ermoved deprecated StructureAssemblyFromModel

src/apps/basic-wrapper/helpers.ts

@@ -67,7 +67,13 @@ export namespace StateHelper {
     }
 
     export function assemble(b: StateBuilder.To<PSO.Molecule.Model>, id?: string) {
-        return b.apply(StateTransforms.Model.StructureAssemblyFromModel, { id: id || 'deposited' }, { tags: 'asm' })
+        const props = {
+            type: {
+                name: 'assembly' as const,
+                params: { id: id || 'deposited' }
+            }
+        }
+        return b.apply(StateTransforms.Model.StructureFromModel, props, { tags: 'asm' })
     }
 
     export function visual(ctx: PluginContext, visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {

src/apps/basic-wrapper/index.ts

@@ -61,10 +61,16 @@ class BasicWrapper {
             ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
             : b.apply(StateTransforms.Model.TrajectoryFromPDB);
 
+        const props = {
+            type: {
+                name: 'assembly' as const,
+                params: { id: assemblyId || 'deposited' }
+            }
+        }
         return parsed
             .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
             .apply(StateTransforms.Model.CustomModelProperties, { autoAttach: [StripedResidues.propertyProvider.descriptor.name], properties: {} }, { ref: 'props', state: { isGhost: false } })
-            .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: 'asm' });
+            .apply(StateTransforms.Model.StructureFromModel, props, { ref: 'asm' });
     }
 
     private visual(visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
@@ -101,8 +107,15 @@ class BasicWrapper {
             tree = state.build();
             this.visual(this.parse(this.download(tree.toRoot(), url), format, assemblyId));
         } else {
+            const props = {
+                type: {
+                    name: 'assembly' as const,
+                    params: { id: assemblyId || 'deposited' }
+                }
+            }
+
             tree = state.build();
-            tree.to('asm').update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId || 'deposited' }));
+            tree.to('asm').update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
         }
 
         await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });

src/apps/demos/lighting/index.ts

@@ -120,9 +120,15 @@ class LightingDemo {
             ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
             : b.apply(StateTransforms.Model.TrajectoryFromPDB);
 
+        const props = {
+            type: {
+                name: 'assembly' as const,
+                params: { id: assemblyId || 'deposited' }
+            }
+        }
         return parsed
             .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
-            .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: 'asm' });
+            .apply(StateTransforms.Model.StructureFromModel, props, { ref: 'asm' });
     }
 
     private visual(visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
@@ -153,8 +159,14 @@ class LightingDemo {
             tree = state.build();
             this.visual(this.parse(this.download(tree.toRoot(), url), format, assemblyId));
         } else {
+            const props = {
+                type: {
+                    name: 'assembly' as const,
+                    params: { id: assemblyId || 'deposited' }
+                }
+            }
             tree = state.build();
-            tree.to('asm').update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId || 'deposited' }));
+            tree.to('asm').update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
         }
 
         await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });

src/examples/proteopedia-wrapper/index.ts

@@ -92,10 +92,16 @@ class MolStarProteopediaWrapper {
 
     private structure(assemblyId: string) {
         const model = this.state.build().to(StateElements.Model);
+        const props = {
+            type: {
+                name: 'assembly' as const,
+                params: { id: assemblyId || 'deposited' }
+            }
+        }
 
         const s = model
             .apply(StateTransforms.Model.CustomModelProperties, { autoAttach: [EvolutionaryConservation.propertyProvider.descriptor.name], properties: {} }, { ref: StateElements.ModelProps, state: { isGhost: false } })
-            .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: StateElements.Assembly });
+            .apply(StateTransforms.Model.StructureFromModel, props, { ref: StateElements.Assembly });
 
         s.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' }, { ref: StateElements.Sequence });
         s.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' }, { ref: StateElements.Het });
@@ -213,7 +219,13 @@ class MolStarProteopediaWrapper {
             const tree = state.build();
             const info = await this.doInfo(true);
             const asmId = (assemblyId === 'preferred' && info && info.preferredAssemblyId) || assemblyId;
-            tree.to(StateElements.Assembly).update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: asmId }));
+            const props = {
+                type: {
+                    name: 'assembly' as const,
+                    params: { id: asmId || 'deposited' }
+                }
+            }
+            tree.to(StateElements.Assembly).update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
             await this.applyState(tree);
         }
 

src/mol-plugin/state/transforms/model.ts

@@ -16,7 +16,6 @@ import Expression from '../../../mol-script/language/expression';
 import { StateObject, StateTransformer } from '../../../mol-state';
 import { RuntimeContext, Task } from '../../../mol-task';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-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';
@@ -32,7 +31,6 @@ import { parseDcd } from '../../../mol-io/reader/dcd/parser';
 import { coordinatesFromDcd } from '../../../mol-model-formats/structure/dcd';
 import { topologyFromPsf } from '../../../mol-model-formats/structure/psf';
 import { deepEqual } from '../../../mol-util';
-import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
 
 export { CoordinatesFromDcd };
 export { TopologyFromPsf };
@@ -45,7 +43,6 @@ export { TrajectoryFrom3DG };
 export { ModelFromTrajectory };
 export { StructureFromTrajectory };
 export { StructureFromModel };
-export { StructureAssemblyFromModel };
 export { TransformStructureConformation };
 export { TransformStructureConformationByMatrix };
 export { StructureSelectionFromExpression };
@@ -290,32 +287,6 @@ const StructureFromModel = PluginStateTransform.BuiltIn({
     }
 });
 
-// TODO: deprecate this in favor of StructureFromModel
-type StructureAssemblyFromModel = typeof StructureAssemblyFromModel
-const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
-    name: 'structure-assembly-from-model',
-    display: { name: 'Structure Assembly', description: 'Create a molecular structure assembly.' },
-    from: SO.Molecule.Model,
-    to: SO.Molecule.Structure,
-    params(a) {
-        if (!a) {
-            return { id: PD.Optional(PD.Text('', { label: 'Assembly Id', description: 'Assembly Id. Value \'deposited\' can be used to specify deposited asymmetric unit.' })) };
-        }
-        const assemblies = ModelSymmetry.Provider.get(a.data)?.assemblies || []
-        const ids = assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]);
-        ids.push(['deposited', 'Deposited']);
-        return {
-            id: PD.Optional(PD.Select(ids[0][0], ids, { label: 'Asm Id', description: 'Assembly Id' }))
-        };
-    }
-})({
-    apply({ a, params }, plugin: PluginContext) {
-        return Task.create('Build Assembly', async ctx => {
-            return ModelStructureRepresentation.create(plugin, ctx, a.data, { name: 'assembly', params });
-        })
-    }
-});
-
 const _translation = Vec3(), _m = Mat4(), _n = Mat4();
 type TransformStructureConformation = typeof TransformStructureConformation
 const TransformStructureConformation = PluginStateTransform.BuiltIn({