diff --git a/src/apps/rednatco/api.ts b/src/apps/rednatco/api.ts
index d58ca246cd2cceacbe928048505644f932e574b3..e6143205e37fb488b8689b33a014ad37be9da291 100644
--- a/src/apps/rednatco/api.ts
+++ b/src/apps/rednatco/api.ts
@@ -1,15 +1,22 @@
+import { Filtering } from './filtering';
+
export namespace ReDNATCOMspApi {
export namespace Commands {
- export type Type = 'deselect-step'|'redraw'|'select-step'|'switch-model';
-
- export type Redraw = { type: 'redraw' }
- export function Redraw(): Redraw { return { type: 'redraw' }; }
+ export type Type = 'deselect-step'|'filter'|'redraw'|'select-step'|'switch-model';
export type DeselectStep = { type: 'deselect-step' }
- export function DeselectStep() {
+ export function DeselectStep(): DeselectStep {
return { type: 'deselect-step' };
}
+ export type Filter = { type: 'filter', filter: Filtering.Filter };
+ export function Filter(filter: Filtering.Filter) {
+ return { type: 'filter', filter };
+ }
+
+ export type Redraw = { type: 'redraw' }
+ export function Redraw(): Redraw { return { type: 'redraw' }; }
+
export type SelectStep = {
type: 'select-step';
stepName: string;
diff --git a/src/apps/rednatco/idents.ts b/src/apps/rednatco/idents.ts
index c1f27f8b6aa902826e83fa4e711bda8f70d5e453..9c7cd3470882bda6428f0456f178ed52342f2c33 100644
--- a/src/apps/rednatco/idents.ts
+++ b/src/apps/rednatco/idents.ts
@@ -1,4 +1,11 @@
-export type ID ='data'|'trajectory'|'model'|'structure'|'visual'|'pyramids'|'superposition';
+export type ID =
+ 'data' | /* Source structural data */
+ 'trajectory' | /* Source data parsed into trajectory */
+ 'model' | /* Currently active model */
+ 'entire-structure' | /* Entire structure (as Molstar structure PSO) of the active model */
+ 'structure' | /* Possibly filtered structure as PSO - this is what shall be used to create visuals from */
+ 'visual' | /* Visual PSO - the thing that is actually drawn on the screen */
+ 'pyramids'|'superposition'; /* Additional identifiers for DNATCO-specific objects */
export type Substructure = 'nucleic'|'protein'|'water'|'selected-slice'|'remainder-slice';
export function ID(id: ID, sub: Substructure|'', ref: string) {
diff --git a/src/apps/rednatco/viewer.ts b/src/apps/rednatco/viewer.ts
index c1e8c797366f76984c30509ecbf460af76894c1d..63aaf14bcc8eca3e52cad8c21d24881897f2233a 100644
--- a/src/apps/rednatco/viewer.ts
+++ b/src/apps/rednatco/viewer.ts
@@ -2,6 +2,7 @@ import * as IDs from './idents';
import * as RefCfmr from './reference-conformers';
import { ReDNATCOMsp, Display, VisualRepresentations } from './index';
import { NtCColors } from './colors';
+import { Filtering } from './filtering';
import { ReferenceConformersPdbs } from './reference-conformers-pdbs';
import { Step } from './step';
import { Superpose } from './superpose';
@@ -840,27 +841,55 @@ export class ReDNATCOMspViewer {
: t.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif, {}, { ref: IDs.ID('trajectory', '', BaseRef) })
)(this.plugin.state.data.build().toRoot().apply(RawData, { data }, { ref: IDs.ID('data', '', BaseRef) }))
.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: display.modelNumber ? display.modelNumber - 1 : 0 }, { ref: IDs.ID('model', '', BaseRef) })
- .apply(StateTransforms.Model.StructureFromModel, {}, { ref: IDs.ID('structure', '', BaseRef) })
+ .apply(StateTransforms.Model.StructureFromModel, {}, { ref: IDs.ID('entire-structure', '', BaseRef) })
// Extract substructures
- .apply(StateTransforms.Model.StructureComplexElement, { type: 'nucleic' }, { ref: IDs.ID('structure', 'nucleic', BaseRef) })
