diff --git a/src/mol-plugin/behavior/dynamic/custom-props.ts b/src/mol-plugin/behavior/dynamic/custom-props.ts
index 7dc6eefd80de94e5f390d467ee542e56aeb5e85c..d82ae6dacb61b9fa6f4a6a22d30c3ab440808219 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props.ts
@@ -25,7 +25,7 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
private provider: CustomPropertyRegistry.Provider = {
option: [StructureQualityReport.Descriptor.name, 'PDBe Structure Quality Report'],
descriptor: StructureQualityReport.Descriptor,
- defaultSelected: false,
+ defaultSelected: this.params.autoAttach,
attachableTo: () => true,
attach: this.attach
}
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 2201de2baf6d9c9a59034c3e437ff6bedcc5769c..6ed4f0f7a06172e3e92d45a126910048785db2ef 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -36,7 +36,7 @@ const DefaultSpec: PluginSpec = {
PluginSpec.Behavior(PluginBehaviors.Representation.SelectLoci),
PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
PluginSpec.Behavior(PluginBehaviors.Camera.FocusLociOnSelect, { minRadius: 20, extraRadius: 4 }),
- PluginSpec.Behavior(PluginBehaviors.CustomProps.PDBeStructureQualityReport, { autoAttach: false })
+ PluginSpec.Behavior(PluginBehaviors.CustomProps.PDBeStructureQualityReport, { autoAttach: true })
]
}
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index 6768bbd6d8e3e068758d2b21e66fda8b4672cb23..13a43c24e53a214869eb60581a98d43403383bd4 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -4,25 +4,20 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
+import { PluginContext } from 'mol-plugin/context';
+import { StateTree, Transformer } from 'mol-state';
import { StateAction } from 'mol-state/action';
+import { StateSelection } from 'mol-state/state/selection';
+import { StateTreeBuilder } from 'mol-state/tree/builder';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
import { PluginStateObject } from '../objects';
import { StateTransforms } from '../transforms';
-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';
-import { StateTree, Transformer } from 'mol-state';
-import { StateTreeBuilder } from 'mol-state/tree/builder';
-import { PolymerIdColorThemeParams } from 'mol-theme/color/polymer-id';
-import { UniformSizeThemeParams } from 'mol-theme/size/uniform';
-import { ElementSymbolColorThemeParams } from 'mol-theme/color/element-symbol';
-import { PhysicalSizeThemeParams } from 'mol-theme/size/physical';
-import { SpacefillParams } from 'mol-repr/structure/representation/spacefill';
+import { StructureRepresentation3DHelpers } from '../transforms/representation';
// TODO: "structure parser provider"
-export { DownloadStructure }
+export { DownloadStructure };
type DownloadStructure = typeof DownloadStructure
const DownloadStructure = StateAction.build({
from: PluginStateObject.Root,
@@ -55,7 +50,7 @@ const DownloadStructure = StateAction.build({
]
})
}
-})(({ params, state }) => {
+})(({ params, state }, ctx: PluginContext) => {
const b = state.build();
const src = params.source;
let url: Transformer.Params<Download>;
@@ -77,69 +72,55 @@ const DownloadStructure = StateAction.build({
}
const data = b.toRoot().apply(StateTransforms.Data.Download, url);
- return state.update(createStructureTree(data, params.source.params.supportProps));
+ return state.update(createStructureTree(ctx, data, params.source.params.supportProps));
});
export const OpenStructure = StateAction.build({
display: { name: 'Open Structure', description: 'Load a structure from file and create its default Assembly and visual' },
from: PluginStateObject.Root,
params: { file: PD.File({ accept: '.cif,.bcif' }) }
-})(({ params, state }) => {
+})(({ params, state }, ctx: PluginContext) => {
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(createStructureTree(data, false));
+ return state.update(createStructureTree(ctx, data, false));
});
-function createStructureTree(b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, supportProps: boolean): StateTree {
+function createStructureTree(ctx: PluginContext, b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, supportProps: boolean): StateTree {
let root = b
.apply(StateTransforms.Data.ParseCif)
- .apply(StateTransforms.Model.TrajectoryFromMmCif, {})
+ .apply(StateTransforms.Model.TrajectoryFromMmCif)
.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 });
if (supportProps) {
- // TODO: implement automatic default property assigment in State.update
- root = root.apply(StateTransforms.Model.CustomModelProperties, { properties: [] });
+ root = root.apply(StateTransforms.Model.CustomModelProperties);
}
- root = root.apply(StateTransforms.Model.StructureAssemblyFromModel);
-
- complexRepresentation(root);
