diff --git a/src/apps/rednatco/api-impl.ts b/src/apps/rednatco/api-impl.ts
new file mode 100644
index 0000000000000000000000000000000000000000..beb2689f220c9a7725a1c92fca3f677771d40070
--- /dev/null
+++ b/src/apps/rednatco/api-impl.ts
@@ -0,0 +1,46 @@
+import { ReDNATCOMsp } from './index';
+import { ReDNATCOMspApi } from './api';
+
+export class ReDNATCOMspApiImpl implements ReDNATCOMspApi.Object {
+ private target: ReDNATCOMsp|undefined = undefined;
+ private onEvent: ((evt: ReDNATCOMspApi.Event) => void)|undefined;
+
+ private check() {
+ if (!this.target)
+ throw new Error('ReDNATCOMsp object not bound');
+ }
+
+ _bind(target: ReDNATCOMsp) {
+ this.target = target;
+ }
+
+ command(cmd: ReDNATCOMspApi.Command) {
+ this.check();
+ this.target!.command(cmd);
+ }
+
+ event(evt: ReDNATCOMspApi.Event) {
+ if (this.onEvent)
+ this.onEvent(evt);
+ }
+
+ init(elemId: string, onEvent?: (evt: ReDNATCOMspApi.Event) => void, onInited?: () => void) {
+ this.onEvent = onEvent;
+ ReDNATCOMsp.init(elemId, onInited);
+ return this;
+ }
+
+ isReady(): boolean {
+ return !!this.target;
+ }
+
+ loadStructure(data: string, type: 'cif'|'pdb') {
+ this.check();
+ this.target!.loadStructure(data, type);
+ }
+
+ query(type: ReDNATCOMspApi.Queries.Type): ReDNATCOMspApi.Response {
+ this.check();
+ return this.target!.apiQuery(type);
+ }
+}
diff --git a/src/apps/rednatco/api.ts b/src/apps/rednatco/api.ts
new file mode 100644
index 0000000000000000000000000000000000000000..b6267aef5fb30478a54696c9ad833f627bf1dd8e
--- /dev/null
+++ b/src/apps/rednatco/api.ts
@@ -0,0 +1,86 @@
+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 DeselectStep = { type: 'deselect-step' }
+ export function DeselectStep() {
+ return { type: 'deselect-step' };
+ }
+
+ export type SelectStep = {
+ type: 'select-step';
+ stepName: string;
+ prevStepName: string|undefined;
+ nextStepName: string|undefined;
+ referenceNtC: string;
+ references: ('sel'|'prev'|'next')[];
+ }
+ export function SelectStep(stepName: string, prevStepName: string|undefined, nextStepName: string|undefined, referenceNtC = '', references = ['sel', 'prev', 'next']): SelectStep {
+ return {
+ type: 'select-step',
+ stepName,
+ prevStepName,
+ nextStepName,
+ referenceNtC,
+ references: references as ('sel'|'prev'|'next')[],
+ };
+ }
+
+ export type SwitchModel = { type: 'switch-model', model: number };
+ export function SwitchModel(model: number): SwitchModel { return { type: 'switch-model', model }; }
+ }
+ export type Command =
+ Commands.DeselectStep |
+ Commands.Redraw |
+ Commands.SelectStep |
+ Commands.SwitchModel;
+
+ export namespace Events {
+ export type Type = 'step-deselected'|'step-requested'|'step-selected';
+
+ export type StepDeselected = { type: 'step-deselected' }
+ export function StepDeselected(): StepDeselected {
+ return { type: 'step-deselected' };
+ }
+
+ export type StepRequested = { type: 'step-requested', name: string }
+ export function StepRequested(name: string): StepRequested {
+ return { type: 'step-requested', name };
+ }
+
+ export type StepSelected = { type: 'step-selected', success: boolean, name: string, rmsd?: number }
+ export function StepSelectedOk(name: string, rmsd?: number): StepSelected {
+ return { type: 'step-selected', success: true, name, rmsd };
+ }
+ export function StepSelectedFail(): StepSelected {
+ return { type: 'step-selected', success: false, name: '' };
+ }
+
+ }
+ export type Event =
+ Events.StepDeselected |
+ Events.StepRequested |
+ Events.StepSelected;
+
+ export namespace Queries {
+ export type Type = 'selected-step';
+
+ export type SelectedStep = { type: 'selected-step', name: string, rmsd?: number }
+ export function SelectedStep(name: string, rmsd?: number): SelectedStep {
+ return { type: 'selected-step', name, rmsd };
+ }
+ }
+ export type Response = Queries.SelectedStep;
+
+ export interface Object {
+ command: (cmd: Command) => void;
+ event: (evt: Event) => void;
+ init: (elemId: string, onEvent?: (evt: Event) => void, onInited?: () => void) => void;
+ isReady: () => boolean;
+ loadStructure: (data: string, type: 'cif'|'pdb') => void;
+ query: (type: Queries.Type) => Response;
+ }
+}
diff --git a/src/apps/rednatco/commands.ts b/src/apps/rednatco/commands.ts
deleted file mode 100644
index 7c48b0ce6e93e562e3d569ee03d241ef6ef19b19..0000000000000000000000000000000000000000
--- a/src/apps/rednatco/commands.ts
+++ /dev/null
@@ -1,30 +0,0 @@
-export namespace Commands {
- export type Type = 'redraw'|'select-step'|'switch-model';
-
- export type Redraw = { type: 'redraw' }
- export function Redraw(): Redraw { return { type: 'redraw' }; }
-
- export type SelectStep = {
- type: 'select-step';
- stepName: string;
- prevStepName: string|null;
- nextStepName: string|null;
- referenceNtC: string;
- references: ('sel'|'prev'|'next')[];
- }
- export function SelectStep(stepName: string, prevStepName: string|null, nextStepName: string|null, referenceNtC = '', references = ['sel', 'prev', 'next']): SelectStep {
- return {
- type: 'select-step',
- stepName,
- prevStepName,
- nextStepName,
- referenceNtC,
- references: references as ('sel'|'prev'|'next')[],
- };
- }
-
- export type SwitchModel = { type: 'switch-model', model: number };
- export function SwitchModel(model: number): SwitchModel { return { type: 'switch-model', model }; }
-
- export type Cmd = Redraw|SelectStep|SwitchModel;
-}
diff --git a/src/apps/rednatco/idents.ts b/src/apps/rednatco/idents.ts
index 6340bfb810f5e653945aa62adcb740a38c659155..c1f27f8b6aa902826e83fa4e711bda8f70d5e453 100644
--- a/src/apps/rednatco/idents.ts
+++ b/src/apps/rednatco/idents.ts
@@ -1,5 +1,5 @@
export type ID ='data'|'trajectory'|'model'|'structure'|'visual'|'pyramids'|'superposition';
-export type Substructure = 'nucleic'|'protein'|'water';
+export type Substructure = 'nucleic'|'protein'|'water'|'selected-slice'|'remainder-slice';
export function ID(id: ID, sub: Substructure|'', ref: string) {
if (sub === '')
diff --git a/src/apps/rednatco/index.tsx b/src/apps/rednatco/index.tsx
index 20925066fa183c433dfb20648e0ca8fdbc9a6c16..c37fcbd2ad4c6f38a695fb2b7361c62c035d6e65 100644
--- a/src/apps/rednatco/index.tsx
+++ b/src/apps/rednatco/index.tsx
@@ -1,62 +1,14 @@
import React from 'react';
import ReactDOM from 'react-dom';
+import { ReDNATCOMspApi as Api } from './api';
+import { ReDNATCOMspApiImpl } from './api-impl';
+import { ReDNATCOMspViewer } from './viewer';
import { NtCColors } from './colors';
import { ColorPicker } from './color-picker';
-import { Commands } from './commands';
import { CollapsibleVertical, PushButton, ToggleButton } from './controls';
-import * as IDs from './idents';
-import * as RefCfmr from './reference-conformers';
-import { ReferenceConformersPdbs } from './reference-conformers-pdbs';
-import { Step } from './step';
-import { Superpose } from './superpose';
-import { Traverse } from './traverse';
import { luminance } from './util';
-import { DnatcoConfalPyramids } from '../../extensions/dnatco';
-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, Structure, StructureElement, StructureProperties, StructureSelection, Trajectory } from '../../mol-model/structure';
-import { Location } from '../../mol-model/structure/structure/element/location';
-import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
-import { PluginBehavior, PluginBehaviors } from '../../mol-plugin/behavior';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginSpec } from '../../mol-plugin/spec';
-import { LociLabel } from '../../mol-plugin-state/manager/loci-label';
-import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
-import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { RawData } from '../../mol-plugin-state/transforms/data';
-import { createPluginUI } from '../../mol-plugin-ui';
-import { PluginUIContext } from '../../mol-plugin-ui/context';
-import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
-import { Representation } from '../../mol-repr/representation';
-import { StateObjectCell, StateObject, StateSelection } from '../../mol-state';
-import { StateTreeSpine } from '../../mol-state/tree/spine';
-import { lociLabel } from '../../mol-theme/label';
import { Color } from '../../mol-util/color';
-import { arrayMax } from '../../mol-util/array';
-import { Binding } from '../../mol-util/binding';
-import { ButtonsType, ModifiersKeys } from '../../mol-util/input/input-observer';
-import { MarkerAction } from '../../mol-util/marker-action';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { ObjectKeys } from '../../mol-util/type-helpers';
import './index.html';
-import './molstar.css';
-import './rednatco-molstar.css';
-
-const Extensions = {
- 'ntc-balls-pyramids-prop': PluginSpec.Behavior(DnatcoConfalPyramids),
-};
-
-const AnimationDurationMsec = 150;
-const BaseRef = 'rdo';
-const RCRef = 'rc';
-const NtCSupPrev = 'ntc-sup-prev';
-const NtCSupSel = 'ntc-sup-sel';
-const NtCSupNext = 'ntc-sup-next';
-const SphereBoundaryHelper = new BoundaryHelper('98');
const ConformersByClass = {
A: ['AA00_Upr', 'AA00_Lwr', 'AA02_Upr', 'AA02_Lwr', 'AA03_Upr', 'AA03_Lwr', 'AA04_Upr', 'AA04_Lwr', 'AA08_Upr', 'AA08_Lwr', 'AA09_Upr', 'AA09_Lwr', 'AA01_Upr', 'AA01_Lwr', 'AA05_Upr', 'AA05_Lwr', 'AA06_Upr', 'AA06_Lwr', 'AA10_Upr', 'AA10_Lwr', 'AA11_Upr', 'AA11_Lwr', 'AA07_Upr', 'AA07_Lwr', 'AA12_Upr', 'AA12_Lwr', 'AA13_Upr', 'AA13_Lwr', 'AB01_Upr', 'AB02_Upr', 'AB03_Upr', 'AB04_Upr', 'AB05_Upr', 'BA01_Lwr', 'BA05_Lwr', 'BA09_Lwr', 'BA08_Lwr', 'BA10_Lwr', 'BA13_Lwr', 'BA16_Lwr', 'BA17_Lwr', 'AAS1_Lwr', 'AB1S_Upr'],
@@ -71,22 +23,7 @@ const ConformersByClass = {
};
type ConformersByClass = typeof ConformersByClass;
-const DefaultChainColor = Color(0xD9D9D9);
-
-class ColorBox extends React.Component<{ caption: string, color: Color }> {
- render() {
- const lum = luminance(this.props.color);
- return (
- <div
- className='rmsp-color-box'
- style={{ backgroundColor: Color.toStyle(this.props.color) }}
- >
- <span style={{ color: lum > 0.6 ? 'black' : 'white' }}>{this.props.caption}</span>
- </div>
- );
- }
-}
-
+export type VisualRepresentations = 'ball-and-stick'|'cartoon';
const Display = {
representation: 'cartoon' as VisualRepresentations,
