diff --git a/src/mol-model/structure/query/queries/internal.ts b/src/mol-model/structure/query/queries/internal.ts
index 0c65b5c62a320928501be94047bb00f6b57a19e1..8cf1078110a6c3c929f56bada9d17a1e2ea8d8bf 100644
--- a/src/mol-model/structure/query/queries/internal.ts
+++ b/src/mol-model/structure/query/queries/internal.ts
@@ -11,13 +11,14 @@ import Structure from '../../structure/structure';
import { StructureQuery } from '../query';
import { StructureSelection } from '../selection';
-export function sequence(): StructureQuery {
+export function atomicSequence(): StructureQuery {
return ctx => {
const { inputStructure } = ctx;
const l = StructureElement.create();
const units: Unit[] = [];
for (const unit of inputStructure.units) {
+ if (unit.kind !== Unit.Kind.Atomic) continue;
l.unit = unit;
const elements = unit.elements;
l.element = elements[0];
@@ -45,6 +46,8 @@ export function water(): StructureQuery {
const units: Unit[] = [];
for (const unit of inputStructure.units) {
+ if (unit.kind !== Unit.Kind.Atomic) continue;
+
l.unit = unit;
const elements = unit.elements;
l.element = elements[0];
@@ -55,13 +58,15 @@ export function water(): StructureQuery {
};
}
-export function lidangs(): StructureQuery {
+export function atomicHet(): StructureQuery {
return ctx => {
const { inputStructure } = ctx;
const l = StructureElement.create();
const units: Unit[] = [];
for (const unit of inputStructure.units) {
+ if (unit.kind !== Unit.Kind.Atomic) continue;
+
l.unit = unit;
const elements = unit.elements;
l.element = elements[0];
@@ -82,3 +87,16 @@ export function lidangs(): StructureQuery {
return StructureSelection.Singletons(inputStructure, new Structure(units));
};
}
+
+export function spheres(): StructureQuery {
+ return ctx => {
+ const { inputStructure } = ctx;
+
+ const units: Unit[] = [];
+ for (const unit of inputStructure.units) {
+ if (unit.kind !== Unit.Kind.Spheres) continue;
+ units.push(unit);
+ }
+ return StructureSelection.Singletons(inputStructure, new Structure(units));
+ };
+}
diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index af037145a351bdf69b37224c336c2ed3bd73f45b..c4a047a20930a742fc3ed15ac737160551d72cc4 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -83,15 +83,19 @@ export class PluginContext {
this.canvas3d.animate();
return true;
} catch (e) {
- this.log(LogEntry.error('' + e));
+ this.log.error('' + e);
console.error(e);
return false;
}
}
- log(e: LogEntry) {
- this.events.log.next(e);
- }
+ readonly log = {
+ entry: (e: LogEntry) => this.events.log.next(e),
+ error: (msg: string) => this.events.log.next(LogEntry.error(msg)),
+ message: (msg: string) => this.events.log.next(LogEntry.message(msg)),
+ info: (msg: string) => this.events.log.next(LogEntry.info(msg)),
+ warn: (msg: string) => this.events.log.next(LogEntry.warning(msg)),
+ };
/**
* This should be used in all transform related request so that it could be "spoofed" to allow
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index d7e521824c97734cdc7ac07a1bb8c2d4c6ef73b8..dca8203d8f5b404202d8ef468bc2c6794547ba02 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -13,7 +13,6 @@ import { PluginSpec } from './spec';
import { DownloadAtomicStructure, CreateComplexRepresentation, OpenAtomicStructure } from './state/actions/basic';
import { StateTransforms } from './state/transforms';
import { PluginBehaviors } from './behavior';
-import { LogEntry } from 'mol-util/log-entry';
function getParam(name: string, regex: string): string {
let r = new RegExp(`${name}=(${regex})[&]?`, 'i');
@@ -55,7 +54,7 @@ async function trySetSnapshot(ctx: PluginContext) {
if (!snapshotUrl) return;
await PluginCommands.State.Snapshots.Fetch.dispatch(ctx, { url: snapshotUrl })
} catch (e) {
- ctx.log(LogEntry.error('Failed to load snapshot.'));
+ ctx.log.error('Failed to load snapshot.');
console.warn('Failed to load snapshot', e);
}
}
\ No newline at end of file
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index f10374d3193f8bec997197dbbcd6b12cc8db12ca..152e549b007cea7a98b58b1235b4530aa0976c5b 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -101,14 +101,20 @@ function atomicStructureTree(b: StateTreeBuilder.To<PluginStateObject.Data.Binar
.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
.apply(StateTransforms.Model.StructureAssemblyFromModel);
- root.apply(StateTransforms.Model.StructureComplexElement, { type: 'sequence' })
+ complexRepresentation(root);
+
+ return root.getTree();
+}
+
+function complexRepresentation(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) } });
- root.apply(StateTransforms.Model.StructureComplexElement, { type: 'ligands' })
+ root.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' })
.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();
+ .apply(StateTransforms.Representation.StructureRepresentation3D, { type: { name: 'ball-and-stick', params: { ...PD.getDefaultValues(BallAndStickParams), alpha: 0.51 } } })
+ root.apply(StateTransforms.Model.StructureComplexElement, { type: 'spheres' });
+ // TODO: create spheres visual
}
export const CreateComplexRepresentation = StateAction.create<PluginStateObject.Molecule.Structure, void, {}>({
@@ -119,13 +125,7 @@ export const CreateComplexRepresentation = StateAction.create<PluginStateObject.
