @@ export namespace ParamDefinition {
return { type: 'conditioned', select: Select<string>(conditionForValue(defaultValue) as string, options), defaultValue, conditionParams, conditionForValue, conditionedValue };
}
- export type Any = Value<any> | Select<any> | MultiSelect<any> | Boolean | Text | Color | Vec3 | Numeric | FileParam | Interval | LineGraph | ColorScale<any> | Group<any> | Mapped<any> | Converted<any, any> | Conditioned<any, any, any>
+ export interface ScriptExpression extends Base<{ language: 'mol-script', expression: string }> {
+ type: 'script-expression'
+ }
+ export function ScriptExpression(defaultValue: ScriptExpression['defaultValue'], info?: Info): ScriptExpression {
+ return setInfo<ScriptExpression>({ type: 'script-expression', defaultValue }, info)
+ }
+
+ export type Any = Value<any> | Select<any> | MultiSelect<any> | Boolean | Text | Color | Vec3 | Numeric | FileParam | Interval | LineGraph | ColorScale<any> | Group<any> | Mapped<any> | Converted<any, any> | Conditioned<any, any, any> | ScriptExpression
export type Params = { [k: string]: Any }
export type Values<T extends Params> = { [k in keyof T]: T[k]['defaultValue'] }
@@ -301,6 +308,9 @@ export namespace ParamDefinition {
return true;
} else if (p.type === 'vec3') {
return Vec3Data.equals(a, b);
+ } else if (p.type === 'script-expression') {
+ const u = a as ScriptExpression['defaultValue'], v = b as ScriptExpression['defaultValue'];
+ return u.language === v.language && u.expression === v.expression;
} else if (typeof a === 'object' && typeof b === 'object') {
return shallowEqual(a, b);
}