@@ -105,19 +42,7 @@ const Display = {
classColors: { ...NtCColors.Classes },
conformerColors: { ...NtCColors.Conformers },
};
-type Display = typeof Display;
-
-type StepInfo = {
- name: string;
- assignedNtC: string;
- closestNtC: string; // Fallback for cases where assignedNtC is NANT
- resNo1: number;
- resNo2: number;
- altId1?: string;
- altId2?: string;
-}
-
-type VisualRepresentations = 'ball-and-stick'|'cartoon';
+export type Display = typeof Display;
function capitalize(s: string) {
if (s.length === 0)
@@ -125,904 +50,17 @@ function capitalize(s: string) {
return s[0].toLocaleUpperCase() + s.slice(1);
}
-function dinucleotideBackbone(loci: StructureElement.Loci, altId1?: string, altId2?: string) {
- const es = loci.elements[0];
- const loc = Location.create(loci.structure, es.unit, es.unit.elements[OrderedSet.getAt(es.indices, 0)]);
- const len = OrderedSet.size(es.indices);
- const indices = new Array<ElementIndex>();
-
- const gather = (atoms: string[], start: number, end: number, altId?: string) => {
- for (const atom of atoms) {
- let idx = start;
- for (; idx < end; idx++) {
- loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
- const _atom = StructureProperties.atom.label_atom_id(loc);
- if (atom === _atom) {
- if (altId) {
- const _altId = StructureProperties.atom.label_alt_id(loc);
- if (_altId !== '' && _altId !== altId)
- continue;
- }
-
- indices.push(loc.element);
- break;
- }
- }
- if (idx === end) {
- console.error(`Cannot find backbone atom ${atom} in first residue of a step`);
- return false;
- }
- }
-
- return true;
- };
-
- // Find split between first and second residue
- const resNo1 = StructureProperties.residue.auth_seq_id(loc);
- let secondIdx = -1;
- for (let idx = 0; idx < len; idx++) {
- loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
- const resNo = StructureProperties.residue.auth_seq_id(loc);
- if (resNo !== resNo1) {
- secondIdx = idx;
- break;
- }
- }
- if (secondIdx === -1)
- return [];
-
- // Gather ElementIndices for backbone atoms of the first residue
- loc.element = es.unit.elements[OrderedSet.getAt(es.indices, 0)];
- const ring1 = RefCfmr.CompoundRings[StructureProperties.atom.label_comp_id(loc) as keyof RefCfmr.CompoundRings];
- if (!ring1)
- return [];
-
- const first = RefCfmr.BackboneAtoms.first.concat(RefCfmr.BackboneAtoms[ring1]);
- if (!gather(first, 0, secondIdx, altId1))
- return [];
-
- loc.element = es.unit.elements[OrderedSet.getAt(es.indices, secondIdx)];
- const ring2 = RefCfmr.CompoundRings[StructureProperties.atom.label_comp_id(loc) as keyof RefCfmr.CompoundRings];
- if (!ring2)
- return [];
-
- const second = RefCfmr.BackboneAtoms.second.concat(RefCfmr.BackboneAtoms[ring2]);
- if (!gather(second, secondIdx, len, altId2))
- return [];
-
- return indices;
-}
-
-function rcref(c: string, where: 'sel'|'prev'|'next'|'' = '') {
- return `${RCRef}-${c}-${where}`;
-}
-
-const ReDNATCOLociLabelProvider = PluginBehavior.create({
- name: 'watlas-loci-label-provider',
- category: 'interaction',
- ctor: class implements PluginBehavior<undefined> {
- private f = {
- label: (loci: Loci) => {
- switch (loci.kind) {
- case 'structure-loci':
- case 'element-loci':
- return lociLabel(loci);
- default:
- return '';
- }
- },
- group: (label: LociLabel) => label.toString().replace(/Model [0-9]+/g, 'Models'),
- priority: 100
- };
- register() { this.ctx.managers.lociLabels.addProvider(this.f); }
- unregister() { this.ctx.managers.lociLabels.removeProvider(this.f); }
- constructor(protected ctx: PluginContext) { }
- },
- display: { name: 'ReDNATCO labeling' }
-});
-
-const ReDNATCOLociSelectionBindings = {
- clickFocus: Binding([Binding.Trigger(ButtonsType.Flag.Secondary)], 'Focus camera on selected loci using ${triggers}'),
- clickSelectOnly: Binding([Binding.Trigger(ButtonsType.Flag.Primary)], 'Select the clicked element using ${triggers}.'),
- clickDeselectAllOnEmpty: Binding([Binding.Trigger(ButtonsType.Flag.Primary)], 'Deselect all when clicking on nothing using ${triggers}.'),
-};
-const ReDNATCOLociSelectionParams = {
- bindings: PD.Value(ReDNATCOLociSelectionBindings, { isHidden: true }),
- onDeselected: PD.Value(() => {}, { isHidden: true }),
- onSelected: PD.Value((loci: Representation.Loci) => {}, { isHidden: true }),
-};
-type ReDNATCOLociSelectionProps = PD.Values<typeof ReDNATCOLociSelectionParams>;
-
-const ReDNATCOLociSelectionProvider = PluginBehavior.create({
- name: 'rednatco-loci-selection-provider',
- category: 'interaction',
- display: { name: 'Interactive step selection' },
- params: () => ReDNATCOLociSelectionParams,
- ctor: class extends PluginBehavior.Handler<ReDNATCOLociSelectionProps> {
- private spine: StateTreeSpine.Impl;
- private lociMarkProvider = (reprLoci: Representation.Loci, action: MarkerAction) => {
- if (!this.ctx.canvas3d) return;
- this.ctx.canvas3d.mark({ loci: reprLoci.loci }, action);
- };
- private applySelectMark(ref: string, clear?: boolean) {
- const cell = this.ctx.state.data.cells.get(ref);
- if (cell && PSO.isRepresentation3D(cell.obj)) {
- this.spine.current = cell;
- const so = this.spine.getRootOfType(PSO.Molecule.Structure);
- if (so) {
- if (clear) {
- this.lociMarkProvider({ loci: Structure.Loci(so.data) }, MarkerAction.Deselect);
- }
- const loci = this.ctx.managers.structure.selection.getLoci(so.data);
- this.lociMarkProvider({ loci }, MarkerAction.Select);
- }
- }
- }
- private focusOnLoci(loci: Representation.Loci) {
- if (!this.ctx.canvas3d)
- return;
-
- const sphere = Loci.getBoundingSphere(loci.loci);
- if (!sphere)
- return;
- const snapshot = this.ctx.canvas3d.camera.getSnapshot();
- snapshot.target = sphere.center;
-
- PluginCommands.Camera.SetSnapshot(this.ctx, { snapshot, durationMs: AnimationDurationMsec });
- }
- register() {
- const lociIsEmpty = (current: Representation.Loci) => Loci.isEmpty(current.loci);
- const lociIsNotEmpty = (current: Representation.Loci) => !Loci.isEmpty(current.loci);
-
- const actions: [keyof typeof ReDNATCOLociSelectionBindings, (current: Representation.Loci) => void, ((current: Representation.Loci) => boolean) | undefined][] = [
- ['clickFocus', current => this.focusOnLoci(current), lociIsNotEmpty],
- [
- 'clickDeselectAllOnEmpty',
- () => {
- this.ctx.managers.interactivity.lociSelects.deselectAll();
- this.params.onDeselected();
- },
- lociIsEmpty
- ],
- [
- 'clickSelectOnly',
- current => {
- this.ctx.managers.interactivity.lociSelects.deselectAll();
- if (current.loci.kind === 'element-loci') {
- this.ctx.managers.interactivity.lociSelects.select(current);
- this.params.onSelected(current);
- }
- },
- lociIsNotEmpty
- ],
- ];
-
- // sort the action so that the ones with more modifiers trigger sooner.
- actions.sort((a, b) => {
- const x = this.params.bindings[a[0]], y = this.params.bindings[b[0]];
- const k = x.triggers.length === 0 ? 0 : arrayMax(x.triggers.map(t => ModifiersKeys.size(t.modifiers)));
- const l = y.triggers.length === 0 ? 0 : arrayMax(y.triggers.map(t => ModifiersKeys.size(t.modifiers)));
- return l - k;
- });
-
- this.subscribeObservable(this.ctx.behaviors.interaction.click, ({ current, button, modifiers }) => {
- if (!this.ctx.canvas3d) return;
-
- // only trigger the 1st action that matches
- for (const [binding, action, condition] of actions) {
- if (Binding.match(this.params.bindings[binding], button, modifiers) && (!condition || condition(current))) {
- action(current);
- break;
- }
- }
- });
-
- this.ctx.managers.interactivity.lociSelects.addProvider(this.lociMarkProvider);
-
- this.subscribeObservable(this.ctx.state.events.object.created, ({ ref }) => this.applySelectMark(ref));
-
- // re-apply select-mark to all representation of an updated structure
- this.subscribeObservable(this.ctx.state.events.object.updated, ({ ref, obj, oldObj, oldData, action }) => {
- const cell = this.ctx.state.data.cells.get(ref);
- if (cell && PSO.Molecule.Structure.is(cell.obj)) {
- const structure: Structure = obj.data;
- const oldStructure: Structure | undefined = action === 'recreate' ? oldObj?.data :
- action === 'in-place' ? oldData : undefined;
- if (oldStructure &&
- Structure.areEquivalent(structure, oldStructure) &&
- Structure.areHierarchiesEqual(structure, oldStructure)) return;
-
- const reprs = this.ctx.state.data.select(StateSelection.Generators.ofType(PSO.Molecule.Structure.Representation3D, ref));
- for (const repr of reprs) this.applySelectMark(repr.transform.ref, true);
- }
- });
-
- }
- unregister() {
- }
- constructor(ctx: PluginContext, params: ReDNATCOLociSelectionProps) {
- super(ctx, params);
- this.spine = new StateTreeSpine.Impl(ctx.state.data.cells);
- }
- },
-});
-
-class ReDNATCOMspViewer {
- private haveMultipleModels = false;
- private steps: StepInfo[] = [];
- private stepNames: Map<string, number> = new Map();
-
- constructor(public plugin: PluginUIContext, interactionContext: { self?: ReDNATCOMspViewer }) {
- interactionContext.self = this;
- }
-
- private currentModelNumber() {
- const model = this.plugin.state.data.cells.get(IDs.ID('model', '', BaseRef))?.obj;
- if (!model)
- return -1;
- return (model as StateObject<Model>).data.modelNum;
- }
-
- private focusOnLoci(loci: StructureElement.Loci) {
- if (!this.plugin.canvas3d)
- return;
-
- const sphere = Loci.getBoundingSphere(loci);
- if (!sphere)
- return;
- const snapshot = this.plugin.canvas3d.camera.getSnapshot();
-
- const v = Vec3();
- const u = Vec3();
- Vec3.set(v, sphere.center[0], sphere.center[1], sphere.center[2]);
- Vec3.set(u, snapshot.position[0], snapshot.position[1], snapshot.position[2]);
- Vec3.sub(u, u, v);
- Vec3.normalize(u, u);
- Vec3.scale(u, u, sphere.radius * 8);
- Vec3.add(v, u, v);
-
- console.log(
- 'Cam',
- 'Center', sphere.center,
- 'Radius', sphere.radius,
- 'Position', v
- );
-
- snapshot.target = sphere.center;
- snapshot.position = v;
-
- PluginCommands.Camera.SetSnapshot(this.plugin, { snapshot, durationMs: AnimationDurationMsec });
- }
-
- private getBuilder(id: IDs.ID, sub: IDs.Substructure|'' = '', ref = BaseRef) {
- return this.plugin.state.data.build().to(IDs.ID(id, sub, ref));
- }
-
- private getStructureParent(cell: StateObjectCell) {
- if (!cell.sourceRef)