+ const structure = root.apply(StateTransforms.Model.StructureAssemblyFromModel);
+ complexRepresentation(ctx, structure);
return root.getTree();
}
-function complexRepresentation(root: StateTreeBuilder.To<PluginStateObject.Molecule.Structure>) {
+function complexRepresentation(ctx: PluginContext, root: StateTreeBuilder.To<PluginStateObject.Molecule.Structure>) {
root.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' })
- .apply(StateTransforms.Representation.StructureRepresentation3D, {
- type: { name: 'cartoon', params: PD.getDefaultValues(CartoonParams) },
- colorTheme: { name: 'polymer-id', params: PD.getDefaultValues(PolymerIdColorThemeParams) },
- sizeTheme: { name: 'uniform', params: PD.getDefaultValues(UniformSizeThemeParams) },
- });
+ .apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'cartoon'));
root.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' })
- .apply(StateTransforms.Representation.StructureRepresentation3D, {
- type: { name: 'ball-and-stick', params: PD.getDefaultValues(BallAndStickParams) },
- colorTheme: { name: 'element-symbol', params: PD.getDefaultValues(ElementSymbolColorThemeParams) },
- sizeTheme: { name: 'uniform', params: PD.getDefaultValues(UniformSizeThemeParams) },
- });
+ .apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick'));
root.apply(StateTransforms.Model.StructureComplexElement, { type: 'water' })
- .apply(StateTransforms.Representation.StructureRepresentation3D, {
- type: { name: 'ball-and-stick', params: { ...PD.getDefaultValues(BallAndStickParams), alpha: 0.51 } },
- colorTheme: { name: 'element-symbol', params: PD.getDefaultValues(ElementSymbolColorThemeParams) },
- sizeTheme: { name: 'uniform', params: PD.getDefaultValues(UniformSizeThemeParams) },
- })
+ .apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick', { alpha: 0.51 }));
root.apply(StateTransforms.Model.StructureComplexElement, { type: 'spheres' })
- .apply(StateTransforms.Representation.StructureRepresentation3D, {
- type: { name: 'spacefill', params: { ...PD.getDefaultValues(SpacefillParams) } },
- colorTheme: { name: 'polymer-id', params: PD.getDefaultValues(PolymerIdColorThemeParams) },
- sizeTheme: { name: 'physical', params: PD.getDefaultValues(PhysicalSizeThemeParams) },
- })
+ .apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'spacefill'));
}
export const CreateComplexRepresentation = StateAction.build({
display: { name: 'Create Complex', description: 'Split the structure into Sequence/Water/Ligands/... ' },
from: PluginStateObject.Molecule.Structure
-})(({ ref, state }) => {
+})(({ ref, state }, ctx: PluginContext) => {
const root = state.build().to(ref);
- complexRepresentation(root);
+ complexRepresentation(ctx, root);
return state.update(root.getTree());
});
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index 1c93b7b63b87f2ffbee56f795117bff6b9640ff1..64c66e6c2660f79facd44cd2a60c6618174bf996 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -14,16 +14,31 @@ import { ParamDefinition as PD } from 'mol-util/param-definition';
import { createTheme } from 'mol-theme/theme';
import { BuiltInStructureRepresentationsName } from 'mol-repr/structure/registry';
import { Structure } from 'mol-model/structure';
+import { UnitsMeshParams } from 'mol-repr/structure/units-visual';
export namespace StructureRepresentation3DHelpers {
- export function getDefaultParams(ctx: PluginContext, name: BuiltInStructureRepresentationsName, structure: Structure): Transformer.Params<StructureRepresentation3D> {
+ export function getDefaultParams(ctx: PluginContext, name: BuiltInStructureRepresentationsName, structure: Structure, meshParams?: Partial<PD.Values<UnitsMeshParams>>): Transformer.Params<StructureRepresentation3D> {
const type = ctx.structureRepresentation.registry.get(name);
const themeDataCtx = { structure };
const colorParams = ctx.structureRepresentation.themeCtx.colorThemeRegistry.get(type.defaultColorTheme).getParams(themeDataCtx);
const sizeParams = ctx.structureRepresentation.themeCtx.sizeThemeRegistry.get(type.defaultSizeTheme).getParams(themeDataCtx)
return ({
- type: { name, params: type.defaultValues },
+ type: { name, params: meshParams ? { ...type.defaultValues, ...meshParams } : type.defaultValues },
+ colorTheme: { name: type.defaultColorTheme, params: PD.getDefaultValues(colorParams) },
+ sizeTheme: { name: type.defaultSizeTheme, params: PD.getDefaultValues(sizeParams) }
+ })
+ }
+
+ export function getDefaultParamsStatic(ctx: PluginContext, name: BuiltInStructureRepresentationsName, meshParams?: Partial<PD.Values<UnitsMeshParams>>): Transformer.Params<StructureRepresentation3D> {
+ const type = ctx.structureRepresentation.registry.get(name);
+
+ // TODO: there should be "static default properties" for the themes.
