diff --git a/src/apps/rednatco/api-impl.ts b/src/apps/rednatco/api-impl.ts
index bed5fbff2daab5e983ce9dae321475cac1b83579..27ce3fd3866ead331a47b5feaeef5e64aed0085d 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' }, 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);
}
diff --git a/src/apps/rednatco/api.ts b/src/apps/rednatco/api.ts
index 1652681da019ee27c21a111cd1a46773b713ed20..ac0de6d82c1f37a642b77d446689c7f5bd13c44f 100644
--- a/src/apps/rednatco/api.ts
+++ b/src/apps/rednatco/api.ts
@@ -1,6 +1,10 @@
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];
}
}
diff --git a/src/apps/rednatco/density-map-controls.tsx b/src/apps/rednatco/density-map-controls.tsx
index 2fee14728e04283d07c7452fd75a26024066f43f..17f7659ce6bed326ee3d3851bf25230dcf9761ee 100644
--- a/src/apps/rednatco/density-map-controls.tsx
+++ b/src/apps/rednatco/density-map-controls.tsx
@@ -1,7 +1,8 @@
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>;
diff --git a/src/apps/rednatco/index.tsx b/src/apps/rednatco/index.tsx
index 7ff9c2329c3c10f05a548124d8efd465b7c2ae2b..8553321ca68c6173cb57d930df3fa39d1b2efdd5 100644
--- a/src/apps/rednatco/index.tsx
+++ b/src/apps/rednatco/index.tsx
@@ -31,21 +31,20 @@ const ConformersByClass = {
};
type ConformersByClass = typeof ConformersByClass;
-type ToolBarItems = 'structure'|'ntc'|'colors'|'density-maps';
+type ToolBarItems = 'structure' | 'ntc' | 'colors' | 'density-maps';
const ViewerToolBar = ToolBar.Specialize<ToolBarItems>();
const DefaultChainColor = Color(0xD9D9D9);
const DefaultDensityMapAlpha = 0.25;
const DefaultWaterColor = Color(0x0BB2FF);
-export type VisualRepresentations = 'ball-and-stick'|'cartoon';
-export type DensityMapRepresentation = 'wireframe'|'solid';
-export type DensityMapKind = '2fo-fc'|'fo-fc'|'em';
+export type VisualRepresentations = 'ball-and-stick' | 'cartoon' | 'ntc-tube';
+export type DensityMapRepresentation = 'wireframe' | 'solid';
export const DefaultDensityDifferencePositiveColor = Color(0x00C300);
export const DefaultDensityDifferenceNegativeColor = Color(0xC30000);
export const DefaultDensityMapColor = Color(0x009DFF);
const DefaultDensityMapDisplay = {
- kind: '2fo-fc' as DensityMapKind,
+ kind: '2fo-fc' as Api.DensityMapKind,
representations: [] as DensityMapRepresentation[],
isoValue: 0,
@@ -56,18 +55,17 @@ export type DensityMapDisplay = typeof DefaultDensityMapDisplay;
const Display = {
structures: {
- representation: 'cartoon' as VisualRepresentations,
-
+ nucleicRepresentation: 'cartoon' as VisualRepresentations,
showNucleic: true,
+
+ proteinRepresentation: 'cartoon' as Omit<VisualRepresentations, 'ntc-tube'>,
showProtein: false,
+
showWater: false,
showPyramids: true,
pyramidsTransparent: false,
- showBalls: false,
- ballsTransparent: false,
-
modelNumber: 1,
classColors: { ...NtCColors.Classes },
@@ -79,12 +77,6 @@ const Display = {
};
export type Display = typeof Display;
-function capitalize(s: string) {
- if (s.length === 0)
- return s;
- return s[0].toLocaleUpperCase() + s.slice(1);
-}
-
interface State {
display: Display;
showControls: boolean;
@@ -92,8 +84,8 @@ interface State {
export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
private currentFilter: Filters.All = Filters.Empty();
private presentConformers: string[] = [];
- private viewer: ReDNATCOMspViewer|undefined = undefined;
- private selectedStep: Api.Payloads.StepSelection|undefined = undefined;
+ private viewer: ReDNATCOMspViewer | undefined = undefined;
+ private selectedStep: Api.Payloads.StepSelection | undefined = undefined;
constructor(props: ReDNATCOMsp.Props) {
super(props);
@@ -111,6 +103,17 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
return updated;
}
+ private finalizeNtCColorUpdate(display: Display) {