- return undefined;
- const parent = this.plugin.state.data.cells.get(cell.sourceRef);
- if (!parent)
- return undefined;
- return parent.obj?.type.name === 'Structure' ? parent.obj : undefined;
- }
-
- private ntcRef(step: StepInfo, where: 'sel'|'prev'|'next') {
- return rcref(step.assignedNtC === 'NANT' ? step.closestNtC : step.assignedNtC, where);
- }
-
- private pyramidsParams(colors: NtCColors.Conformers, visible: Map<string, boolean>, transparent: boolean) {
- const typeParams = {} as PD.Values<ConfalPyramidsParams>;
- for (const k of Reflect.ownKeys(ConfalPyramidsParams) as (keyof ConfalPyramidsParams)[]) {
- if (ConfalPyramidsParams[k].type === 'boolean')
- (typeParams[k] as any) = visible.get(k) ?? ConfalPyramidsParams[k]['defaultValue'];
- }
-
- return {
- type: { name: 'confal-pyramids', params: { ...typeParams, alpha: transparent ? 0.5 : 1.0 } },
- colorTheme: {
- name: 'confal-pyramids',
- params: {
- colors: {
- name: 'custom',
- params: colors,
- },
- },
- },
- };
- }
-
- private resetCameraRadius() {
- if (!this.plugin.canvas3d)
- return;
-
- const spheres = [];
- for (const [ref, cell] of Array.from(this.plugin.state.data.cells)) {
- if (!IDs.isVisual(ref))
- continue;
- const parent = this.getStructureParent(cell);
- if (parent) {
- const loci = StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(parent.data, parent.data));
- const s = Loci.getBoundingSphere(loci);
- if (s)
- spheres.push(s);
- }
- }
-
- if (spheres.length === 0)
- return;
-
- SphereBoundaryHelper.reset();
- for (const s of spheres)
- SphereBoundaryHelper.includePositionRadius(s.center, s.radius);
- SphereBoundaryHelper.finishedIncludeStep();
- for (const s of spheres)
- SphereBoundaryHelper.radiusPositionRadius(s.center, s.radius);
- const bs = SphereBoundaryHelper.getSphere();
-
- const snapshot = this.plugin.canvas3d.camera.getSnapshot();
- snapshot.radius = bs.radius;
- snapshot.target = bs.center;
- PluginCommands.Camera.SetSnapshot(this.plugin, { snapshot, durationMs: AnimationDurationMsec });
- }
-
- private substructureVisuals(representation: 'ball-and-stick'|'cartoon') {
- switch (representation) {
- case 'cartoon':
- return {
- type: {
- name: 'cartoon',
- params: { sizeFactor: 0.2, sizeAspectRatio: 0.35, aromaticBonds: false },
- },
- colorTheme: { name: 'uniform', params: { color: DefaultChainColor } }
- };
- case 'ball-and-stick':
- return {
- type: {
- name: 'ball-and-stick',
- params: { sizeFactor: 0.2, sizeAspectRatio: 0.35, aromaticBonds: false },
- },
- colorTheme: { name: 'element-symbol', params: { carbonColor: { name: 'custom', params: DefaultChainColor } } },
- };
- }
- }
-
- private superpose(reference: StructureElement.Loci, stru: StructureElement.Loci, altId1?: string, altId2?: string) {
- const refElems = dinucleotideBackbone(reference);
- const struElems = dinucleotideBackbone(stru, altId1, altId2);
-
- return Superpose.superposition(
- { elements: refElems, conformation: reference.elements[0].unit.conformation },
- { elements: struElems, conformation: stru.elements[0].unit.conformation }
- );
- }
-
- static async create(target: HTMLElement) {
- const interactCtx: { self?: ReDNATCOMspViewer } = { self: undefined };
- const defaultSpec = DefaultPluginUISpec();
- const spec: PluginUISpec = {
- ...defaultSpec,
- behaviors: [
- PluginSpec.Behavior(ReDNATCOLociLabelProvider),
- PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci),
- PluginSpec.Behavior(
- ReDNATCOLociSelectionProvider,
- {
- bindings: ReDNATCOLociSelectionBindings,
- onDeselected: () => interactCtx.self!.onDeselected(),
- onSelected: (loci) => interactCtx.self!.onLociSelected(loci),
- }
- ),
- ...ObjectKeys(Extensions).map(k => Extensions[k]),
- ],
- components: {
- ...defaultSpec.components,
- controls: {
- ...defaultSpec.components?.controls,
- top: 'none',
- right: 'none',
- bottom: 'none',
- left: 'none'
- },
- },
- layout: {
- initial: {
- isExpanded: false,
- showControls: false,
- },
- },
- };
-
- const plugin = await createPluginUI(target, spec);
-
- plugin.managers.interactivity.setProps({ granularity: 'two-residues' });
- plugin.selectionMode = true;
-
- return new ReDNATCOMspViewer(plugin, interactCtx);
- }
-
- async changeNtCColors(display: Partial<Display>) {
- if (!this.has('pyramids', 'nucleic'))
- return;
-
- const b = this.plugin.state.data.build().to(IDs.ID('pyramids', 'nucleic', BaseRef));
- b.update(
- StateTransforms.Representation.StructureRepresentation3D,
- old => ({
- ...old,
- colorTheme: {
- name: 'confal-pyramids',
- params: {
- colors: {
- name: 'custom',
- params: display.conformerColors ?? NtCColors.Conformers,
- },
- },
- },
- })
- );
-
- await b.commit();
- }
-
- async changePyramids(display: Partial<Display>) {
- if (display.showPyramids) {
- if (!this.has('pyramids', 'nucleic')) {
- const b = this.getBuilder('structure', 'nucleic');
- if (b) {
- b.apply(
- StateTransforms.Representation.StructureRepresentation3D,
- this.pyramidsParams(display.conformerColors ?? NtCColors.Conformers, new Map(), display.pyramidsTransparent ?? false),
- { ref: IDs.ID('pyramids', 'nucleic', BaseRef) }
- );
- await b.commit();
- }
- } else {
- const b = this.getBuilder('pyramids', 'nucleic');
- b.update(
- StateTransforms.Representation.StructureRepresentation3D,
- old => ({
- ...old,
- ...this.pyramidsParams(display.conformerColors ?? NtCColors.Conformers, new Map(), display.pyramidsTransparent ?? false),
- })
- );
- await b.commit();
- }
- } else
- await PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.data, ref: IDs.ID('pyramids', 'nucleic', BaseRef) });
- }
-
- async changeRepresentation(display: Partial<Display>) {
- const b = this.plugin.state.data.build();
- const repr = display.representation ?? 'cartoon';
-
- for (const sub of ['nucleic', 'protein'] as IDs.Substructure[]) {
- if (this.has('visual', sub)) {
- b.to(IDs.ID('visual', sub, BaseRef))
- .update(
- StateTransforms.Representation.StructureRepresentation3D,
- old => ({
- ...old,
- ...this.substructureVisuals(repr),
- })
- );
- }
- }
-
- await b.commit();
- }
-
- focusOnSelectedStep() {
- // Focus camera on the selection
- const sel = this.plugin.state.data.cells.get(IDs.ID('superposition', '', NtCSupSel));
- const prev = this.plugin.state.data.cells.get(IDs.ID('superposition', '', NtCSupPrev));
- const next = this.plugin.state.data.cells.get(IDs.ID('superposition', '', NtCSupNext));
-
- const prevLoci = prev?.obj ? StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(prev.obj!.data, prev.obj!.data)) : EmptyLoci;
- const nextLoci = next?.obj ? StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(next.obj!.data, next.obj!.data)) : EmptyLoci;
- let focusOn = sel?.obj ? StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(sel!.obj!.data, sel!.obj!.data)) : EmptyLoci;
- if (focusOn.kind === 'empty-loci')
- return;
-
- if (prevLoci.kind === 'element-loci')
- focusOn = StructureElement.Loci.union(focusOn, prevLoci);
- if (nextLoci.kind === 'element-loci')
- focusOn = StructureElement.Loci.union(focusOn, nextLoci);
-
- this.focusOnLoci(focusOn);
- }
-
- gatherStepInfo(): { steps: StepInfo[], stepNames: Map<string, number> }|undefined {
- const obj = this.plugin.state.data.cells.get(IDs.ID('model', '', BaseRef))?.obj;
- if (!obj)
- return void 0;
- const model = (obj as StateObject<Model>);
- const sourceData = model.data.sourceData;
- if (!MmcifFormat.is(sourceData))
- return void 0;
-
- const tableSum = sourceData.data.frame.categories['ndb_struct_ntc_step_summary'];
- const tableStep = sourceData.data.frame.categories['ndb_struct_ntc_step'];
- if (!tableSum || !tableStep) {
- console.warn('NtC information not present');
- return void 0;
- }
-
- const _ids = tableStep.getField('id');
- const _names = tableStep.getField('name');
- const _authSeqId1 = tableStep.getField('auth_seq_id_1');
- const _authSeqId2 = tableStep.getField('auth_seq_id_2');
- const _labelAltId1 = tableStep.getField('label_alt_id_1');
- const _labelAltId2 = tableStep.getField('label_alt_id_2');
- const _stepIds = tableSum.getField('step_id');
- const _assignedNtCs = tableSum.getField('assigned_NtC');
- const _closestNtCs = tableSum.getField('closest_NtC');
- if (!_ids || !_names || !_stepIds || !_assignedNtCs || !_closestNtCs || !_labelAltId1 || !_labelAltId2 || !_authSeqId1 || !_authSeqId2) {
- console.warn('Expected fields are not present in NtC categories');
- return void 0;
- }
-
- const ids = _ids.toIntArray();
- const names = _names.toStringArray();
- const authSeqId1 = _authSeqId1.toIntArray();
- const authSeqId2 = _authSeqId2.toIntArray();
- const labelAltId1 = _labelAltId1.toStringArray();
- const labelAltId2 = _labelAltId2.toStringArray();
- const stepIds = _stepIds.toIntArray();
- const assignedNtCs = _assignedNtCs.toStringArray();
- const closestNtCs = _closestNtCs.toStringArray();
- const len = ids.length;
-
- const stepNames = new Map<string, number>();
- const steps = new Array<StepInfo>(len);
-
- for (let idx = 0; idx < len; idx++) {
- const id = ids[idx];
- const name = names[idx];
- for (let jdx = 0; jdx < len; jdx++) {
- if (stepIds[jdx] === id) {
- const assignedNtC = assignedNtCs[jdx];
- const closestNtC = closestNtCs[jdx];
- const resNo1 = authSeqId1[jdx];
- const resNo2 = authSeqId2[jdx];
- const altId1 = labelAltId1[jdx] === '' ? void 0 : labelAltId1[jdx];
- const altId2 = labelAltId2[jdx] === '' ? void 0 : labelAltId2[jdx];
-
- // We're assuming that steps are ID'd with a contigious, monotonic sequence starting from 1
- steps[id - 1] = { name, assignedNtC, closestNtC, resNo1, resNo2, altId1, altId2 };
- stepNames.set(name, id - 1);
- break;
- }
- }
- }
-
- return { steps, stepNames };
- }
-
- getModelCount() {
- const obj = this.plugin.state.data.cells.get(IDs.ID('trajectory', '', BaseRef))?.obj;
- if (!obj)
- return 0;
- return (obj as StateObject<Trajectory>).data.frameCount;
- }
-
- getPresentConformers() {
- const obj = this.plugin.state.data.cells.get(IDs.ID('model', '', BaseRef))?.obj;
- if (!obj)
- return [];
- const model = (obj as StateObject<Model>);
- const modelNum = model.data.modelNum;
- const sourceData = model.data.sourceData;
- if (MmcifFormat.is(sourceData)) {
