From df9540b89be29684bf99929c3a0f600c7d8f2fef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Mal=C3=BD?= <michal.maly@ibt.cas.cz>
Date: Wed, 9 Nov 2022 18:48:52 +0100
Subject: [PATCH] ReDNATCO plugin stage 32
---
src/apps/rednatco/api-impl.ts | 4 ++--
src/apps/rednatco/api.ts | 2 +-
src/apps/rednatco/idents.ts | 7 ++++++
src/apps/rednatco/index.tsx | 4 ++--
src/apps/rednatco/viewer.ts | 43 ++++++++++++++++++++++++++++++++---
5 files changed, 52 insertions(+), 8 deletions(-)
diff --git a/src/apps/rednatco/api-impl.ts b/src/apps/rednatco/api-impl.ts
index a24cca51f..4121bb9e9 100644
--- a/src/apps/rednatco/api-impl.ts
+++ b/src/apps/rednatco/api-impl.ts
@@ -34,9 +34,9 @@ export class ReDNATCOMspApiImpl implements ReDNATCOMspApi.Object {
return !!this.target;
}
- loadStructure(data: string, type: 'cif'|'pdb') {
+ loadStructure(coords: { data: string, type: 'cif'|'pdb' }, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6' }|null) {
this.check();
- this.target!.loadStructure(data, type);
+ this.target!.loadStructure(coords, densityMap);
}
query<T extends ReDNATCOMspApi.Queries.Type>(type: T): ReDNATCOMspApi.ResponseTypes[T] {
diff --git a/src/apps/rednatco/api.ts b/src/apps/rednatco/api.ts
index dcf9854ac..549b8a448 100644
--- a/src/apps/rednatco/api.ts
+++ b/src/apps/rednatco/api.ts
@@ -126,7 +126,7 @@ export namespace ReDNATCOMspApi {
event: (evt: Event) => void;
init: (elemId: string, onEvent?: (evt: Event) => void) => void;
isReady: () => boolean;
- loadStructure: (data: string, type: 'cif'|'pdb') => void;
+ loadStructure: (coords: { data: string, type: 'cif'|'pdb'}, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6' }|null) => void;
query: <T extends Queries.Type>(type: T) => ResponseTypes[T];
}
}
diff --git a/src/apps/rednatco/idents.ts b/src/apps/rednatco/idents.ts
index 96a74d6be..91b5b4c91 100644
--- a/src/apps/rednatco/idents.ts
+++ b/src/apps/rednatco/idents.ts
@@ -8,6 +8,7 @@ export type ID =
'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) {
@@ -16,6 +17,12 @@ export function ID(id: ID, sub: Substructure|'', ref: string) {
return `${ref}_${sub}_${id}`;
}
+export type DensityID = 'data'|'volume'|'visual';
+
+export function DensityID(id: DensityID, ref: string) {
+ return `${ref}_density-map_${id}`;
+}
+
export function isVisual(ident: string) {
return ident.endsWith('_visual');
}
diff --git a/src/apps/rednatco/index.tsx b/src/apps/rednatco/index.tsx
index ae047f25b..e5a86b0ae 100644
--- a/src/apps/rednatco/index.tsx
+++ b/src/apps/rednatco/index.tsx
@@ -204,9 +204,9 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
}
}
- loadStructure(data: string, type: 'pdb'|'cif') {
+ loadStructure(coords: { data: string, type: 'pdb'|'cif' }, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6' }|null) {
if (this.viewer) {
- this.viewer.loadStructure(data, type, this.state.display).then(() => {
+ this.viewer.loadStructure(coords, densityMap, this.state.display).then(() => {
this.presentConformers = this.viewer!.getPresentConformers();
this.forceUpdate();
ReDNATCOMspApi.event(Api.Events.StructureLoaded());
diff --git a/src/apps/rednatco/viewer.ts b/src/apps/rednatco/viewer.ts
index 06195b5df..8c609374f 100644
--- a/src/apps/rednatco/viewer.ts
+++ b/src/apps/rednatco/viewer.ts
@@ -16,6 +16,7 @@ import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
import { Vec3 } from '../../mol-math/linear-algebra/3d';
import { EmptyLoci, Loci } from '../../mol-model/loci';
import { ElementIndex, Model, StructureElement, StructureProperties, StructureSelection, Trajectory } from '../../mol-model/structure';
+// import { Volume } from '../../mol-model/volume';
import { structureUnion, structureSubtract } from '../../mol-model/structure/query/utils/structure-set';
import { Location } from '../../mol-model/structure/structure/element/location';
import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
@@ -799,16 +800,20 @@ export class ReDNATCOMspViewer {
return this.has('structure', '', BaseRef);
}
- async loadStructure(data: string, type: 'pdb'|'cif', display: Display) {
+ async loadStructure(
+ coords: { data: string, type: 'pdb'|'cif' },
+ densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6' }|null,
+ display: Display
+ ) {
// TODO: Remove the currently loaded structure
const chainColor = Color(display.chainColor);
const waterColor = Color(display.waterColor);
- const b = (t => type === 'pdb'
+ const b = (t => coords.type === 'pdb'
? t.apply(StateTransforms.Model.TrajectoryFromPDB, {}, { ref: IDs.ID('trajectory', '', BaseRef) })
: 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) }))
+ )(this.plugin.state.data.build().toRoot().apply(RawData, { data: coords.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('entire-structure', '', BaseRef) })
// Extract substructures
@@ -885,6 +890,38 @@ export class ReDNATCOMspViewer {
await b3.commit();
+ // Load density map, if any
+ if (densityMap) {
+ const [ParseTransform, VolumeTransform] = densityMap.type === 'ccp4'
+ ? [StateTransforms.Data.ParseCcp4, StateTransforms.Volume.VolumeFromCcp4]
+ : [StateTransforms.Data.ParseDsn6, StateTransforms.Volume.VolumeFromDsn6];
+ const b4 = this.plugin.state.data.build();
+ b4.toRoot()
+ .apply(RawData, { data: densityMap.data }, { ref: IDs.DensityID('data', BaseRef) })
+ .apply(ParseTransform)
+ .apply(VolumeTransform, {}, { ref: IDs.DensityID('volume', BaseRef) })
+ .apply(
+ StateTransforms.Representation.VolumeRepresentation3D,
+ {
+ type: {
+ name: 'isosurface',
+ params: {
+ alpha: 0.5,
+ visuals: ['wireframe'],
+ sizeFactor: 0.75,
+ }
+ },
+ colorTheme: {
+ name: 'uniform',
+ params: { value: Color(0x000000) },
+ },
+ },
+ { ref: IDs.DensityID('visual', BaseRef) }
+ );
+
+ await b4.commit();
+ }
+
this.haveMultipleModels = this.getModelCount() > 1;
const ntcInfo = this.gatherStepInfo();
--
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