+ this.viewer!.changeNtCColors(display).then(() => {
+ if (display.structures.showNucleic && display.structures.nucleicRepresentation === 'ntc-tube') {
+ this.viewer!.changeChainColor(['nucleic'], display).then(() => {
+ this.setState({ ...this.state, display });
+ });
+ } else
+ this.setState({ ...this.state, display });
+ });
+ }
+
private updateChainColor(color: number) {
const display: Display = {
...this.state.display,
@@ -120,11 +123,11 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
},
};
- this.viewer!.changeChainColor(display);
+ this.viewer!.changeChainColor(['nucleic', 'protein'], display);
this.setState({ ...this.state, display });
}
- private updateClassColor(changes: { cls: keyof NtCColors.Classes, color: number }|{ cls: keyof NtCColors.Classes, color: number }[]) {
+ private updateClassColor(changes: { cls: keyof NtCColors.Classes, color: number } | { cls: keyof NtCColors.Classes, color: number }[]) {
const classColors = { ...this.state.display.structures.classColors };
const isArray = Array.isArray(changes);
@@ -144,11 +147,10 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
display.structures.classColors = classColors;
display.structures.conformerColors = conformerColors;
- this.viewer!.changeNtCColors(display);
- this.setState({ ...this.state, display });
+ this.finalizeNtCColorUpdate(display);
}
- private updateConformerColor(changes: { conformer: keyof NtCColors.Conformers, color: number }|{ conformer: keyof NtCColors.Conformers, color: number }[]) {
+ private updateConformerColor(changes: { conformer: keyof NtCColors.Conformers, color: number } | { conformer: keyof NtCColors.Conformers, color: number }[]) {
const conformerColors = { ...this.state.display.structures.conformerColors };
if (Array.isArray(changes))
changes.forEach(item => conformerColors[item.conformer] = Color(item.color));
@@ -158,8 +160,7 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
const display = { ...this.state.display };
display.structures.conformerColors = conformerColors;
- this.viewer!.changeNtCColors(display);
- this.setState({ ...this.state, display });
+ this.finalizeNtCColorUpdate(display);
}
private updateWaterColor(color: number) {
@@ -191,6 +192,10 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
if (!this.viewer)
return;
+ for (const p in cmd) {
+ console.log(`${p}: ${cmd[p as keyof typeof cmd]}`);
+ }
+
if (cmd.type === 'redraw')
window.dispatchEvent(new Event('resize'));
else if (cmd.type === 'deselect-step') {
@@ -233,7 +238,7 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
}
}
- loadStructure(coords: { data: string, type: 'pdb'|'cif' }, densityMaps: { data: Uint8Array, type: 'ccp4'|'dsn6', kind: '2fo-fc'|'fo-fc'|'em' }[]|null) {
+ loadStructure(coords: { data: string, type: Api.CoordinatesFormat }, densityMaps: { data: Uint8Array, type: Api.DensityMapFormat, kind: Api.DensityMapKind }[] | null) {
if (this.viewer) {
const display = { ...this.state.display };
if (densityMaps) {
@@ -306,38 +311,80 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
icon: './imgs/nucleic.svg',
content:
<ToolBarContent style={{ width: '10em' }}>
+ <div className='rmsp-control-line'>
+ <div className='rmsp-control-item'>
+ <ToggleButton
+ text='Nucleic'
+ enabled={hasNucleic}
+ switchedOn={this.state.display.structures.showNucleic}
+ onClicked={() => {
+ const display = { ...this.state.display };
+ display.structures.showNucleic = !display.structures.showNucleic,
+ this.viewer!.toggleSubstructure('nucleic', display).then(() => {
+ this.setState({ ...this.state, display });
+ });
+ }}
+ />
+ </div>
+ </div>
<div className='rmsp-control-line'>
<div className='rmsp-control-item'>
<PushButton
- text={capitalize(this.state.display.structures.representation)}