- const tableSum = sourceData.data.frame.categories['ndb_struct_ntc_step_summary'];
- const tableStep = sourceData.data.frame.categories['ndb_struct_ntc_step'];
- if (!tableSum || !tableStep) {
- console.warn('NtC information not present');
- return [];
- }
-
- const _stepIds = tableSum.getField('step_id');
- const _assignedNtCs = tableSum.getField('assigned_NtC');
- const _ids = tableStep.getField('id');
- const _modelNos = tableStep.getField('PDB_model_number');
- if (!_stepIds || !_assignedNtCs || !_ids || !_modelNos) {
- console.warn('Expected fields are not present in NtC categories');
- return [];
- }
-
- const stepIds = _stepIds.toIntArray();
- const assignedNtCs = _assignedNtCs.toStringArray();
- const ids = _ids.toIntArray();
- const modelNos = _modelNos.toIntArray();
-
- const present = new Array<string>();
- for (let row = 0; row < stepIds.length; row++) {
- const idx = ids.indexOf(stepIds[row]);
- if (modelNos[idx] === modelNum) {
- const ntc = assignedNtCs[row];
- if (!present.includes(ntc))
- present.push(ntc);
- }
- }
-
- present.sort();
- return present;
- }
- return [];
- }
-
- has(id: IDs.ID, sub: IDs.Substructure|'' = '', ref = BaseRef) {
- return !!this.plugin.state.data.cells.get(IDs.ID(id, sub, ref))?.obj?.data;
- }
-
- isReady() {
- return this.has('structure', '', BaseRef);
- }
-
- async loadStructure(data: string, type: 'pdb'|'cif', display: Partial<Display>) {
- // TODO: Remove the currently loaded structure
-
- const b = (t => 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) }))
- .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) })
- // 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
- await b.commit();
-
- // Create default visuals
- const bb = this.plugin.state.data.build();
- if (display.showNucleic && this.has('structure', 'nucleic')) {
- bb.to(IDs.ID('structure', 'nucleic', BaseRef))
- .apply(
- StateTransforms.Representation.StructureRepresentation3D,
- this.substructureVisuals('cartoon'),
- { ref: IDs.ID('visual', 'nucleic', BaseRef) }
- )
- if (display.showPyramids) {
- bb.to(IDs.ID('structure', 'nucleic', BaseRef))
- .apply(
- StateTransforms.Representation.StructureRepresentation3D,
- this.pyramidsParams(display.conformerColors ?? NtCColors.Conformers, new Map(), false),
- { ref: IDs.ID('pyramids', 'nucleic', BaseRef) }
- );
- }
- }
- if (display.showProtein && this.has('structure', 'protein')) {
- bb.to(IDs.ID('structure', 'protein', BaseRef))
- .apply(
- StateTransforms.Representation.StructureRepresentation3D,
- this.substructureVisuals('cartoon'),
- { ref: IDs.ID('visual', 'protein', BaseRef) }
- );
- }
- if (display.showWater && this.has('structure', 'water')) {
- bb.to(IDs.ID('structure', 'water', BaseRef))
- .apply(
- StateTransforms.Representation.StructureRepresentation3D,
- this.substructureVisuals('ball-and-stick'),
- { ref: IDs.ID('visual', 'water', BaseRef) }
- );
- }
-
- await bb.commit();
-
- this.haveMultipleModels = this.getModelCount() > 1;
-
- const ntcInfo = this.gatherStepInfo();
- if (!ntcInfo) {
- this.steps.length = 0;
- this.stepNames.clear();
- } else {
- this.steps = ntcInfo.steps;
- this.stepNames = ntcInfo.stepNames;
- }
- }
-
- async loadReferenceConformers() {
- const b = this.plugin.state.data.build().toRoot();
-
- for (const c in ReferenceConformersPdbs) {
- const cfmr = ReferenceConformersPdbs[c as keyof typeof ReferenceConformersPdbs];
- const bRef = rcref(c);
- const mRef = IDs.ID('model', '', bRef);
- b.toRoot();
- b.apply(RawData, { data: cfmr, label: `Reference ${c}` }, { ref: IDs.ID('data', '', bRef) })
- .apply(StateTransforms.Model.TrajectoryFromPDB, {}, { ref: IDs.ID('trajectory', '', bRef) })
- .apply(StateTransforms.Model.ModelFromTrajectory, {}, { ref: mRef })
- .apply(StateTransforms.Model.StructureFromModel, {}, { ref: IDs.ID('structure', '', rcref(c, 'sel')) })
- .to(mRef)
- .apply(StateTransforms.Model.StructureFromModel, {}, { ref: IDs.ID('structure', '', rcref(c, 'prev')) })
- .to(mRef)
- .apply(StateTransforms.Model.StructureFromModel, {}, { ref: IDs.ID('structure', '', rcref(c, 'next')) });
- }
-
- await b.commit();
- }
-
- async onDeselected() {
- await this.plugin.state.data.build()
- .delete(IDs.ID('superposition', '', NtCSupSel))
- .delete(IDs.ID('superposition', '', NtCSupPrev))
- .delete(IDs.ID('superposition', '', NtCSupNext))
- .commit();
-
- this.resetCameraRadius();
- }
-
- async onLociSelected(selected: Representation.Loci) {
- const loci = Loci.normalize(selected.loci, 'two-residues');
-
- if (loci.kind === 'element-loci') {
- // TODO: This cannot call superposeReferences directly
- // Instead, we must make a callback via the API
- // and have the listener decide what to do with this event
- const stepDesc = Step.describe(loci);
- if (!stepDesc)
- return;
- const stepName = Step.name(stepDesc, this.haveMultipleModels);
- await this.superposeReferences(stepName, null, null, '', []);
- this.focusOnSelectedStep();
- }
- }
-
- async switchModel(display: Partial<Display>) {
- if (display.modelNumber && display.modelNumber === this.currentModelNumber())
- return;
-
- const b = this.plugin.state.data.build()
- .delete(IDs.ID('superposition', '', NtCSupSel))
- .delete(IDs.ID('superposition', '', NtCSupPrev))
- .delete(IDs.ID('superposition', '', NtCSupNext))
- .to(IDs.ID('model', '', BaseRef))
- .update(
- StateTransforms.Model.ModelFromTrajectory,
- old => ({
- ...old,
- modelIndex: display.modelNumber ? display.modelNumber - 1 : 0
- })
- );
-
- await b.commit();
- }
-
- async superposeReferences(stepName: string, prevStepName: string|null, nextStepName: string|null, referenceNtc: string, references: ('sel'|'prev'|'next')[]) {
- const ReferenceVisuals = (color: number) => {
- return {
- type: { name: 'ball-and-stick', params: { sizeFactor: 0.15, aromaticBonds: false } },
- colorTheme: { name: 'uniform', params: { value: Color(color) } },
- };
- };
-
- const stepDesc = Step.fromName(stepName);
- if (!stepDesc)
- return;
- const stepIdx = this.stepNames.get(stepName);
- if (stepIdx === undefined) {
- console.error(`Unknown step name ${stepName}`);
- return;
- }
-
- if (stepDesc.model !== this.currentModelNumber()) {
- const b = this.getBuilder('model')
- .update(
- StateTransforms.Model.ModelFromTrajectory,
- old => ({
- ...old,
- modelIndex: stepDesc.model - 1,
- })
- );
- await b.commit();
- }
-
- const entireStru = this.plugin.state.data.cells.get(IDs.ID('structure', 'nucleic', BaseRef))!.obj!;
- const loci = Traverse.findResidue(
- stepDesc.chain,
- stepDesc.resNo1,
- stepDesc.altId1,
- StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(entireStru.data, entireStru.data)),
- 'auth'
+class ColorBox extends React.Component<{ caption: string, color: Color }> {
+ render() {
+ const lum = luminance(this.props.color);
+ return (
+ <div
+ className='rmsp-color-box'
+ style={{ backgroundColor: Color.toStyle(this.props.color) }}
+ >
+ <span style={{ color: lum > 0.6 ? 'black' : 'white' }}>{this.props.caption}</span>
+ </div>
);
- if (loci.kind !== 'element-loci')
- return;
- const selLoci = Loci.normalize(loci, 'two-residues');
- if (selLoci.kind !== 'element-loci')
- return;
-
- // HACK: This is a temporary hack until we get prev-next steps mapping into the plugin
- let stepPrev = undefined;
- if (prevStepName) {
- const idx = this.stepNames.get(prevStepName);
- stepPrev = (idx !== undefined) ? this.steps[idx] : undefined;
- }
- let stepNext = undefined;
- if (nextStepName) {
- const idx = this.stepNames.get(nextStepName);
- stepNext = (idx !== undefined) ? this.steps[idx] : undefined;
- }
-
- const step = this.steps[stepIdx];
-
- const ntcRefSel = step ? this.ntcRef(step, 'sel') : void 0;
- const ntcRefPrev = stepPrev ? this.ntcRef(stepPrev, 'prev') : void 0;
- const ntcRefNext = stepNext ? this.ntcRef(stepNext, 'next') : void 0;
-
- if (!ntcRefSel) {
- console.error(`stepIdx ${stepIdx} does not map to a known step`);
- return;
- }
-
- const b = this.plugin.state.data.build()
- .delete(IDs.ID('superposition', '', NtCSupSel))
- .delete(IDs.ID('superposition', '', NtCSupPrev))
- .delete(IDs.ID('superposition', '', NtCSupNext));
-
- const addReference = (ntcRef: string, superposRef: string, loci: Loci, altId1: string|undefined, altId2: string|undefined, color: number) => {
- const refStru = this.plugin.state.data.cells.get(IDs.ID('structure', '', ntcRef))!.obj!;
- const refLoci = StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(refStru.data, refStru.data));
-
- if (loci.kind === 'element-loci' && Step.is(loci)) {
- const { bTransform, rmsd } = this.superpose(refLoci, loci, altId1, altId2);
- if (isNaN(bTransform[0])) {
- console.error(`Cannot superpose reference conformer ${ntcRef} onto selection`);
- return;
- }
- b.to(IDs.ID('structure', '', ntcRef))
- .apply(
- StateTransforms.Model.TransformStructureConformation,
- { transform: { name: 'matrix', params: { data: bTransform, transpose: false } } },
- { ref: IDs.ID('superposition', '', superposRef) }
- ).apply(
- StateTransforms.Representation.StructureRepresentation3D,
- ReferenceVisuals(color),
- { ref: IDs.ID('visual', '', superposRef) }
- );
- return rmsd;
- }
- };
-
- const rmsd = addReference(ntcRefSel, NtCSupSel, selLoci, stepDesc.altId1, stepDesc.altId2, 0x008000);
- if (ntcRefPrev) {
- const { altId1, altId2 } = stepPrev!;
- addReference(ntcRefPrev, NtCSupPrev, Loci.normalize(Traverse.residue(-1, altId1, selLoci), 'two-residues'), altId1, altId2, 0x0000FF);
- }
- if (ntcRefNext) {
- const { altId1, altId2 } = stepNext!;
- addReference(ntcRefNext, NtCSupNext, Loci.normalize(Traverse.residue(1, altId1, selLoci), 'two-residues'), altId1, altId2, 0x00FFFF);
- }
-
- await b.commit();
-
- return rmsd;
- }
-
- async toggleSubstructure(sub: IDs.Substructure, display: Partial<Display>) {
- const show = sub === 'nucleic' ? !!display.showNucleic :
- sub === 'protein' ? !!display.showProtein : !!display.showWater;
- const repr = display.representation ?? 'cartoon';
-
- if (show) {
- const b = this.getBuilder('structure', sub);
- const visuals = this.substructureVisuals(sub === 'water' ? 'ball-and-stick' : repr);
- if (b) {
- b.apply(
- StateTransforms.Representation.StructureRepresentation3D,
- visuals,
