From b88bf9bdf2373d41b3ddcc775d442360516d861c Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 5 Aug 2019 15:08:43 -0700
Subject: [PATCH] LociStructureSelection based on StructureElement.Query
---
src/mol-plugin/state/transforms/model.ts | 49 +++++++++++++++++++-----
1 file changed, 40 insertions(+), 9 deletions(-)
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index ddc20811a..3868b91a3 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -27,7 +27,6 @@ import { transpileMolScript } from '../../../mol-script/script/mol-script/symbol
import { shapeFromPly } from '../../../mol-model-formats/shape/ply';
import { SymmetryOperator } from '../../../mol-math/geometry';
import { ensureSecondaryStructure } from './helpers';
-import { formatMolScript } from '../../../mol-script/language/expression-formatter';
export { TrajectoryFromBlob };
export { TrajectoryFromMmCif };
@@ -41,6 +40,7 @@ export { TransformStructureConformation };
export { TransformStructureConformationByMatrix };
export { StructureSelection };
export { UserStructureSelection };
+export { LociStructureSelection };
export { StructureComplexElement };
export { CustomModelProperties };
export { CustomStructureProperties };
@@ -369,7 +369,7 @@ 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.' },
+ display: { name: 'Structure Selection', description: 'Create a molecular structure from the specified query expression string.' },
from: SO.Molecule.Structure,
to: SO.Molecule.Structure,
params: {
@@ -387,13 +387,6 @@ const UserStructureSelection = PluginStateTransform.BuiltIn({
const result = compiled(new QueryContext(a.data));
const s = Sel.unionStructure(result);
- // TODO for debug purposes only, later move to StructureSelection where the expression is not visible to the user
- let loci = Structure.toStructureElementLoci(Structure.Loci(s))
- if (s.parent) loci = StructureElement.Loci.remap(loci, s.parent)
- const expression = formatMolScript(StructureElement.Loci.toScriptExpression(loci))
- console.log({ before: params.query.expression, after: expression })
- params.query.expression = expression
-
const props = { label: `${params.label || 'Selection'}`, description: structureDesc(s) };
return new SO.Molecule.Structure(s, props);
},
@@ -425,6 +418,44 @@ function updateStructureFromQuery(query: QueryFn<Sel>, src: Structure, obj: SO.M
return true;
}
+type LociStructureSelection = typeof LociStructureSelection
+const LociStructureSelection = PluginStateTransform.BuiltIn({
+ name: 'loci-structure-selection',
+ display: { name: 'Structure Selection', description: 'Create a molecular structure from the specified structure-element query.' },
+ from: SO.Molecule.Structure,
+ to: SO.Molecule.Structure,
+ params: {
+ query: PD.Value<StructureElement.Query>(StructureElement.Query.Empty, { isHidden: true }),
+ label: PD.Optional(PD.Text('', { isHidden: true }))
+ }
+})({
+ apply({ a, params, cache }) {
+ (cache as { source: Structure }).source = a.data;
+
+ const s = StructureElement.Query.toStructure(params.query, a.data);
+ if (s.elementCount === 0) return StateObject.Null;
+
+ const props = { label: `${params.label || 'Selection'}`, description: structureDesc(s) };
+ return new SO.Molecule.Structure(s, props);
+ },
+ update: ({ a, b, oldParams, newParams, cache }) => {
+ if (!StructureElement.Query.areEqual(oldParams.query, newParams.query)) return StateTransformer.UpdateResult.Recreate;
+
+ if ((cache as { source: Structure }).source === a.data) {
+ return StateTransformer.UpdateResult.Unchanged;
+ }
+ (cache as { source: Structure }).source = a.data;
+
+ const s = StructureElement.Query.toStructure(newParams.query, a.data);
+ if (s.elementCount === 0) return StateTransformer.UpdateResult.Null;
+
+ b.label = `${newParams.label || 'Selection'}`;
+ b.description = structureDesc(s);
+ b.data = s;
+ return StateTransformer.UpdateResult.Updated;
+ }
+});
+
namespace StructureComplexElement {
export type Types = 'atomic-sequence' | 'water' | 'atomic-het' | 'spheres'
}
--
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