- enabled={ready}
+ text='Cartoon'
+ enabled={ready && this.state.display.structures.showNucleic}
onClicked={() => {
const display = { ...this.state.display };
- display.structures.representation = display.structures.representation === 'cartoon' ? 'ball-and-stick' : 'cartoon';
- this.viewer!.changeRepresentation(display);
- this.setState({ ...this.state, display });
+ if (display.structures.nucleicRepresentation !== 'cartoon') {
+ display.structures.nucleicRepresentation = 'cartoon';
+ this.viewer!.changeRepresentation('nucleic', display).then(() => {
+ this.setState({ ...this.state, display });
+ });
+ }
}}
/>
</div>
</div>
-
- <div className='rmsp-control-vertical-spacer' />
-
<div className='rmsp-control-line'>
<div className='rmsp-control-item'>
- <ToggleButton
- text='Nucleic'
- enabled={hasNucleic}
- switchedOn={this.state.display.structures.showNucleic}
+ <PushButton
+ text='Ball-and-stick'
+ enabled={ready && this.state.display.structures.showNucleic}
onClicked={() => {
const display = { ...this.state.display };
- display.structures.showNucleic = !display.structures.showNucleic,
- this.viewer!.toggleSubstructure('nucleic', display);
- this.setState({ ...this.state, display });
+ if (display.structures.nucleicRepresentation !== 'ball-and-stick') {
+ display.structures.nucleicRepresentation = 'ball-and-stick';
+ this.viewer!.changeRepresentation('nucleic', display).then(() => {
+ this.setState({ ...this.state, display });
+ });
+ }
+ }}
+ />
+ </div>
+ </div>
+ <div className='rmsp-control-line'>
+ <div className='rmsp-control-item'>
+ <PushButton
+ text='NtC tube'
+ enabled={ready && this.state.display.structures.showNucleic}
+ onClicked={() => {
+ const display = { ...this.state.display };
+ if (display.structures.nucleicRepresentation !== 'ntc-tube') {
+ display.structures.nucleicRepresentation = 'ntc-tube';
+ this.viewer!.changeRepresentation('nucleic', display).then(() => {
+ display.structures.showPyramids = false;
+
+ this.viewer!.changePyramids(display).then(() => {
+ this.setState({ ...this.state, display });
+ });
+ });
+ }
}}
/>
</div>
</div>
+
+ <div className='rmsp-control-vertical-spacer' />
+
<div className='rmsp-control-line'>
<div className='rmsp-control-item'>
<ToggleButton
@@ -347,12 +394,50 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
onClicked={() => {
const display = { ...this.state.display };
display.structures.showProtein = !display.structures.showProtein,
- this.viewer!.toggleSubstructure('protein', display);
- this.setState({ ...this.state, display });
+ this.viewer!.toggleSubstructure('protein', display).then(() => {
+ this.setState({ ...this.state, display });
+ });
}}
/>
</div>
</div>
+ <div className='rmsp-control-line'>
+ <div className='rmsp-control-item'>
+ <PushButton
+ text='Cartoon'
+ enabled={ready && this.state.display.structures.showProtein}
+ onClicked={() => {
+ const display = { ...this.state.display };
+ if (display.structures.proteinRepresentation !== 'cartoon') {
+ display.structures.proteinRepresentation = 'cartoon';
+ this.viewer!.changeRepresentation('protein', display).then(() => {
+ this.setState({ ...this.state, display });
+ });
+ }
+ }}
+ />
+ </div>
+ </div>
+ <div className='rmsp-control-line'>
+ <div className='rmsp-control-item'>
+ <PushButton
+ text='Ball-and-stick'
+ enabled={ready && this.state.display.structures.showProtein}
+ onClicked={() => {
+ const display = { ...this.state.display };
+ if (display.structures.proteinRepresentation !== 'ball-and-stick') {
+ display.structures.proteinRepresentation = 'ball-and-stick';
+ this.viewer!.changeRepresentation('protein', display).then(() => {
+ this.setState({ ...this.state, display });
+ });
+ }
+ }}
+ />
+ </div>
+ </div>
+