},
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 } } });
-
+ complexRepresentation(root);
return state.update(root.getTree());
}
});
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 0c29e936769d896809048c88086573ab9c60410b..9f5efdddd610324cd62d8f1bd75c08f9917dd821 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -13,6 +13,7 @@ import Expression from 'mol-script/language/expression';
import { compile } from 'mol-script/runtime/query/compiler';
import { MolScriptBuilder } from 'mol-script/language/builder';
import { StateObject } from 'mol-state';
+import { PluginContext } from 'mol-plugin/context';
export { TrajectoryFromMmCif }
namespace TrajectoryFromMmCif { export interface Params { blockHeader?: string } }
@@ -102,15 +103,21 @@ const StructureAssemblyFromModel = PluginStateTransform.Create<SO.Molecule.Model
const ids = model.symmetry.assemblies.map(a => [a.id, a.id] as [string, string]);
return { id: PD.Select(ids.length ? ids[0][0] : '', ids, { label: 'Asm Id', description: 'Assembly Id' }) };
},
- apply({ a, params }) {
+ apply({ a, params }, plugin: PluginContext) {
return Task.create('Build Assembly', async ctx => {
- let id = params.id;
+ let id = (params.id || '').trim();
const model = a.data;
if (!id && model.symmetry.assemblies.length) id = model.symmetry.assemblies[0].id;
- const asm = ModelSymmetry.findAssembly(model, id || '');
- if (!asm) throw new Error(`Assembly '${id}' not found`);
+ const asm = ModelSymmetry.findAssembly(model, id);
+ if (id && !asm) throw new Error(`Assembly '${id}' not found`);
const base = Structure.ofModel(model);
+ if (!asm) {
+ plugin.log.warn(`Model '${a.label}' has no assembly, returning default structure.`);
+ const label = { label: a.data.label, description: structureDesc(base) };
+ return new SO.Molecule.Structure(base, label);
+ }
+
const s = await StructureSymmetry.buildAssembly(base, id!).runInContext(ctx);
const label = { label: `Assembly ${id}`, description: structureDesc(s) };
return new SO.Molecule.Structure(s, label);
@@ -143,7 +150,7 @@ const StructureSelection = PluginStateTransform.Create<SO.Molecule.Structure, SO
});
export { StructureComplexElement }
-namespace StructureComplexElement { export interface Params { type: 'sequence' | 'water' | 'ligands' } }
+namespace StructureComplexElement { export interface Params { type: 'atomic-sequence' | 'water' | 'atomic-het' | 'spheres' } }
const StructureComplexElement = PluginStateTransform.Create<SO.Molecule.Structure, SO.Molecule.Structure, StructureComplexElement.Params>({
name: 'structure-complex-element',
display: {
@@ -158,9 +165,10 @@ const StructureComplexElement = PluginStateTransform.Create<SO.Molecule.Structur
let query: StructureQuery, label: string;
switch (params.type) {
- case 'sequence': query = Queries.internal.sequence(); label = 'Sequence'; break;
+ case 'atomic-sequence': query = Queries.internal.atomicSequence(); label = 'Sequence'; break;
case 'water': query = Queries.internal.water(); label = 'Water'; break;
- case 'ligands': query = Queries.internal.lidangs(); label = 'Ligands'; break;
+ case 'atomic-het': query = Queries.internal.atomicHet(); label = 'HET Groups/Ligands'; break;
+ case 'spheres': query = Queries.internal.spheres(); label = 'Coarse Spheres'; break;
default: throw new Error(`${params.type} is a valid complex element.`);
}
diff --git a/src/mol-plugin/ui/state.tsx b/src/mol-plugin/ui/state.tsx
index 031a3a54b572f8b16681f5652bf43366cb9648e1..d22304a0aeec92b8540b2c4b6090886977947513 100644
--- a/src/mol-plugin/ui/state.tsx
+++ b/src/mol-plugin/ui/state.tsx
@@ -9,7 +9,6 @@ import * as React from 'react';
import { PluginComponent } from './base';
import { shallowEqual } from 'mol-util';
import { List } from 'immutable';
-import { LogEntry } from 'mol-util/log-entry';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ParameterControls } from './controls/parameters';
import { Subject } from 'rxjs';
@@ -58,7 +57,7 @@ class StateSnapshotControls extends PluginComponent<{ serverUrl: string, serverC
this.setState({ isUploading: true });
await PluginCommands.State.Snapshots.Upload.dispatch(this.plugin, { name: this.state.name, description: this.state.description, serverUrl: this.state.serverUrl });
this.setState({ isUploading: false });
- this.plugin.log(LogEntry.message('Snapshot uploaded.'));
+ this.plugin.log.message('Snapshot uploaded.');
UploadedEvent.next();
}
@@ -128,7 +127,7 @@ class RemoteStateSnapshotList extends PluginComponent<{ serverUrl: string }, { e
}))),
isFetching: false })
} catch (e) {
- this.plugin.log(LogEntry.error('Fetching Remote Snapshots: ' + e));
+ this.plugin.log.error('Fetching Remote Snapshots: ' + e);
this.setState({ entries: List<RemoteEntry>(), isFetching: false })
}
}