- { ref: IDs.ID('visual', sub, BaseRef) }
- );
- await b.commit();
- }
- } else {
- await PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.data, ref: IDs.ID('visual', sub, BaseRef) });
- this.resetCameraRadius();
- }
}
}
@@ -1030,9 +68,19 @@ interface State {
display: Display;
showControls: boolean;
}
-class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
+export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
private presentConformers: string[] = [];
- private viewer: ReDNATCOMspViewer|null = null;
+ private viewer: ReDNATCOMspViewer|undefined = undefined;
+ private selectedStep: { name: string, rmsd?: number }|undefined;
+
+ constructor(props: ReDNATCOMsp.Props) {
+ super(props);
+
+ this.state = {
+ display: { ...Display },
+ showControls: false,
+ };
+ }
private classColorToConformers(k: keyof ConformersByClass, color: Color) {
const updated: Partial<NtCColors.Conformers> = {};
@@ -1074,15 +122,36 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
this.setState({ ...this.state, display });
}
- async command(cmd: Commands.Cmd) {
+ apiQuery(type: Api.Queries.Type): Api.Response {
+ if (type === 'selected-step') {
+ if (this.selectedStep)
+ return Api.Queries.SelectedStep(this.selectedStep.name, this.selectedStep.rmsd);
+ return Api.Queries.SelectedStep('');
+ }
+
+ // TODO: This cannot happen - figure out how to assert on this
+ return Api.Queries.SelectedStep('');
+ }
+
+ async command(cmd: Api.Command) {
if (!this.viewer)
return;
if (cmd.type === 'redraw')
window.dispatchEvent(new Event('resize'));
- else if (cmd.type === 'select-step') {
- await this.viewer.superposeReferences(cmd.stepName, cmd.prevStepName, cmd.nextStepName, cmd.referenceNtC, cmd.references);
+ else if (cmd.type === 'deselect-step') {
+ await this.viewer.actionDeselectStep(this.state.display);
+ } else if (cmd.type === 'select-step') {
+ const ret = await this.viewer.actionSelectStep(cmd.stepName, cmd.prevStepName, cmd.nextStepName, cmd.referenceNtC, cmd.references, this.state.display);
+ if (!ret) {
+ ReDNATCOMspApi.event(Api.Events.StepSelectedFail());
+ return;
+ }
+
this.viewer.focusOnSelectedStep();
+ this.selectedStep = { name: cmd.stepName, rmsd: ret.rmsd };
+
+ ReDNATCOMspApi.event(Api.Events.StepSelectedOk(this.selectedStep.name, this.selectedStep.rmsd));
} else if (cmd.type === 'switch-model') {
if (cmd.model < 1 || cmd.model > this.viewer.getModelCount())
return;
@@ -1097,15 +166,6 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
}
}
- constructor(props: ReDNATCOMsp.Props) {
- super(props);
-
- this.state = {
- display: { ...Display },
- showControls: false,
- };
- }
-
loadStructure(data: string, type: 'pdb'|'cif') {
if (this.viewer)
this.viewer.loadStructure(data, type, this.state.display).then(() => {
@@ -1114,10 +174,19 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
});
}
+ viewerStepDeselected() {
+ this.viewer!.actionDeselectStep(this.state.display);
+ ReDNATCOMspApi.event(Api.Events.StepDeselected());
+ }
+
+ viewerStepSelected(stepName: string) {
+ ReDNATCOMspApi.event(Api.Events.StepRequested(stepName));
+ }
+
componentDidMount() {
if (!this.viewer) {
const elem = document.getElementById(this.props.elemId + '-viewer');
- ReDNATCOMspViewer.create(elem!).then(viewer => {
+ ReDNATCOMspViewer.create(elem!, this).then(viewer => {
this.viewer = viewer;
this.viewer.loadReferenceConformers().then(() => {
ReDNATCOMspApi._bind(this);
@@ -1341,7 +410,7 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
}
}
-namespace ReDNATCOMsp {
+export namespace ReDNATCOMsp {
export interface Props {
elemId: string;
onInited?: () => void;
@@ -1356,32 +425,4 @@ namespace ReDNATCOMsp {
}
}
-class _ReDNATCOMspApi {
- private target: ReDNATCOMsp|null = null;
-
- private check() {
- if (!this.target)
- throw new Error('ReDNATCOMsp object not bound');
- }
-
- _bind(target: ReDNATCOMsp) {
- this.target = target;
- }
-
- command(cmd: Commands.Cmd) {
- this.check();
- this.target!.command(cmd);
- }
-
- init(elemId: string, onInited?: () => void) {
- ReDNATCOMsp.init(elemId, onInited);
- return this;
- }
-
- loadStructure(data: string) {
- this.check();
- this.target!.loadStructure(data, 'cif');
- }
-}
-
-export const ReDNATCOMspApi = new _ReDNATCOMspApi();
+export const ReDNATCOMspApi = new ReDNATCOMspApiImpl();
diff --git a/src/apps/rednatco/traverse.ts b/src/apps/rednatco/traverse.ts
index e4eafbfcdc3927acf55e1d4e13ce548c0753eb85..913b679694f8c8affc7d5a751c056ca9e0aa3eb3 100644
--- a/src/apps/rednatco/traverse.ts
+++ b/src/apps/rednatco/traverse.ts
@@ -66,6 +66,14 @@ export namespace Traverse {
return EmptyLoci;
}
+ export function findStep(asymId: string, seqId: number, altId: string|undefined, loci: StructureElement.Loci, source: 'label'|'auth') {
+ const sel = findResidue(asymId, seqId, altId, loci, source);
+ if (sel.kind === 'empty-loci')
+ return sel;
+
+ return Loci.normalize(sel, 'two-residues');
+ }
+
export function residue(shift: number, altId: string|undefined, cursor: StructureElement.Loci) {
for (const e of cursor.elements) {
const entireUnit = cursor.structure.units[e.unit.id];
diff --git a/src/apps/rednatco/viewer.ts b/src/apps/rednatco/viewer.ts
new file mode 100644
index 0000000000000000000000000000000000000000..01d5e8f06506008c69574dd54b427eb40823044b
--- /dev/null
+++ b/src/apps/rednatco/viewer.ts
@@ -0,0 +1,1084 @@
+import * as IDs from './idents';
+import * as RefCfmr from './reference-conformers';
+import { ReDNATCOMsp, Display, VisualRepresentations } from './index';
+import { NtCColors } from './colors';
+import { ReferenceConformersPdbs } from './reference-conformers-pdbs';
+import { Step } from './step';
+import { Superpose } from './superpose';
+import { Traverse } from './traverse';
+import { DnatcoConfalPyramids } from '../../extensions/dnatco';
+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, Structure, StructureElement, StructureProperties, StructureSelection, Trajectory } from '../../mol-model/structure';
+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';
+import { PluginBehavior, PluginBehaviors } from '../../mol-plugin/behavior';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
+import { PluginSpec } from '../../mol-plugin/spec';
+import { LociLabel } from '../../mol-plugin-state/manager/loci-label';
+import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { RawData } from '../../mol-plugin-state/transforms/data';
+import { createPluginUI } from '../../mol-plugin-ui';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
+import { Representation } from '../../mol-repr/representation';
+import { StateObjectCell, StateObject, StateSelection, StateTransformer } from '../../mol-state';
+import { StateBuilder } from '../../mol-state/state/builder';
+import { StateTreeSpine } from '../../mol-state/tree/spine';
+import { lociLabel } from '../../mol-theme/label';
+import { arrayMax } from '../../mol-util/array';
+import { Binding } from '../../mol-util/binding';
+import { Color } from '../../mol-util/color';
+import { ButtonsType, ModifiersKeys } from '../../mol-util/input/input-observer';
+import { MarkerAction } from '../../mol-util/marker-action';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+import './molstar.css';
+import './rednatco-molstar.css';
+
+const Extensions = {
+ 'ntc-balls-pyramids-prop': PluginSpec.Behavior(DnatcoConfalPyramids),
+};
+
+const AnimationDurationMsec = 150;
+const BaseRef = 'rdo';
+const RCRef = 'rc';
+const NtCSupPrev = 'ntc-sup-prev';
+const NtCSupSel = 'ntc-sup-sel';
+const NtCSupNext = 'ntc-sup-next';
+const SphereBoundaryHelper = new BoundaryHelper('98');
+
+const DefaultChainColor = Color(0xD9D9D9);
+
+type StepInfo = {
+ name: string;
+ assignedNtC: string;
+ closestNtC: string; // Fallback for cases where assignedNtC is NANT
+ chain: string;
+ resNo1: number;
+ resNo2: number;
+ altId1?: string;
+ altId2?: string;
+ model: number;
+}
+
+type StepWithStructure = {
+ step: StepInfo;
+ loci: StructureElement.Loci;
+}
+
+function dinucleotideBackbone(loci: StructureElement.Loci, altId1?: string, altId2?: string) {
+ const es = loci.elements[0];
+ const loc = Location.create(loci.structure, es.unit, es.unit.elements[OrderedSet.getAt(es.indices, 0)]);
+ const len = OrderedSet.size(es.indices);
+ const indices = new Array<ElementIndex>();
+
+ const gather = (atoms: string[], start: number, end: number, altId?: string) => {
+ for (const atom of atoms) {
+ let idx = start;
+ for (; idx < end; idx++) {
+ loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
+ const _atom = StructureProperties.atom.label_atom_id(loc);
+ if (atom === _atom) {
+ if (altId) {
+ const _altId = StructureProperties.atom.label_alt_id(loc);
+ if (_altId !== '' && _altId !== altId)
+ continue;
+ }
+
+ indices.push(loc.element);
+ break;
+ }
+ }
+ if (idx === end) {
+ console.error(`Cannot find backbone atom ${atom} in first residue of a step`);
+ return false;
+ }
+ }
+
+ return true;
+ };
+
+ // Find split between first and second residue
+ const resNo1 = StructureProperties.residue.auth_seq_id(loc);
+ let secondIdx = -1;
+ for (let idx = 0; idx < len; idx++) {
+ loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
+ const resNo = StructureProperties.residue.auth_seq_id(loc);
+ if (resNo !== resNo1) {
+ secondIdx = idx;
+ break;
+ }
+ }
+ if (secondIdx === -1)
+ return [];
+
+ // Gather ElementIndices for backbone atoms of the first residue
+ loc.element = es.unit.elements[OrderedSet.getAt(es.indices, 0)];
+ const ring1 = RefCfmr.CompoundRings[StructureProperties.atom.label_comp_id(loc) as keyof RefCfmr.CompoundRings];
+ if (!ring1)
+ return [];
+
+ const first = RefCfmr.BackboneAtoms.first.concat(RefCfmr.BackboneAtoms[ring1]);
+ if (!gather(first, 0, secondIdx, altId1))
+ return [];
+
+ loc.element = es.unit.elements[OrderedSet.getAt(es.indices, secondIdx)];
+ const ring2 = RefCfmr.CompoundRings[StructureProperties.atom.label_comp_id(loc) as keyof RefCfmr.CompoundRings];
+ if (!ring2)
+ return [];
+
+ const second = RefCfmr.BackboneAtoms.second.concat(RefCfmr.BackboneAtoms[ring2]);
+ if (!gather(second, secondIdx, len, altId2))
+ return [];
+
+ return indices;
+}
+
+function rcref(c: string, where: 'sel'|'prev'|'next'|'' = '') {