+ <div className='rmsp-control-vertical-spacer' />
+
<div className='rmsp-control-line'>
<div className='rmsp-control-item'>
<ToggleButton
@@ -362,8 +447,9 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
onClicked={() => {
const display = { ...this.state.display };
display.structures.showWater = !this.state.display.structures.showWater;
- this.viewer!.toggleSubstructure('water', display);
- this.setState({ ...this.state, display });
+ this.viewer!.toggleSubstructure('water', display).then(() => {
+ this.setState({ ...this.state, display });
+ });
}}
/>
</div>
@@ -387,8 +473,9 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
onClicked={() => {
const display = { ...this.state.display };
display.structures.showPyramids = !display.structures.showPyramids;
- this.viewer!.changePyramids(display);
- this.setState({ ...this.state, display });
+ this.viewer!.changePyramids(display).then(() => {
+ this.setState({ ...this.state, display });
+ });
}}
/>
</div>
@@ -401,39 +488,9 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
onClicked={() => {
const display = { ...this.state.display };
display.structures.pyramidsTransparent = !display.structures.pyramidsTransparent;
- this.viewer!.changePyramids(display);
- this.setState({ ...this.state, display });
- }}
- />
- </div>
- </div>
-
- <div className='rmsp-control-vertical-spacer' />
-
- <div className='rmsp-control-vertical-section-caption'>
- Balls
- </div>
- <div className='rmsp-control-line'>
- <div className='rmsp-control-item'>
- <ToggleButton
- text='Balls'
- enabled={false}
- switchedOn={false}
- onClicked={() => {}}
- />
- </div>
- </div>
- <div className='rmsp-control-line'>
- <div className='rmsp-control-item'>
- <PushButton
- text={this.state.display.structures.ballsTransparent ? 'Transp.' : 'Solid'}
- enabled={this.state.display.structures.showBalls}
- onClicked={() => {
- const display = { ...this.state.display };
- display.structures.showBalls = !display.structures.showBalls;
-
- /* No balls today... */
- this.setState({ ...this.state, display });
+ this.viewer!.changePyramids(display).then(() => {
+ this.setState({ ...this.state, display });
+ });
}}
/>
</div>
diff --git a/src/apps/rednatco/traverse.ts b/src/apps/rednatco/traverse.ts
index 547a81d758deed809eba5d53e4d5b2f27c99e7c5..ec907d85a62ff88df8216b3e3392ee898c9bc6fa 100644
--- a/src/apps/rednatco/traverse.ts
+++ b/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')
diff --git a/src/apps/rednatco/viewer.ts b/src/apps/rednatco/viewer.ts
index 5bc5ced8cd728d63c2020905f3da23b493be08e2..2e3ea7b4be0175a777f44d729ddd3562e4721489 100644
--- a/src/apps/rednatco/viewer.ts
+++ b/src/apps/rednatco/viewer.ts
@@ -11,12 +11,14 @@ import { Superpose } from './superpose';
import { Traverse } from './traverse';
import { isoBounds, prettyIso } from './util';
import { DnatcoNtCs } from '../../extensions/dnatco';
+import { DnatcoTypes } from '../../extensions/dnatco/types';
+import { NtCTubeTypes } from '../../extensions/dnatco/ntc-tube/types';
import { ConfalPyramidsParams } from '../../extensions/dnatco/confal-pyramids/representation';
import { OrderedSet } from '../../mol-data/int/ordered-set';
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 { ElementIndex, Model, Structure, 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';
@@ -35,6 +37,9 @@ import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
import { Representation } from '../../mol-repr/representation';
import { StateObjectCell, StateObject, StateTransformer } from '../../mol-state';
import { StateBuilder } from '../../mol-state/state/builder';
+import { Script } from '../../mol-script/script';
+import { MolScriptBuilder as MSB } from '../../mol-script/language/builder';