+ const themeDataCtx = { };
+ const colorParams = ctx.structureRepresentation.themeCtx.colorThemeRegistry.get(type.defaultColorTheme).getParams(themeDataCtx);
+ const sizeParams = ctx.structureRepresentation.themeCtx.sizeThemeRegistry.get(type.defaultSizeTheme).getParams(themeDataCtx)
+ return ({
+ type: { name, params: meshParams ? { ...type.defaultValues, ...meshParams } : type.defaultValues },
colorTheme: { name: type.defaultColorTheme, params: PD.getDefaultValues(colorParams) },
sizeTheme: { name: type.defaultSizeTheme, params: PD.getDefaultValues(sizeParams) }
})
diff --git a/src/mol-state/state.ts b/src/mol-state/state.ts
index 75f801a682472e0cffe640268c5b49ba8122cbfa..a08f5f0d0d2aa20b28f22e99243c1e65e48becc6 100644
--- a/src/mol-state/state.ts
+++ b/src/mol-state/state.ts
@@ -18,6 +18,7 @@ import { StateActionManager } from './action/manager';
import { TransientTree } from './tree/transient';
import { LogEntry } from 'mol-util/log-entry';
import { now, formatTimespan } from 'mol-util/now';
+import { ParamDefinition } from 'mol-util/param-definition';
export { State }
@@ -498,6 +499,16 @@ async function updateSubtree(ctx: UpdateContext, root: Ref) {
}
}
+function resolveDefaultParams(ctx: UpdateContext, transform: Transform, src: StateObject) {
+ const prms = transform.transformer.definition.params;
+ const defaults = prms
+ ? ParamDefinition.getDefaultValues(prms(src, ctx.parent.globalContext))
+ : { };
+ // TODO: this should probably be resolved each time separately the transform is applied.
+ // the params should be cached in the cell?
+ (transform.params as any) = defaults;
+}
+
async function updateNode(ctx: UpdateContext, currentRef: Ref): Promise<UpdateNodeResult> {
const { oldTree, tree } = ctx;
const current = ctx.cells.get(currentRef)!;
@@ -514,6 +525,10 @@ async function updateNode(ctx: UpdateContext, currentRef: Ref): Promise<UpdateNo
const parent = parentCell.obj!;
current.sourceRef = parentCell.transform.ref;
+ if (!transform.params) {
+ resolveDefaultParams(ctx, transform, parent);
+ }
+
if (!oldTree.transforms.has(currentRef)) {
const obj = await createObject(ctx, currentRef, transform.transformer, parent, transform.params);
current.obj = obj;
diff --git a/src/mol-state/transform.ts b/src/mol-state/transform.ts
index dc290b1d3655d3d32ea73a9a74616af47f765356..6637949f202f7260a609bfecbb42153606eed6f6 100644
--- a/src/mol-state/transform.ts
+++ b/src/mol-state/transform.ts
@@ -40,7 +40,7 @@ export namespace Transform {
transformer,
props: (options && options.props) || { },
ref,
- params: params || {} as any,
+ params: params as any,
version: UUID.create22()
}
}
diff --git a/src/mol-state/tree/builder.ts b/src/mol-state/tree/builder.ts
index fcca72f35476165fe593bcd5e2f6c75623a81ade..2eb22efd86b5797c1845f75603646ca94af8ff79 100644
--- a/src/mol-state/tree/builder.ts
+++ b/src/mol-state/tree/builder.ts
@@ -51,6 +51,12 @@ namespace StateTreeBuilder {
export class To<A extends StateObject> implements StateTreeBuilder {
get editInfo() { return this.state.editInfo; }
+ readonly ref: Transform.Ref;
+
+ /**
+ * Apply the transformed to the parent node
+ * If no params are specified (params <- undefined), default params are lazily resolved.
+ */
apply<T extends Transformer<A, any, any>>(tr: T, params?: Transformer.Params<T>, options?: Partial<Transform.Options>, initialCellState?: Partial<StateObjectCell.State>): To<Transformer.To<T>> {
const t = tr.apply(this.ref, params, options);
this.state.tree.add(t, initialCellState);
@@ -84,7 +90,8 @@ namespace StateTreeBuilder {
getTree(): StateTree { return this.state.tree.asImmutable(); }
- constructor(private state: State, private ref: Transform.Ref, private root: Root) {
+ constructor(private state: State, ref: Transform.Ref, private root: Root) {
+ this.ref = ref;
if (!this.state.tree.transforms.has(ref)) {
throw new Error(`Could not find node '${ref}'.`);
}