+ return `${RCRef}-${c}-${where}`;
+}
+
+const ReDNATCOLociLabelProvider = PluginBehavior.create({
+ name: 'watlas-loci-label-provider',
+ category: 'interaction',
+ ctor: class implements PluginBehavior<undefined> {
+ private f = {
+ label: (loci: Loci) => {
+ switch (loci.kind) {
+ case 'structure-loci':
+ case 'element-loci':
+ return lociLabel(loci);
+ default:
+ return '';
+ }
+ },
+ group: (label: LociLabel) => label.toString().replace(/Model [0-9]+/g, 'Models'),
+ priority: 100
+ };
+ register() { this.ctx.managers.lociLabels.addProvider(this.f); }
+ unregister() { this.ctx.managers.lociLabels.removeProvider(this.f); }
+ constructor(protected ctx: PluginContext) { }
+ },
+ display: { name: 'ReDNATCO labeling' }
+});
+
+const ReDNATCOLociSelectionBindings = {
+ clickFocus: Binding([Binding.Trigger(ButtonsType.Flag.Secondary)], 'Focus camera on selected loci using ${triggers}'),
+ clickSelectOnly: Binding([Binding.Trigger(ButtonsType.Flag.Primary)], 'Select the clicked element using ${triggers}.'),
+ clickDeselectAllOnEmpty: Binding([Binding.Trigger(ButtonsType.Flag.Primary)], 'Deselect all when clicking on nothing using ${triggers}.'),
+};
+const ReDNATCOLociSelectionParams = {
+ bindings: PD.Value(ReDNATCOLociSelectionBindings, { isHidden: true }),
+ onDeselected: PD.Value(() => {}, { isHidden: true }),
+ onSelected: PD.Value((loci: Representation.Loci) => {}, { isHidden: true }),
+};
+type ReDNATCOLociSelectionProps = PD.Values<typeof ReDNATCOLociSelectionParams>;
+
+const ReDNATCOLociSelectionProvider = PluginBehavior.create({
+ name: 'rednatco-loci-selection-provider',
+ category: 'interaction',
+ display: { name: 'Interactive step selection' },
+ params: () => ReDNATCOLociSelectionParams,
+ ctor: class extends PluginBehavior.Handler<ReDNATCOLociSelectionProps> {
+ private spine: StateTreeSpine.Impl;
+ private lociMarkProvider = (reprLoci: Representation.Loci, action: MarkerAction) => {
+ if (!this.ctx.canvas3d) return;
+ this.ctx.canvas3d.mark({ loci: reprLoci.loci }, action);
+ };
+ private applySelectMark(ref: string, clear?: boolean) {
+ const cell = this.ctx.state.data.cells.get(ref);
+ if (cell && PSO.isRepresentation3D(cell.obj)) {
+ this.spine.current = cell;
+ const so = this.spine.getRootOfType(PSO.Molecule.Structure);
+ if (so) {
+ if (clear) {
+ this.lociMarkProvider({ loci: Structure.Loci(so.data) }, MarkerAction.Deselect);
+ }
+ const loci = this.ctx.managers.structure.selection.getLoci(so.data);
+ this.lociMarkProvider({ loci }, MarkerAction.Select);
+ }
+ }
+ }
+ private focusOnLoci(loci: Representation.Loci) {
+ if (!this.ctx.canvas3d)
+ return;
+
+ const sphere = Loci.getBoundingSphere(loci.loci);
+ if (!sphere)
+ return;
+ const snapshot = this.ctx.canvas3d.camera.getSnapshot();
+ snapshot.target = sphere.center;
+
+ PluginCommands.Camera.SetSnapshot(this.ctx, { snapshot, durationMs: AnimationDurationMsec });
+ }
+ register() {
+ const lociIsEmpty = (current: Representation.Loci) => Loci.isEmpty(current.loci);
+ const lociIsNotEmpty = (current: Representation.Loci) => !Loci.isEmpty(current.loci);
+
+ const actions: [keyof typeof ReDNATCOLociSelectionBindings, (current: Representation.Loci) => void, ((current: Representation.Loci) => boolean) | undefined][] = [
+ ['clickFocus', current => this.focusOnLoci(current), lociIsNotEmpty],
+ [
+ 'clickDeselectAllOnEmpty',
+ () => {
+ this.ctx.managers.interactivity.lociSelects.deselectAll();
+ this.params.onDeselected();
+ },
+ lociIsEmpty
+ ],
+ [
+ 'clickSelectOnly',
+ current => {
+ this.ctx.managers.interactivity.lociSelects.deselectAll();
+ if (current.loci.kind === 'element-loci') {
+ this.ctx.managers.interactivity.lociSelects.select(current);
+ this.params.onSelected(current);
+ }
+ },
+ lociIsNotEmpty
+ ],
+ ];
+
+ // sort the action so that the ones with more modifiers trigger sooner.
+ actions.sort((a, b) => {
+ const x = this.params.bindings[a[0]], y = this.params.bindings[b[0]];
+ const k = x.triggers.length === 0 ? 0 : arrayMax(x.triggers.map(t => ModifiersKeys.size(t.modifiers)));
+ const l = y.triggers.length === 0 ? 0 : arrayMax(y.triggers.map(t => ModifiersKeys.size(t.modifiers)));
+ return l - k;
+ });
+
+ this.subscribeObservable(this.ctx.behaviors.interaction.click, ({ current, button, modifiers }) => {
+ if (!this.ctx.canvas3d) return;
+
+ // only trigger the 1st action that matches
+ for (const [binding, action, condition] of actions) {
+ if (Binding.match(this.params.bindings[binding], button, modifiers) && (!condition || condition(current))) {
+ action(current);
+ break;
+ }
+ }
+ });
+
+ this.ctx.managers.interactivity.lociSelects.addProvider(this.lociMarkProvider);
+
+ this.subscribeObservable(this.ctx.state.events.object.created, ({ ref }) => this.applySelectMark(ref));
+
+ // re-apply select-mark to all representation of an updated structure
+ this.subscribeObservable(this.ctx.state.events.object.updated, ({ ref, obj, oldObj, oldData, action }) => {
+ const cell = this.ctx.state.data.cells.get(ref);
+ if (cell && PSO.Molecule.Structure.is(cell.obj)) {
+ const structure: Structure = obj.data;
+ const oldStructure: Structure | undefined = action === 'recreate' ? oldObj?.data :
+ action === 'in-place' ? oldData : undefined;
+ if (oldStructure &&
+ Structure.areEquivalent(structure, oldStructure) &&
+ Structure.areHierarchiesEqual(structure, oldStructure)) return;
+
+ const reprs = this.ctx.state.data.select(StateSelection.Generators.ofType(PSO.Molecule.Structure.Representation3D, ref));
+ for (const repr of reprs) this.applySelectMark(repr.transform.ref, true);
+ }
+ });
+
+ }
+ unregister() {
+ }
+ constructor(ctx: PluginContext, params: ReDNATCOLociSelectionProps) {
+ super(ctx, params);
+ this.spine = new StateTreeSpine.Impl(ctx.state.data.cells);
+ }
+ },
+});
+
+export class ReDNATCOMspViewer {
+ private haveMultipleModels = false;
+ private steps: StepInfo[] = [];
+ private stepNames: Map<string, number> = new Map();
+ private app: ReDNATCOMsp;
+
+ constructor(public plugin: PluginUIContext, interactionContext: { self?: ReDNATCOMspViewer }, app: ReDNATCOMsp) {
+ interactionContext.self = this;
+ this.app = app;
+ }
+
+ private currentModelNumber() {
+ const model = this.plugin.state.data.cells.get(IDs.ID('model', '', BaseRef))?.obj;
+ if (!model)
+ return -1;
+ return (model as StateObject<Model>).data.modelNum;
+ }
+
+ private focusOnLoci(loci: StructureElement.Loci) {
+ if (!this.plugin.canvas3d)
+ return;
+
+ const sphere = Loci.getBoundingSphere(loci);
+ if (!sphere)
+ return;
+ const snapshot = this.plugin.canvas3d.camera.getSnapshot();
+
+ const v = Vec3();
+ const u = Vec3();
+ Vec3.set(v, sphere.center[0], sphere.center[1], sphere.center[2]);
+ Vec3.set(u, snapshot.position[0], snapshot.position[1], snapshot.position[2]);
+ Vec3.sub(u, u, v);
+ Vec3.normalize(u, u);
+ Vec3.scale(u, u, sphere.radius * 8);
+ Vec3.add(v, u, v);
+
+ console.log(
+ 'Cam',
+ 'Center', sphere.center,
+ 'Radius', sphere.radius,
+ 'Position', v
+ );
+
+ snapshot.target = sphere.center;
+ snapshot.position = v;
+
+ PluginCommands.Camera.SetSnapshot(this.plugin, { snapshot, durationMs: AnimationDurationMsec });
+ }
+
+ private getBuilder(id: IDs.ID, sub: IDs.Substructure|'' = '', ref = BaseRef) {
+ return this.plugin.state.data.build().to(IDs.ID(id, sub, ref));
+ }
+
+ private getStructureParent(cell: StateObjectCell) {
+ if (!cell.sourceRef)
+ return undefined;
+ const parent = this.plugin.state.data.cells.get(cell.sourceRef);
+ if (!parent)
+ return undefined;
+ return parent.obj?.type.name === 'Structure' ? parent.obj : undefined;
+ }
+
+ private ntcRef(step: StepInfo, where: 'sel'|'prev'|'next') {
+ return rcref(step.assignedNtC === 'NANT' ? step.closestNtC : step.assignedNtC, where);
+ }
+
+ private pyramidsParams(colors: NtCColors.Conformers, visible: Map<string, boolean>, transparent: boolean) {
+ const typeParams = {} as PD.Values<ConfalPyramidsParams>;
+ for (const k of Reflect.ownKeys(ConfalPyramidsParams) as (keyof ConfalPyramidsParams)[]) {
+ if (ConfalPyramidsParams[k].type === 'boolean')
+ (typeParams[k] as any) = visible.get(k) ?? ConfalPyramidsParams[k]['defaultValue'];
+ }
+
+ return {
+ type: { name: 'confal-pyramids', params: { ...typeParams, alpha: transparent ? 0.5 : 1.0 } },
+ colorTheme: {
+ name: 'confal-pyramids',
+ params: {
+ colors: {
+ name: 'custom',
+ params: colors,
+ },
+ },
+ },
+ };
+ }
+
+ private resetCameraRadius() {
+ if (!this.plugin.canvas3d)
+ return;
+
+ const spheres = [];
+ for (const [ref, cell] of Array.from(this.plugin.state.data.cells)) {
+ if (!IDs.isVisual(ref))
+ continue;
+ const parent = this.getStructureParent(cell);
+ if (parent) {
+ const loci = StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(parent.data, parent.data));
+ const s = Loci.getBoundingSphere(loci);
+ if (s)
+ spheres.push(s);
+ }
+ }
+
+ if (spheres.length === 0)
+ return;
+
+ SphereBoundaryHelper.reset();
+ for (const s of spheres)
+ SphereBoundaryHelper.includePositionRadius(s.center, s.radius);
+ SphereBoundaryHelper.finishedIncludeStep();
+ for (const s of spheres)
+ SphereBoundaryHelper.radiusPositionRadius(s.center, s.radius);
+ const bs = SphereBoundaryHelper.getSphere();
+
+ const snapshot = this.plugin.canvas3d.camera.getSnapshot();
+ snapshot.radius = bs.radius;
+ snapshot.target = bs.center;
+ PluginCommands.Camera.SetSnapshot(this.plugin, { snapshot, durationMs: AnimationDurationMsec });
+ }
+
+ private stepFromName(name: string) {
+ const idx = this.stepNames.get(name);
+ if (idx === undefined)
+ return undefined;
+
+ return this.steps[idx];
+ }
+
+ private substructureVisuals(representation: 'ball-and-stick'|'cartoon') {
+ switch (representation) {
+ case 'cartoon':
+ return {
+ type: {
+ name: 'cartoon',
+ params: { sizeFactor: 0.2, sizeAspectRatio: 0.35, aromaticBonds: false },
+ },
+ colorTheme: { name: 'uniform', params: { color: DefaultChainColor } }
+ };
+ case 'ball-and-stick':
+ return {
+ type: {
+ name: 'ball-and-stick',
+ params: { sizeFactor: 0.2, sizeAspectRatio: 0.35, aromaticBonds: false },
+ },
+ colorTheme: { name: 'element-symbol', params: { carbonColor: { name: 'custom', params: DefaultChainColor } } },