+import { formatMolScript } from '../../mol-script/language/expression-formatter';
import { lociLabel } from '../../mol-theme/label';
import { arrayMax } from '../../mol-util/array';
import { Binding } from '../../mol-util/binding';
@@ -57,6 +62,31 @@ const NtCSupSel = 'ntc-sup-sel';
const NtCSupNext = 'ntc-sup-next';
const SphereBoundaryHelper = new BoundaryHelper('98');
+function ntcStepToElementLoci(step: DnatcoTypes.Step, stru: Structure) {
+ let expr = MSB.core.rel.eq([MSB.struct.atomProperty.macromolecular.auth_asym_id(), step.auth_asym_id_1]);
+ expr = MSB.core.logic.and([
+ MSB.core.rel.eq([MSB.struct.atomProperty.macromolecular.auth_seq_id(), step.auth_seq_id_1]),
+ expr
+ ]);
+ expr = MSB.core.logic.and([
+ MSB.core.rel.eq([MSB.struct.atomProperty.macromolecular.label_alt_id(), step.label_alt_id_1]),
+ expr
+ ]);
+ expr = MSB.struct.generator.atomGroups({ 'atom-test': expr, 'group-by': MSB.struct.atomProperty.macromolecular.label_asym_id() });
+
+ return Loci.normalize(
+ Script.toLoci(
+ Script(formatMolScript(expr), 'mol-script'),
+ stru
+ ),
+ 'two-residues'
+ );
+}
+
+function rcref(c: string, where: 'sel' | 'prev' | 'next' | '' = '') {
+ return `${RCRef}-${c}-${where}`;
+}
+
function superpositionAtomsIndices(loci: StructureElement.Loci) {
const es = loci.elements[0];
const loc = Location.create(loci.structure, es.unit, es.unit.elements[OrderedSet.getAt(es.indices, 0)]);
@@ -120,8 +150,16 @@ function superpositionAtomsIndices(loci: StructureElement.Loci) {
return indices;
}
-function rcref(c: string, where: 'sel' | 'prev' | 'next' | '' = '') {
- return `${RCRef}-${c}-${where}`;
+function visualForSubstructure(sub: IDs.Substructure, display: Display) {
+ if (sub === 'nucleic') {
+ return display.structures.nucleicRepresentation === 'ntc-tube'
+ ? SubstructureVisual.NtC('ntc-tube', display.structures.conformerColors)
+ : SubstructureVisual.BuiltIn(display.structures.nucleicRepresentation, Color(display.structures.chainColor));
+ } else if (sub === 'protein') {
+ return SubstructureVisual.BuiltIn(display.structures.proteinRepresentation, Color(display.structures.chainColor));
+ } else /* water */ {
+ return SubstructureVisual.BuiltIn('ball-and-stick', Color(display.structures.waterColor));
+ }
}
const ReDNATCOLociLabelProvider = PluginBehavior.create({
@@ -199,6 +237,9 @@ const ReDNATCOLociSelectionProvider = PluginBehavior.create({
this.ctx.managers.interactivity.lociSelects.deselectAll();
if (current.loci.kind === 'element-loci') {
this.params.onSelected(current);
+ } else if (current.loci.kind === 'data-loci') {
+ console.log(current.loci.tag, current.loci.data);
+ this.params.onSelected(current);
}
},
lociIsNotEmpty
@@ -233,6 +274,28 @@ const ReDNATCOLociSelectionProvider = PluginBehavior.create({
},
});
+export namespace SubstructureVisual {
+ export type BuiltIn = {
+ type: 'built-in',
+ repr: Omit<VisualRepresentations, 'ntc-tube'>,
+ color: Color
+ }
+ export function BuiltIn(repr: BuiltIn['repr'], color: BuiltIn['color']): BuiltIn {
+ return { type: 'built-in', repr, color };
+ }
+
+ export type NtC = {
+ type: 'ntc',
+ repr: 'ntc-tube',
+ colors: NtCColors.Conformers
+ }
+ export function NtC(repr: NtC['repr'], colors: NtC['colors']): NtC {
+ return { type: 'ntc', repr, colors };
+ }
+
+ export type Types = BuiltIn | NtC;
+}
+
export class ReDNATCOMspViewer {
private haveMultipleModels = false;
private steps: Step.ExtendedDescription[] = [];
@@ -374,29 +437,50 @@ export class ReDNATCOMspViewer {
return this.steps[idx];
}
- private substructureVisuals(representation: 'ball-and-stick' | 'cartoon', color: Color) {
- switch (representation) {
- case 'cartoon':
- return {
- type: {
- name: 'cartoon',
- params: { sizeFactor: 0.2, sizeAspectRatio: 0.35, aromaticBonds: false },
