From fa0c29c1d12387b68c4b9ddc6d05e024c4f3e62e Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 27 Nov 2019 13:52:19 +0100
Subject: [PATCH] mol-plugin: DownloadStructure now uses StructureFromModel
---
src/mol-plugin/state/actions/structure.ts | 16 +++++++++++-----
src/mol-plugin/state/representation/model.ts | 18 +++++++++---------
src/mol-plugin/state/transforms/model.ts | 7 +++----
3 files changed, 23 insertions(+), 18 deletions(-)
diff --git a/src/mol-plugin/state/actions/structure.ts b/src/mol-plugin/state/actions/structure.ts
index 7c1913100..1697e593b 100644
--- a/src/mol-plugin/state/actions/structure.ts
+++ b/src/mol-plugin/state/actions/structure.ts
@@ -18,6 +18,7 @@ import { FileInfo } from '../../../mol-util/file-info';
import { Task } from '../../../mol-task';
import { StructureElement } from '../../../mol-model/structure';
import { createDefaultStructureComplex } from '../../util/structure-complex-helper';
+import { ModelStructureRepresentation } from '../representation/model';
export const MmcifProvider: DataFormatProvider<any> = {
label: 'mmCIF',
@@ -90,16 +91,20 @@ type StructureFormat = 'pdb' | 'cif' | 'gro' | '3dg'
//
+const DownloadModelRepresentationOptions = ModelStructureRepresentation.getParams(void 0, 'assembly').kind;
+
const DownloadStructurePdbIdSourceOptions = PD.Group({
+ structure: DownloadModelRepresentationOptions,
supportProps: PD.Optional(PD.Boolean(false)),
asTrajectory: PD.Optional(PD.Boolean(false, { description: 'Load all entries into a single trajectory.' }))
});
+
export { DownloadStructure };
type DownloadStructure = typeof DownloadStructure
const DownloadStructure = StateAction.build({
from: PluginStateObject.Root,
- display: { name: 'Download Structure', description: 'Load a structure from the provided source and create its default Assembly and visual.' },
+ display: { name: 'Download Structure', description: 'Load a structure from the provided source and create its representation.' },
params: {
source: PD.MappedStatic('bcif-static', {
'pdbe-updated': PD.Group({
@@ -127,6 +132,7 @@ const DownloadStructure = StateAction.build({
format: PD.Select('cif', [['cif', 'CIF'], ['pdb', 'PDB']] as ['cif' | 'pdb', string][]),
isBinary: PD.Boolean(false),
options: PD.Group({
+ structure: DownloadModelRepresentationOptions,
supportProps: PD.Optional(PD.Boolean(false))
})
}, { isFlat: true })
@@ -191,12 +197,12 @@ const DownloadStructure = StateAction.build({
if (downloadParams.length > 0 && asTrajectory) {
const traj = createSingleTrajectoryModel(downloadParams, b);
- createStructureTree(ctx, traj, supportProps);
+ createStructureTree(ctx, traj, supportProps, src.params.options.structure);
} else {
for (const download of downloadParams) {
const data = b.toRoot().apply(StateTransforms.Data.Download, download, { state: { isGhost: true } });
const traj = createModelTree(data, format);
- createStructureTree(ctx, traj, supportProps)
+ createStructureTree(ctx, traj, supportProps, src.params.options.structure)
}
}
return state.updateTree(b, { revertIfAborted: true });
@@ -246,12 +252,12 @@ export function createModelTree(b: StateBuilder.To<PluginStateObject.Data.Binary
return parsed.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 });
}
-function createStructureTree(ctx: PluginContext, b: StateBuilder.To<PluginStateObject.Molecule.Model>, supportProps: boolean) {
+function createStructureTree(ctx: PluginContext, b: StateBuilder.To<PluginStateObject.Molecule.Model>, supportProps: boolean, params?: ModelStructureRepresentation.Params) {
let root = b;
if (supportProps) {
root = root.apply(StateTransforms.Model.CustomModelProperties);
}
- const structure = root.apply(StateTransforms.Model.StructureAssemblyFromModel);
+ const structure = root.apply(StateTransforms.Model.StructureFromModel, { kind: params || { name: 'assembly', params: { } } });