+ };
+ }
+ }
+
+ private superpose(reference: StructureElement.Loci, stru: StructureElement.Loci, altId1?: string, altId2?: string) {
+ const refElems = dinucleotideBackbone(reference);
+ const struElems = dinucleotideBackbone(stru, altId1, altId2);
+
+ return Superpose.superposition(
+ { elements: refElems, conformation: reference.elements[0].unit.conformation },
+ { elements: struElems, conformation: stru.elements[0].unit.conformation }
+ );
+ }
+
+ private async toggleNucleicSubstructure(show: boolean, repr: VisualRepresentations) {
+ if (this.has('structure', 'remainder-slice', BaseRef)) {
+ const b = this.getBuilder('structure', 'remainder-slice');
+ if (show) {
+ b.apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ this.substructureVisuals(repr),
+ { ref: IDs.ID('visual', 'remainder-slice', BaseRef) }
+ );
+ } else
+ b.delete(IDs.ID('visual', 'remainder-slice', BaseRef));
+
+ await b.commit();
+ } else {
+ const b = this.getBuilder('structure', 'nucleic');
+
+ if (show) {
+ b.apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ this.substructureVisuals(repr),
+ { ref: IDs.ID('visual', 'nucleic', BaseRef) }
+ );
+ } else
+ b.delete(IDs.ID('visual', 'nucleic', BaseRef));
+
+ await b.commit();
+ }
+ }
+
+ private toStepWithStructure(name: string, struLoci: StructureElement.Loci): StepWithStructure|undefined {
+ const step = this.stepFromName(name);
+ if (!step)
+ return void 0;
+
+ const loci = Traverse.findStep(
+ step.chain,
+ step.resNo1,
+ step.altId1,
+ struLoci,
+ 'auth'
+ );
+ if (loci.kind === 'element-loci')
+ return { step, loci };
+
+ return void 0;
+ }
+
+ static async create(target: HTMLElement, app: ReDNATCOMsp) {
+ const interactCtx: { self?: ReDNATCOMspViewer } = { self: undefined };
+ const defaultSpec = DefaultPluginUISpec();
+ const spec: PluginUISpec = {
+ ...defaultSpec,
+ behaviors: [
+ PluginSpec.Behavior(ReDNATCOLociLabelProvider),
+ PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci),
+ PluginSpec.Behavior(
+ ReDNATCOLociSelectionProvider,
+ {
+ bindings: ReDNATCOLociSelectionBindings,
+ onDeselected: () => interactCtx.self!.onDeselected(),
+ onSelected: (loci) => interactCtx.self!.onLociSelected(loci),
+ }
+ ),
+ ...ObjectKeys(Extensions).map(k => Extensions[k]),
+ ],
+ components: {
+ ...defaultSpec.components,
+ controls: {
+ ...defaultSpec.components?.controls,
+ top: 'none',
+ right: 'none',
+ bottom: 'none',
+ left: 'none'
+ },
+ },
+ layout: {
+ initial: {
+ isExpanded: false,
+ showControls: false,
+ },
+ },
+ };
+
+ const plugin = await createPluginUI(target, spec);
+
+ plugin.managers.interactivity.setProps({ granularity: 'two-residues' });
+ plugin.selectionMode = true;
+
+ return new ReDNATCOMspViewer(plugin, interactCtx, app);
+ }
+
+ async changeNtCColors(display: Partial<Display>) {
+ if (!this.has('pyramids', 'nucleic'))
+ return;
+
+ const b = this.plugin.state.data.build().to(IDs.ID('pyramids', 'nucleic', BaseRef));
+ b.update(
+ StateTransforms.Representation.StructureRepresentation3D,
+ old => ({
+ ...old,
+ colorTheme: {
+ name: 'confal-pyramids',
+ params: {
+ colors: {
+ name: 'custom',
+ params: display.conformerColors ?? NtCColors.Conformers,
+ },
+ },
+ },
+ })
+ );
+
+ await b.commit();
+ }
+
+ async changePyramids(display: Partial<Display>) {
+ if (display.showPyramids) {
+ if (!this.has('pyramids', 'nucleic')) {
+ const b = this.getBuilder('structure', 'nucleic');
+ if (b) {
+ b.apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ this.pyramidsParams(display.conformerColors ?? NtCColors.Conformers, new Map(), display.pyramidsTransparent ?? false),
+ { ref: IDs.ID('pyramids', 'nucleic', BaseRef) }
+ );
+ await b.commit();
+ }
+ } else {
+ const b = this.getBuilder('pyramids', 'nucleic');
+ b.update(
+ StateTransforms.Representation.StructureRepresentation3D,
+ old => ({
+ ...old,
+ ...this.pyramidsParams(display.conformerColors ?? NtCColors.Conformers, new Map(), display.pyramidsTransparent ?? false),
+ })
+ );
+ await b.commit();
+ }
+ } else
+ await PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.data, ref: IDs.ID('pyramids', 'nucleic', BaseRef) });
+ }
+
+ async changeRepresentation(display: Partial<Display>) {
+ const b = this.plugin.state.data.build();
+ const repr = display.representation ?? 'cartoon';
+
+ for (const sub of ['nucleic', 'protein'] as IDs.Substructure[]) {
+ if (this.has('visual', sub)) {
+ b.to(IDs.ID('visual', sub, BaseRef))
+ .update(
+ StateTransforms.Representation.StructureRepresentation3D,
+ old => ({
+ ...old,
+ ...this.substructureVisuals(repr),
+ })
+ );
+ }
+ }
+
+ await b.commit();
+ }
+
+ focusOnSelectedStep() {
+ // Focus camera on the selection
+ const sel = this.plugin.state.data.cells.get(IDs.ID('superposition', '', NtCSupSel));
+ const prev = this.plugin.state.data.cells.get(IDs.ID('superposition', '', NtCSupPrev));
+ const next = this.plugin.state.data.cells.get(IDs.ID('superposition', '', NtCSupNext));
+
+ const prevLoci = prev?.obj ? StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(prev.obj!.data, prev.obj!.data)) : EmptyLoci;
+ const nextLoci = next?.obj ? StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(next.obj!.data, next.obj!.data)) : EmptyLoci;
+ let focusOn = sel?.obj ? StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(sel!.obj!.data, sel!.obj!.data)) : EmptyLoci;
+ if (focusOn.kind === 'empty-loci')
+ return;
+
+ if (prevLoci.kind === 'element-loci')
+ focusOn = StructureElement.Loci.union(focusOn, prevLoci);
+ if (nextLoci.kind === 'element-loci')
+ focusOn = StructureElement.Loci.union(focusOn, nextLoci);
+
+ this.focusOnLoci(focusOn);
+ }
+
+ gatherStepInfo(): { steps: StepInfo[], stepNames: Map<string, number> }|undefined {
+ const obj = this.plugin.state.data.cells.get(IDs.ID('model', '', BaseRef))?.obj;
+ if (!obj)
+ return void 0;
+ const model = (obj as StateObject<Model>);
+ const sourceData = model.data.sourceData;
+ if (!MmcifFormat.is(sourceData))
+ return void 0;
+
+ const tableSum = sourceData.data.frame.categories['ndb_struct_ntc_step_summary'];
+ const tableStep = sourceData.data.frame.categories['ndb_struct_ntc_step'];
+ if (!tableSum || !tableStep) {
+ console.warn('NtC information not present');
+ return void 0;
+ }
+
+ const _ids = tableStep.getField('id');
+ const _names = tableStep.getField('name');
+ const _chains = tableStep.getField('auth_asym_id_1');
+ const _authSeqId1 = tableStep.getField('auth_seq_id_1');
+ const _authSeqId2 = tableStep.getField('auth_seq_id_2');
+ const _labelAltId1 = tableStep.getField('label_alt_id_1');
+ const _labelAltId2 = tableStep.getField('label_alt_id_2');
+ const _stepIds = tableSum.getField('step_id');
+ const _assignedNtCs = tableSum.getField('assigned_NtC');
+ const _closestNtCs = tableSum.getField('closest_NtC');
+ const _models = tableStep.getField('PDB_model_number');
+ if (!_ids || !_names || !_chains || !_stepIds || !_assignedNtCs || !_closestNtCs || !_labelAltId1 || !_labelAltId2 || !_authSeqId1 || !_authSeqId2 || !_models) {
+ console.warn('Expected fields are not present in NtC categories');
+ return void 0;
+ }
+
+ const ids = _ids.toIntArray();
+ const names = _names.toStringArray();
+ const chains = _chains.toStringArray();
+ const authSeqId1 = _authSeqId1.toIntArray();
+ const authSeqId2 = _authSeqId2.toIntArray();
+ const labelAltId1 = _labelAltId1.toStringArray();
+ const labelAltId2 = _labelAltId2.toStringArray();
+ const stepIds = _stepIds.toIntArray();
+ const assignedNtCs = _assignedNtCs.toStringArray();
+ const closestNtCs = _closestNtCs.toStringArray();
+ const models = _models.toIntArray();
+ const len = ids.length;
+
+ const stepNames = new Map<string, number>();
+ const steps = new Array<StepInfo>(len);
+
+ for (let idx = 0; idx < len; idx++) {
+ const id = ids[idx];
+ const name = names[idx];
+ for (let jdx = 0; jdx < len; jdx++) {
+ if (stepIds[jdx] === id) {
+ const assignedNtC = assignedNtCs[jdx];
+ const closestNtC = closestNtCs[jdx];
+ const chain = chains[jdx];
+ const resNo1 = authSeqId1[jdx];
+ const resNo2 = authSeqId2[jdx];
+ const altId1 = labelAltId1[jdx] === '' ? void 0 : labelAltId1[jdx];
+ const altId2 = labelAltId2[jdx] === '' ? void 0 : labelAltId2[jdx];
+ const model = models[jdx];
+
+ // We're assuming that steps are ID'd with a contigious, monotonic sequence starting from 1
+ steps[id - 1] = {
+ name,
+ assignedNtC,
+ closestNtC,
+ chain,
+ resNo1,
+ resNo2,
+ altId1,
+ altId2,
+ model
+ };
+ stepNames.set(name, id - 1);
+ break;
+ }
+ }
+ }
+
+ return { steps, stepNames };
+ }
+
+ getModelCount() {
+ const obj = this.plugin.state.data.cells.get(IDs.ID('trajectory', '', BaseRef))?.obj;
+ if (!obj)
+ return 0;
+ return (obj as StateObject<Trajectory>).data.frameCount;
+ }
+
+ getPresentConformers() {
+ const obj = this.plugin.state.data.cells.get(IDs.ID('model', '', BaseRef))?.obj;
+ if (!obj)
+ return [];
+ const model = (obj as StateObject<Model>);
+ const modelNum = model.data.modelNum;
+ const sourceData = model.data.sourceData;
+ if (MmcifFormat.is(sourceData)) {
+ const tableSum = sourceData.data.frame.categories['ndb_struct_ntc_step_summary'];
+ const tableStep = sourceData.data.frame.categories['ndb_struct_ntc_step'];
+ if (!tableSum || !tableStep) {
+ console.warn('NtC information not present');
+ return [];
+ }
+
+ const _stepIds = tableSum.getField('step_id');
+ const _assignedNtCs = tableSum.getField('assigned_NtC');
+ const _ids = tableStep.getField('id');
+ const _modelNos = tableStep.getField('PDB_model_number');
+ if (!_stepIds || !_assignedNtCs || !_ids || !_modelNos) {
+ console.warn('Expected fields are not present in NtC categories');
+ return [];
+ }
+
+ const stepIds = _stepIds.toIntArray();
+ const assignedNtCs = _assignedNtCs.toStringArray();
+ const ids = _ids.toIntArray();
+ const modelNos = _modelNos.toIntArray();
+
+ const present = new Array<string>();
+ for (let row = 0; row < stepIds.length; row++) {
+ const idx = ids.indexOf(stepIds[row]);
+ if (modelNos[idx] === modelNum) {
+ const ntc = assignedNtCs[row];
+ if (!present.includes(ntc))
+ present.push(ntc);
+ }
+ }
+
+ present.sort();
+ return present;
+ }
+ return [];
+ }
+
+ has(id: IDs.ID, sub: IDs.Substructure|'' = '', ref = BaseRef) {
