From 884f2fb3e354a16ed81b42f1cdccc3d51310ba3e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Mal=C3=BD?= <michal.maly@ibt.cas.cz>
Date: Fri, 11 Nov 2022 20:52:14 +0100
Subject: [PATCH] ReDNATCO plugin stage 34
---
src/apps/rednatco/api-impl.ts | 2 +-
src/apps/rednatco/api.ts | 2 +-
src/apps/rednatco/index.tsx | 2 +-
src/apps/rednatco/viewer.ts | 40 ++++++++++++++++++++++-------------
4 files changed, 28 insertions(+), 18 deletions(-)
diff --git a/src/apps/rednatco/api-impl.ts b/src/apps/rednatco/api-impl.ts
index 4121bb9e9..fa36829f0 100644
--- a/src/apps/rednatco/api-impl.ts
+++ b/src/apps/rednatco/api-impl.ts
@@ -34,7 +34,7 @@ export class ReDNATCOMspApiImpl implements ReDNATCOMspApi.Object {
return !!this.target;
}
- loadStructure(coords: { data: string, type: 'cif'|'pdb' }, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6' }|null) {
+ loadStructure(coords: { data: string, type: 'cif'|'pdb' }, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6'|'ds' }|null) {
this.check();
this.target!.loadStructure(coords, densityMap);
}
diff --git a/src/apps/rednatco/api.ts b/src/apps/rednatco/api.ts
index 549b8a448..07d281d5a 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: (coords: { data: string, type: 'cif'|'pdb'}, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6' }|null) => void;
+ loadStructure: (coords: { data: string, type: 'cif'|'pdb'}, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6'|'ds' }|null) => void;
query: <T extends Queries.Type>(type: T) => ResponseTypes[T];
}
}
diff --git a/src/apps/rednatco/index.tsx b/src/apps/rednatco/index.tsx
index de537d688..f6dda49d1 100644
--- a/src/apps/rednatco/index.tsx
+++ b/src/apps/rednatco/index.tsx
@@ -226,7 +226,7 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
}
}
- loadStructure(coords: { data: string, type: 'pdb'|'cif' }, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6' }|null) {
+ loadStructure(coords: { data: string, type: 'pdb'|'cif' }, densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6'|'ds' }|null) {
if (this.viewer) {
this.viewer.loadStructure(coords, densityMap, this.state.display).then(() => {
this.presentConformers = this.viewer!.getPresentConformers();
diff --git a/src/apps/rednatco/viewer.ts b/src/apps/rednatco/viewer.ts
index 209e78ddc..63514a690 100644
--- a/src/apps/rednatco/viewer.ts
+++ b/src/apps/rednatco/viewer.ts
@@ -852,7 +852,7 @@ export class ReDNATCOMspViewer {
async loadStructure(
coords: { data: string, type: 'pdb'|'cif' },
- densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6' }|null,
+ densityMap: { data: Uint8Array, type: 'ccp4'|'dsn6'|'ds' }|null,
display: Display
) {
// TODO: Remove the currently loaded structure
@@ -942,28 +942,38 @@ export class ReDNATCOMspViewer {
// 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) });
-
- await b4.commit(); // Load the density map now so we can probe the stats;
+ // This is ridiculous but anything saner breaks type checker
+ if (densityMap.type === 'ccp4') {
+ await this.plugin.state.data.build().toRoot()
+ .apply(RawData, { data: densityMap.data }, { ref: IDs.DensityID('data', BaseRef) })
+ .apply(StateTransforms.Data.ParseCcp4)
+ .apply(StateTransforms.Volume.VolumeFromCcp4, {}, { ref: IDs.DensityID('volume', BaseRef) })
+ .commit();
+ } else if (densityMap.type === 'dsn6') {
+ await this.plugin.state.data.build().toRoot()
+ .apply(RawData, { data: densityMap.data }, { ref: IDs.DensityID('data', BaseRef) })
+ .apply(StateTransforms.Data.ParseDsn6)
+ .apply(StateTransforms.Volume.VolumeFromDsn6, {}, { ref: IDs.DensityID('volume', BaseRef) })
+ .commit();
+ } else if (densityMap.type === 'ds') {
+ await this.plugin.state.data.build().toRoot()
+ .apply(RawData, { data: densityMap.data }, { ref: IDs.DensityID('data', BaseRef) })
+ .apply(StateTransforms.Data.ParseCif)
+ .apply(StateTransforms.Volume.VolumeFromDensityServerCif, {}, { ref: IDs.DensityID('volume', BaseRef) })
+ .commit();
+ }
+
const isoRange = this.densityMapIsoRange()!;
const bounds = isoBounds(isoRange.min, isoRange.max);
const iso = prettyIso(((isoRange.max - isoRange.min) / 2) + isoRange.min, bounds.step);
- const b5 = this.plugin.state.data.build().to(IDs.DensityID('volume', BaseRef))
+ await this.plugin.state.data.build().to(IDs.DensityID('volume', BaseRef))
.apply(
StateTransforms.Representation.VolumeRepresentation3D,
this.densityMapVisuals(display.densityMap),
{ ref: IDs.DensityID('visual', BaseRef) }
- );
-
- await b5.commit();
+ )
+ .commit();
display.densityMap.representations = ['wireframe'];
display.densityMap.isoValue = iso;
--
GitLab