- },
- colorTheme: { name: 'uniform', params: { value: color } }
- };
- case 'ball-and-stick':
- return {
- type: {
- name: 'ball-and-stick',
- params: {
- sizeFactor: 0.2,
- sizeAspectRatio: 0.35,
- excludeTypes: ['hydrogen-bond', 'aromatic'],
- aromaticBonds: false,
+ private substructureVisuals(visual: SubstructureVisual.Types) {
+ if (visual.type === 'built-in') {
+ switch (visual.repr) {
+ case 'cartoon':
+ return {
+ type: {
+ name: 'cartoon',
+ params: { sizeFactor: 0.2, sizeAspectRatio: 0.35, aromaticBonds: false },
},
- },
- colorTheme: { name: 'element-symbol', params: { carbonColor: { name: 'custom', params: color } } },
- };
+ colorTheme: { name: 'uniform', params: { value: visual.color } }
+ };
+ case 'ball-and-stick':
+ return {
+ type: {
+ name: 'ball-and-stick',
+ params: {
+ sizeFactor: 0.2,
+ sizeAspectRatio: 0.35,
+ excludeTypes: ['hydrogen-bond', 'aromatic'],
+ aromaticBonds: false,
+ },
+ },
+ colorTheme: { name: 'element-symbol', params: { carbonColor: { name: 'custom', params: visual.color } } },
+ };
+ }
+ } else if (visual.type === 'ntc') {
+ switch (visual.repr) {
+ case 'ntc-tube':
+ return {
+ type: {
+ name: 'ntc-tube',
+ params: {},
+ },
+ colorTheme: {
+ name: 'ntc-tube',
+ params: {
+ colors: {
+ name: 'custom',
+ params: visual.colors,
+ },
+ },
+ },
+ };
+ }
}
}
@@ -410,13 +494,13 @@ export class ReDNATCOMspViewer {
);
}
- private async toggleNucleicSubstructure(show: boolean, repr: VisualRepresentations, color: Color) {
+ private async toggleNucleicSubstructure(show: boolean, visual: SubstructureVisual.Types) {
if (this.has('structure', 'remainder-slice', BaseRef)) {
const b = this.getBuilder('structure', 'remainder-slice');
if (show) {
b.apply(
StateTransforms.Representation.StructureRepresentation3D,
- this.substructureVisuals(repr, color),
+ this.substructureVisuals(visual),
{ ref: IDs.ID('visual', 'remainder-slice', BaseRef) }
);
} else
@@ -429,7 +513,7 @@ export class ReDNATCOMspViewer {
if (show) {
b.apply(
StateTransforms.Representation.StructureRepresentation3D,
- this.substructureVisuals(repr, color),
+ this.substructureVisuals(visual),
{ ref: IDs.ID('visual', 'nucleic', BaseRef) }
);
} else
@@ -515,18 +599,21 @@ export class ReDNATCOMspViewer {
return new ReDNATCOMspViewer(plugin, interactCtx, app);
}
- async changeChainColor(display: Display) {
+ async changeChainColor(subs: IDs.Substructure[], display: Display) {
+ const b = this.plugin.state.data.build();
+
const color = Color(display.structures.chainColor);
- const b = this.plugin.state.data.build();
- for (const sub of ['nucleic', 'protein'] as IDs.Substructure[]) {
+ for (const sub of subs) {
+ const vis = visualForSubstructure(sub, display);
+
if (this.has('visual', sub)) {
b.to(IDs.ID('visual', sub, BaseRef))
.update(
StateTransforms.Representation.StructureRepresentation3D,
old => ({
...old,
- ...this.substructureVisuals(display.structures.representation, color),
+ ...this.substructureVisuals(vis),
})
);
}
@@ -538,17 +625,20 @@ export class ReDNATCOMspViewer {
StateTransforms.Representation.StructureRepresentation3D,
old => ({
...old,
- ...this.substructureVisuals('ball-and-stick', color),
+ ...this.substructureVisuals(SubstructureVisual.BuiltIn('ball-and-stick', color)),
})
);
}
+
if (this.has('visual', 'remainder-slice', BaseRef)) {
+ const vis = visualForSubstructure('nucleic', display);
+
b.to(IDs.ID('visual', 'remainder-slice', BaseRef))
.update(
StateTransforms.Representation.StructureRepresentation3D,
old => ({
...old,
- ...this.substructureVisuals(display.structures.representation, color),
+ ...this.substructureVisuals(vis),
})
);
}
@@ -625,35 +715,34 @@ export class ReDNATCOMspViewer {
}
}
- async changeRepresentation(display: Display) {
