Use NtC tube and separate representations for nucleic and protein

substructures

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' }, densityMaps: { data: Uint8Array, type: 'ccp4' | 'dsn6', kind: '2fo-fc' | 'fo-fc' | 'em' }[] | null) {
+    loadStructure(coords: { data: string, type: ReDNATCOMspApi.CoordinatesFormat }, densityMaps: { data: Uint8Array, type: ReDNATCOMspApi.DensityMapFormat, kind: ReDNATCOMspApi.DensityMapKind }[] | null) {
         this.check();
         this.target!.loadStructure(coords, densityMaps);
     }

src/apps/rednatco/api.ts

 import { Filters } from './filters';
 
 export namespace ReDNATCOMspApi {
+    export type CoordinatesFormat = 'cif' | 'pdb';
+    export type DensityMapFormat = 'ccp4' | 'dsn6';
+    export type DensityMapKind = '2fo-fc' | 'fo-fc' | 'em';
+
     export namespace Payloads {
         export type StepSelection = {
             name: string;
@@ -126,7 +130,7 @@ export namespace ReDNATCOMspApi {
         event: (evt: Event) => void;
         init: (elemId: string, onEvent?: (evt: Event) => void) => void;
         isReady: () => boolean;
-        loadStructure: (coords: { data: string, type: 'cif' | 'pdb'}, densityMaps: { data: Uint8Array, type: 'ccp4' | 'dsn6', kind: '2fo-fc' | 'fo-fc' | 'em' }[] | null) => void;
+        loadStructure: (coords: { data: string, type: CoordinatesFormat }, densityMaps: { data: Uint8Array, type: DensityMapFormat, kind: DensityMapKind }[] | null) => void;
         query: <T extends Queries.Type>(type: T) => ResponseTypes[T];
     }
 }

src/apps/rednatco/density-map-controls.tsx

 import React from 'react';
+import { ReDNATCOMspApi as Api } from './api';
 import { ColorPicker } from './color-picker';
 import { ColorBox, RangeSlider, SpinBox, ToggleButton } from './controls';
-import { DensityMapDisplay, DensityMapKind } from './index';
+import { DensityMapDisplay } from './index';
 import { isoBounds, isoToFixed } from './util';
 import { ReDNATCOMspViewer as Viewer } from './viewer';
 import { Color } from '../../mol-util/color';
@@ -135,7 +136,7 @@ export class DensityMapControls extends React.Component<DensityMapControls.Props
         return ctrls;
     }
 
-    private mapName(kind: DensityMapKind) {
+    private mapName(kind: Api.DensityMapKind) {
         switch (kind) {
             case '2fo-fc':
                 return <span>2Fo-Fc</span>;

src/apps/rednatco/traverse.ts

@@ -23,7 +23,7 @@ export namespace Traverse {
 
     // TODO: We will be able to use a function from DnatcoUtils once it gets upstreamed
     const _loc = StructureElement.Location.create();
-    export function findResidue(asymId: string, seqId: number, altId: string|undefined, insCode: string, loci: StructureElement.Loci, source: 'label'|'auth') {
+    export function findResidue(asymId: string, seqId: number, altId: string | undefined, insCode: string, loci: StructureElement.Loci, source: 'label' | 'auth') {
         _loc.structure = loci.structure;
         for (const e of loci.elements) {
             _loc.unit = e.unit;
@@ -76,9 +76,9 @@ export namespace Traverse {
 
     export function findStep(
         asymId: string,
-        seqId1: number, altId1: string|undefined, insCode1: string,
-        seqId2: number, altId2: string|undefined, insCode2: string,
-        loci: StructureElement.Loci, source: 'label'|'auth'
+        seqId1: number, altId1: string | undefined, insCode1: string,
+        seqId2: number, altId2: string | undefined, insCode2: string,
+        loci: StructureElement.Loci, source: 'label' | 'auth'
     ) {
         const first = findResidue(asymId, seqId1, altId1, insCode1, loci, source);
         if (first.kind === 'empty-loci')

src/extensions/dnatco/behavior.ts

@@ -56,4 +56,3 @@ export const DnatcoNtCs = PluginBehavior.create<{ autoAttach: boolean, showToolT
         showToolTip: PD.Boolean(true)
     })
 });
-