- .to(IDs.ID('structure', '', BaseRef))
- .apply(StateTransforms.Model.StructureComplexElement, { type: 'protein' }, { ref: IDs.ID('structure', 'protein', BaseRef) })
- .to(IDs.ID('structure', '', BaseRef))
- .apply(StateTransforms.Model.StructureComplexElement, { type: 'water' }, { ref: IDs.ID('structure', 'water', BaseRef) });
- // Commit now so that we can check whether individual substructures are available
+ .apply(StateTransforms.Model.StructureComplexElement, { type: 'nucleic' }, { ref: IDs.ID('entire-structure', 'nucleic', BaseRef) })
+ .to(IDs.ID('entire-structure', '', BaseRef))
+ .apply(StateTransforms.Model.StructureComplexElement, { type: 'protein' }, { ref: IDs.ID('entire-structure', 'protein', BaseRef) })
+ .to(IDs.ID('entire-structure', '', BaseRef))
+ .apply(StateTransforms.Model.StructureComplexElement, { type: 'water' }, { ref: IDs.ID('entire-structure', 'water', BaseRef) });
+ // Commit now so that we can check whether individual substructures are available and apply filters
await b.commit();
+ // Create the "possibly filtered" structure PSOs
+ const b2 = this.plugin.state.data.build();
+ if (this.has('entire-structure', 'nucleic')) {
+ b2.to(IDs.ID('entire-structure', 'nucleic', BaseRef))
+ .apply(
+ StateTransforms.Model.StructureSelectionFromExpression,
+ { expression: Filtering.toExpression(Filtering.EmptyFilter()) },
+ { ref: IDs.ID('structure', 'nucleic', BaseRef) }
+ );
+ }
+ if (this.has('entire-structure', 'protein')) {
+ b2.to(IDs.ID('entire-structure', 'protein', BaseRef))
+ .apply(
+ StateTransforms.Model.StructureSelectionFromExpression,
+ { expression: Filtering.toExpression(Filtering.EmptyFilter()) },
+ { ref: IDs.ID('structure', 'protein', BaseRef) }
+ );
+ }
+ if (this.has('entire-structure', 'water')) {
+ b2.to(IDs.ID('entire-structure', 'water', BaseRef))
+ .apply(
+ StateTransforms.Model.StructureSelectionFromExpression,
+ { expression: Filtering.toExpression(Filtering.EmptyFilter()) },
+ { ref: IDs.ID('structure', 'water', BaseRef) }
+ );
+ }
+ await b2.commit();
+
// Create default visuals
- const bb = this.plugin.state.data.build();
+ const b3 = this.plugin.state.data.build();
if (display.showNucleic && this.has('structure', 'nucleic')) {
- bb.to(IDs.ID('structure', 'nucleic', BaseRef))
+ b3.to(IDs.ID('structure', 'nucleic', BaseRef))
.apply(
StateTransforms.Representation.StructureRepresentation3D,
this.substructureVisuals('cartoon', chainColor),
{ ref: IDs.ID('visual', 'nucleic', BaseRef) }
);
if (display.showPyramids) {
- bb.to(IDs.ID('structure', 'nucleic', BaseRef))
+ b3.to(IDs.ID('structure', 'nucleic', BaseRef))
.apply(
StateTransforms.Representation.StructureRepresentation3D,
this.pyramidsParams(display.conformerColors ?? NtCColors.Conformers, new Map(), false),
@@ -869,7 +898,7 @@ export class ReDNATCOMspViewer {
}
}
if (display.showProtein && this.has('structure', 'protein')) {
- bb.to(IDs.ID('structure', 'protein', BaseRef))
+ b3.to(IDs.ID('structure', 'protein', BaseRef))
.apply(
StateTransforms.Representation.StructureRepresentation3D,
this.substructureVisuals('cartoon', chainColor),
@@ -877,7 +906,7 @@ export class ReDNATCOMspViewer {
);
}
if (display.showWater && this.has('structure', 'water')) {
- bb.to(IDs.ID('structure', 'water', BaseRef))
+ b3.to(IDs.ID('structure', 'water', BaseRef))
.apply(
StateTransforms.Representation.StructureRepresentation3D,
this.waterVisuals(waterColor),
@@ -885,7 +914,7 @@ export class ReDNATCOMspViewer {
);
}
- await bb.commit();
+ await b3.commit();
this.haveMultipleModels = this.getModelCount() > 1;