+ async changeRepresentation(sub: IDs.Substructure, display: Display) {
const b = this.plugin.state.data.build();
- const repr = display.structures.representation;
- const color = Color(display.structures.chainColor);
+ const vis = visualForSubstructure(sub, display);
- for (const sub of ['nucleic', 'protein'] as IDs.Substructure[]) {
- if (this.has('visual', sub)) {
- b.to(IDs.ID('visual', sub, BaseRef))
+ if (this.has('visual', sub)) {
+ b.to(IDs.ID('visual', sub, BaseRef))
+ .update(
+ StateTransforms.Representation.StructureRepresentation3D,
+ old => ({
+ ...old,
+ ...this.substructureVisuals(vis),
+ })
+ );
+ }
+
+ if (sub === 'nucleic') {
+ if (this.has('visual', 'remainder-slice', BaseRef)) {
+ b.to(IDs.ID('visual', 'remainder-slice', BaseRef))
.update(
StateTransforms.Representation.StructureRepresentation3D,
old => ({
...old,
- ...this.substructureVisuals(repr, color),
+ ...this.substructureVisuals(vis),
})
);
}
}
- if (this.has('visual', 'remainder-slice', BaseRef)) {
- b.to(IDs.ID('visual', 'remainder-slice', BaseRef))
- .update(
- StateTransforms.Representation.StructureRepresentation3D,
- old => ({
- ...old,
- ...this.substructureVisuals(repr, color),
- })
- );
- }
-
await b.commit();
}
@@ -878,8 +967,8 @@ export class ReDNATCOMspViewer {
}
async loadStructure(
- coords: { data: string, type: 'pdb' | 'cif' },
- densityMaps: { data: Uint8Array, type: 'ccp4' | 'dsn6', kind: '2fo-fc' | 'fo-fc' | 'em' }[] | null,
+ coords: { data: string, type: Api.CoordinatesFormat },
+ densityMaps: { data: Uint8Array, type: Api.DensityMapFormat, kind: Api.DensityMapKind }[] | null,
display: Display
) {
// TODO: Remove the currently loaded structure
@@ -936,7 +1025,7 @@ export class ReDNATCOMspViewer {
b3.to(IDs.ID('structure', 'nucleic', BaseRef))
.apply(
StateTransforms.Representation.StructureRepresentation3D,
- this.substructureVisuals('cartoon', chainColor),
+ this.substructureVisuals(SubstructureVisual.BuiltIn('cartoon', chainColor)),
{ ref: IDs.ID('visual', 'nucleic', BaseRef) }
);
if (display.structures.showPyramids) {
@@ -952,7 +1041,7 @@ export class ReDNATCOMspViewer {
b3.to(IDs.ID('structure', 'protein', BaseRef))
.apply(
StateTransforms.Representation.StructureRepresentation3D,
- this.substructureVisuals('cartoon', chainColor),
+ this.substructureVisuals(SubstructureVisual.BuiltIn('cartoon', chainColor)),
{ ref: IDs.ID('visual', 'protein', BaseRef) }
);
}
@@ -1060,10 +1149,30 @@ export class ReDNATCOMspViewer {
}
async onLociSelected(selected: Representation.Loci) {
- const loci = Loci.normalize(selected.loci, 'two-residues');
-
- if (loci.kind === 'element-loci') {
- const stepDesc = Step.describe(loci, this.haveMultipleModels);
+ const normalized = (() => {
+ if (selected.loci.kind === 'data-loci') {
+ if (selected.loci.tag === 'dnatco-tube-segment-data') {
+ const stru = this.plugin.state.data.cells.get(IDs.ID('entire-structure', 'nucleic', BaseRef));
+ if (stru) {
+ const tubeLoci = selected.loci as NtCTubeTypes.Loci;
+ const stepIdx = tubeLoci.elements[0] / 4; // There are 4 tube segments per step
+ const step = tubeLoci.data[stepIdx];
+ if (step)
+ return ntcStepToElementLoci(step, stru.obj!.data);
+ else
+ return EmptyLoci;
+ }
+ return EmptyLoci;
+ } else
+ return EmptyLoci;
+ } else if (selected.loci.kind === 'element-loci')
+ return Loci.normalize(selected.loci, 'two-residues');
+ else
+ return EmptyLoci;
+ })();
+
+ if (normalized.kind === 'element-loci') {
+ const stepDesc = Step.describe(normalized, this.haveMultipleModels);
if (stepDesc && this.stepNames.has(stepDesc.name))
this.notifyStepSelected(stepDesc.name);
}
@@ -1118,8 +1227,6 @@ export class ReDNATCOMspViewer {
.commit();
await this.toggleSubstructure('nucleic', display);
-
- this.resetCameraRadius();
}