createDefaultStructureComplex(ctx, structure);
return root;
diff --git a/src/mol-plugin/state/representation/model.ts b/src/mol-plugin/state/representation/model.ts
index 6edb77f75..2f2d0718d 100644
--- a/src/mol-plugin/state/representation/model.ts
+++ b/src/mol-plugin/state/representation/model.ts
@@ -54,7 +54,7 @@ export namespace ModelStructureRepresentation {
};
}
- export type Params = PD.Values<ReturnType<typeof getParams>>
+ export type Params = PD.Values<ReturnType<typeof getParams>>['kind']
async function buildAssembly(plugin: PluginContext, ctx: RuntimeContext, model: Model, id?: string) {
let asm: Assembly | undefined = void 0;
@@ -106,21 +106,21 @@ export namespace ModelStructureRepresentation {
}
export async function create(plugin: PluginContext, ctx: RuntimeContext, model: Model, params?: Params): Promise<SO.Molecule.Structure> {
- if (!params || !params.kind || params.kind.name === 'deposited') {
+ if (!params || params.name === 'deposited') {
const s = Structure.ofModel(model);
await ensureSecondaryStructure(s);
return new SO.Molecule.Structure(s, { label: 'Deposited', description: Structure.elementDescription(s) });
}
- if (params.kind.name === 'assembly') {
- return buildAssembly(plugin, ctx, model, params.kind.params.id)
+ if (params.name === 'assembly') {
+ return buildAssembly(plugin, ctx, model, params.params.id)
}
- if (params.kind.name === 'symmetry') {
- return buildSymmetry(ctx, model, params.kind.params.ijkMin, params.kind.params.ijkMax)
+ if (params.name === 'symmetry') {
+ return buildSymmetry(ctx, model, params.params.ijkMin, params.params.ijkMax)
}
- if (params.kind.name === 'symmetry-mates') {
- return buildSymmetryMates(ctx, model, params.kind.params.radius)
+ if (params.name === 'symmetry-mates') {
+ return buildSymmetryMates(ctx, model, params.params.radius)
}
- throw new Error(`Unknown represetation type: ${(params.kind as any).name}`);
+ throw new Error(`Unknown represetation type: ${(params as any).name}`);
}
}
\ No newline at end of file
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 940d2b1a2..49815e97a 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -9,8 +9,7 @@ import { parsePDB } from '../../../mol-io/reader/pdb/parser';
import { Vec3, Mat4, Quat } from '../../../mol-math/linear-algebra';
import { trajectoryFromMmCIF } from '../../../mol-model-formats/structure/mmcif';
import { trajectoryFromPDB } from '../../../mol-model-formats/structure/pdb';
-import { Model, ModelSymmetry, Queries, QueryContext, Structure, StructureQuery, StructureSelection as Sel, StructureSymmetry, StructureElement } from '../../../mol-model/structure';
-import { Assembly } from '../../../mol-model/structure/model/properties/symmetry';
+import { Model, Queries, QueryContext, Structure, StructureQuery, StructureSelection as Sel, StructureElement } from '../../../mol-model/structure';
import { PluginContext } from '../../../mol-plugin/context';
import { MolScriptBuilder } from '../../../mol-script/language/builder';
import Expression from '../../../mol-script/language/expression';
@@ -209,7 +208,7 @@ const StructureFromModel = PluginStateTransform.BuiltIn({
})({
apply({ a, params }, plugin: PluginContext) {
return Task.create('Build Structure', async ctx => {
- return ModelStructureRepresentation.create(plugin, ctx, a.data, params);
+ return ModelStructureRepresentation.create(plugin, ctx, a.data, params && params.kind);
})
}
});
@@ -235,7 +234,7 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
})({
apply({ a, params }, plugin: PluginContext) {
return Task.create('Build Assembly', async ctx => {
- return ModelStructureRepresentation.create(plugin, ctx, a.data, { kind: { name: 'assembly', params } });
+ return ModelStructureRepresentation.create(plugin, ctx, a.data, { name: 'assembly', params });
})
}
});
--
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