async actionSelectStep(stepSel: Api.Payloads.StepSelection, prevSel: Api.Payloads.StepSelection | undefined, nextSel: Api.Payloads.StepSelection | undefined, display: Display) {
@@ -1172,7 +1279,7 @@ export class ReDNATCOMspViewer {
)
.apply(
StateTransforms.Representation.StructureRepresentation3D,
- this.substructureVisuals('ball-and-stick', chainColor),
+ this.substructureVisuals(SubstructureVisual.BuiltIn('ball-and-stick', chainColor)),
{ ref: IDs.ID('visual', 'selected-slice', BaseRef) }
)
.to(entireStruCell)
@@ -1184,10 +1291,14 @@ export class ReDNATCOMspViewer {
// Only show the remainder if the nucleic substructure is shown
if (display.structures.showNucleic) {
+ const vis = display.structures.nucleicRepresentation === 'ntc-tube'
+ ? SubstructureVisual.NtC('ntc-tube', display.structures.conformerColors)
+ : SubstructureVisual.BuiltIn(display.structures.nucleicRepresentation, Color(display.structures.chainColor));
+
b.to(IDs.ID('structure', 'remainder-slice', BaseRef))
.apply(
StateTransforms.Representation.StructureRepresentation3D,
- this.substructureVisuals(display.structures.representation, chainColor),
+ this.substructureVisuals(vis),
{ ref: IDs.ID('visual', 'remainder-slice', BaseRef) }
)
.delete(IDs.ID('visual', 'nucleic', BaseRef));
@@ -1284,27 +1395,43 @@ export class ReDNATCOMspViewer {
}
async toggleSubstructure(sub: IDs.Substructure, display: Display) {
- const show = sub === 'nucleic' ? !!display.structures.showNucleic :
- sub === 'protein' ? !!display.structures.showProtein : !!display.structures.showWater;
- const repr = display.structures.representation;
-
- if (sub === 'nucleic')
- this.toggleNucleicSubstructure(show, repr, Color(display.structures.chainColor));
- else {
- if (show) {
+ if (sub === 'nucleic') {
+ const show = display.structures.showNucleic;
+ const vis = display.structures.nucleicRepresentation === 'ntc-tube'
+ ? SubstructureVisual.NtC('ntc-tube', display.structures.conformerColors)
+ : SubstructureVisual.BuiltIn(display.structures.nucleicRepresentation, Color(display.structures.chainColor));
+
+ await this.toggleNucleicSubstructure(show, vis);
+ this.resetCameraRadius();
+ } else if (sub === 'protein') {
+ if (!display.structures.showProtein) {
+ await PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.data, ref: IDs.ID('visual', sub, BaseRef) });
+ this.resetCameraRadius();
+ } else {
const b = this.getBuilder('structure', sub);
- const visuals = sub === 'water' ? this.waterVisuals(Color(display.structures.waterColor)) : this.substructureVisuals(repr, Color(display.structures.chainColor));
if (b) {
b.apply(
StateTransforms.Representation.StructureRepresentation3D,
- visuals,
+ this.substructureVisuals(SubstructureVisual.BuiltIn(display.structures.proteinRepresentation, display.structures.chainColor)),
{ ref: IDs.ID('visual', sub, BaseRef) }
);
await b.commit();
}
- } else {
+ }
+ } else if (sub === 'water') {
+ if (!display.structures.showWater) {
await PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.data, ref: IDs.ID('visual', sub, BaseRef) });
this.resetCameraRadius();
+ } else {
+ const b = this.getBuilder('structure', sub);
+ if (b) {
+ b.apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ this.waterVisuals(display.structures.waterColor),
+ { ref: IDs.ID('visual', sub, BaseRef) }
+ );
+ await b.commit();
+ }
}
}
}
diff --git a/src/extensions/dnatco/behavior.ts b/src/extensions/dnatco/behavior.ts
index bbe33f8e9c5c8d700a08926962303d2bc5a7e620..e47d71450aada4f584808877e9a1b25c8d3f43db 100644
--- a/src/extensions/dnatco/behavior.ts
+++ b/src/extensions/dnatco/behavior.ts
@@ -56,4 +56,3 @@ export const DnatcoNtCs = PluginBehavior.create<{ autoAttach: boolean, showToolT
showToolTip: PD.Boolean(true)
})
});
-