+ return !!this.plugin.state.data.cells.get(IDs.ID(id, sub, ref))?.obj?.data;
+ }
+
+ isReady() {
+ return this.has('structure', '', BaseRef);
+ }
+
+ async loadStructure(data: string, type: 'pdb'|'cif', display: Partial<Display>) {
+ // TODO: Remove the currently loaded structure
+
+ const b = (t => 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) }))
+ .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) })
+ // 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
+ await b.commit();
+
+ // Create default visuals
+ const bb = this.plugin.state.data.build();
+ if (display.showNucleic && this.has('structure', 'nucleic')) {
+ bb.to(IDs.ID('structure', 'nucleic', BaseRef))
+ .apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ this.substructureVisuals('cartoon'),
+ { ref: IDs.ID('visual', 'nucleic', BaseRef) }
+ );
+ if (display.showPyramids) {
+ bb.to(IDs.ID('structure', 'nucleic', BaseRef))
+ .apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ this.pyramidsParams(display.conformerColors ?? NtCColors.Conformers, new Map(), false),
+ { ref: IDs.ID('pyramids', 'nucleic', BaseRef) }
+ );
+ }
+ }
+ if (display.showProtein && this.has('structure', 'protein')) {
+ bb.to(IDs.ID('structure', 'protein', BaseRef))
+ .apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ this.substructureVisuals('cartoon'),
+ { ref: IDs.ID('visual', 'protein', BaseRef) }
+ );
+ }
+ if (display.showWater && this.has('structure', 'water')) {
+ bb.to(IDs.ID('structure', 'water', BaseRef))
+ .apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ this.substructureVisuals('ball-and-stick'),
+ { ref: IDs.ID('visual', 'water', BaseRef) }
+ );
+ }
+
+ await bb.commit();
+
+ this.haveMultipleModels = this.getModelCount() > 1;
+
+ const ntcInfo = this.gatherStepInfo();
+ if (!ntcInfo) {
+ this.steps.length = 0;
+ this.stepNames.clear();
+ } else {
+ this.steps = ntcInfo.steps;
+ this.stepNames = ntcInfo.stepNames;
+ }
+ }
+
+ async loadReferenceConformers() {
+ const b = this.plugin.state.data.build().toRoot();
+
+ for (const c in ReferenceConformersPdbs) {
+ const cfmr = ReferenceConformersPdbs[c as keyof typeof ReferenceConformersPdbs];
+ const bRef = rcref(c);
+ const mRef = IDs.ID('model', '', bRef);
+ b.toRoot();
+ b.apply(RawData, { data: cfmr, label: `Reference ${c}` }, { ref: IDs.ID('data', '', bRef) })
+ .apply(StateTransforms.Model.TrajectoryFromPDB, {}, { ref: IDs.ID('trajectory', '', bRef) })
+ .apply(StateTransforms.Model.ModelFromTrajectory, {}, { ref: mRef })
+ .apply(StateTransforms.Model.StructureFromModel, {}, { ref: IDs.ID('structure', '', rcref(c, 'sel')) })
+ .to(mRef)
+ .apply(StateTransforms.Model.StructureFromModel, {}, { ref: IDs.ID('structure', '', rcref(c, 'prev')) })
+ .to(mRef)
+ .apply(StateTransforms.Model.StructureFromModel, {}, { ref: IDs.ID('structure', '', rcref(c, 'next')) });
+ }
+
+ await b.commit();
+ }
+
+ async onDeselected() {
+ this.app.viewerStepDeselected();
+ }
+
+ async onLociSelected(selected: Representation.Loci) {
+ const loci = Loci.normalize(selected.loci, 'two-residues');
+
+ if (loci.kind === 'element-loci') {
+ const stepDesc = Step.describe(loci);
+ if (stepDesc) {
+ const stepName = Step.name(stepDesc, this.haveMultipleModels);
+ this.app.viewerStepSelected(stepName);
+ }
+ }
+ }
+
+ async actionDeselectStep(display: Partial<Display>) {
+ await this.plugin.state.data.build()
+ .delete(IDs.ID('superposition', '', NtCSupSel))
+ .delete(IDs.ID('superposition', '', NtCSupPrev))
+ .delete(IDs.ID('superposition', '', NtCSupNext))
+ .delete(IDs.ID('structure', 'selected-slice', BaseRef))
+ .delete(IDs.ID('structure', 'remainder-slice', BaseRef))
+ .commit();
+
+ await this.toggleSubstructure('nucleic', { showNucleic: !!display.showNucleic });
+
+ this.resetCameraRadius();
+ }
+
+ async actionSelectStep(stepName: string, stepNamePrev: string|undefined, stepNameNext: string|undefined, referenceNtc: string, references: ('sel'|'prev'|'next')[], display: Partial<Display>): Promise<{ rmsd: number }|undefined> {
+ const stepCurrent = this.stepFromName(stepName);
+ if (!stepCurrent)
+ return void 0;
+
+ // Switch to a different model if the selected step is from a different model
+ // This is the first thing we need to do
+ if (stepCurrent.model !== this.currentModelNumber())
+ await this.switchModel({ modelNumber: stepCurrent.model });
+
+ const entireStruCell = this.plugin.state.data.cells.get(IDs.ID('structure', 'nucleic', BaseRef));
+ if (!entireStruCell)
+ return void 0;
+ const stru = entireStruCell.obj!.data!;
+ const struLoci = StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(stru, stru));
+
+ const lociCurrent = Traverse.findStep(
+ stepCurrent.chain,
+ stepCurrent.resNo1,
+ stepCurrent.altId1,
+ struLoci,
+ 'auth'
+ );
+ if (lociCurrent.kind !== 'element-loci')
+ return void 0;
+
+ const current = {
+ step: stepCurrent,
+ loci: lociCurrent,
+ };
+
+ const prev = stepNamePrev ? this.toStepWithStructure(stepNamePrev, struLoci) : undefined;
+ const next = stepNameNext ? this.toStepWithStructure(stepNameNext, struLoci) : undefined;
+
+ const toUnionize = [StructureElement.Loci.toStructure(current.loci)];
+ if (prev)
+ toUnionize.push(StructureElement.Loci.toStructure(prev.loci));
+ if (next)
+ toUnionize.push(StructureElement.Loci.toStructure(next.loci));
+
+ const slice = structureUnion(stru, toUnionize);
+ const stepBundle = StructureElement.Bundle.fromSubStructure(stru, slice);
+
+ const subtracted = structureSubtract(stru, slice);
+ const remainderBundle = StructureElement.Bundle.fromSubStructure(stru, subtracted);
+
+ const b = this.plugin.state.data.build();
+ b.to(entireStruCell)
+ .apply(
+ StateTransforms.Model.StructureSelectionFromBundle,
+ { bundle: stepBundle, label: 'Step' },
+ { ref: IDs.ID('structure', 'selected-slice', BaseRef) }
+ )
+ .apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ this.substructureVisuals('ball-and-stick'),
+ { ref: IDs.ID('visual', 'selected-slice', BaseRef) }
+ )
+ .to(entireStruCell)
+ .apply(
+ StateTransforms.Model.StructureSelectionFromBundle,
+ { bundle: remainderBundle, label: 'Remainder' },
+ { ref: IDs.ID('structure', 'remainder-slice', BaseRef) }
+ );
+
+ // Only show the remainder if the nucleic substructure is shown
+ if (display.showNucleic) {
+ b.to(IDs.ID('structure', 'remainder-slice', BaseRef))
+ .apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ this.substructureVisuals('cartoon'),
+ { ref: IDs.ID('visual', 'remainder-slice', BaseRef) }
+ )
+ .delete(IDs.ID('visual', 'nucleic', BaseRef));
+ }
+
+ const rmsd = this.superposeReferences(b.toRoot(), current, prev, next, referenceNtc, references);
+ if (!rmsd)
+ return void 0;
+
+ await b.commit();
+
+ return { rmsd };
+ }
+
+ async switchModel(display: Partial<Display>) {
+ if (display.modelNumber && display.modelNumber === this.currentModelNumber())
+ return;
+
+ const b = this.plugin.state.data.build()
+ .delete(IDs.ID('superposition', '', NtCSupSel))
+ .delete(IDs.ID('superposition', '', NtCSupPrev))
+ .delete(IDs.ID('superposition', '', NtCSupNext))
+ .to(IDs.ID('model', '', BaseRef))
+ .update(
+ StateTransforms.Model.ModelFromTrajectory,
+ old => ({
+ ...old,
+ modelIndex: display.modelNumber ? display.modelNumber - 1 : 0
+ })
+ );
+
+ await b.commit();
+ }
+
+ superposeReferences<A extends StateObject, T extends StateTransformer>(b: StateBuilder.To<A, T>, current: StepWithStructure, prev: StepWithStructure|undefined, next: StepWithStructure|undefined, referenceNtc: string, references: ('sel'|'prev'|'next')[]) {
+ const ReferenceVisuals = (color: number) => {
+ return {
+ type: { name: 'ball-and-stick', params: { sizeFactor: 0.15, aromaticBonds: false } },
+ colorTheme: { name: 'uniform', params: { value: Color(color) } },
+ };
+ };
+
+ const ntcRefSel = this.ntcRef(current.step, 'sel')!;
+ const ntcRefPrev = prev ? this.ntcRef(prev.step, 'prev') : undefined;
+ const ntcRefNext = next ? this.ntcRef(next?.step, 'next') : undefined;
+
+ b.delete(IDs.ID('superposition', '', NtCSupSel))
+ .delete(IDs.ID('superposition', '', NtCSupPrev))
+ .delete(IDs.ID('superposition', '', NtCSupNext));
+
+ const addReference = (ntcRef: string, superposRef: string, loci: StructureElement.Loci, altId1: string|undefined, altId2: string|undefined, color: number) => {
+ const refStru = this.plugin.state.data.cells.get(IDs.ID('structure', '', ntcRef))!.obj!;
+ const refLoci = StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(refStru.data, refStru.data));
+
+ if (Step.is(loci)) {
+ const { bTransform, rmsd } = this.superpose(refLoci, loci, altId1, altId2);
+ if (isNaN(bTransform[0])) {
+ console.error(`Cannot superpose reference conformer ${ntcRef} onto selection`);
+ return void 0;
+ }
+ b.to(IDs.ID('structure', '', ntcRef))
+ .apply(
+ StateTransforms.Model.TransformStructureConformation,
+ { transform: { name: 'matrix', params: { data: bTransform, transpose: false } } },
+ { ref: IDs.ID('superposition', '', superposRef) }
+ ).apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ ReferenceVisuals(color),
+ { ref: IDs.ID('visual', '', superposRef) }
+ );
+ return rmsd;
+ }
+ };
+
+ const rmsd = addReference(ntcRefSel, NtCSupSel, current.loci, current.step.altId1, current.step.altId2, 0x008000);
+ if (ntcRefPrev) {
+ const { altId1, altId2 } = prev!.step;
+ addReference(ntcRefPrev, NtCSupPrev, prev!.loci, altId1, altId2, 0x0000FF);
+ }
+ if (ntcRefNext) {
+ const { altId1, altId2 } = next!.step;
+ addReference(ntcRefNext, NtCSupNext, next!.loci, altId1, altId2, 0x00FFFF);
+ }
+
+ return rmsd;
+ }
+
+ async toggleSubstructure(sub: IDs.Substructure, display: Partial<Display>) {
+ const show = sub === 'nucleic' ? !!display.showNucleic :
+ sub === 'protein' ? !!display.showProtein : !!display.showWater;
+ const repr = display.representation ?? 'cartoon';
+
+ if (sub === 'nucleic')
+ this.toggleNucleicSubstructure(show, repr);
+ else {
+ if (show) {
+ const b = this.getBuilder('structure', sub);
+ const visuals = this.substructureVisuals(sub === 'water' ? 'ball-and-stick' : repr);
+ if (b) {
+ b.apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ visuals,
+ { ref: IDs.ID('visual', sub, BaseRef) }
+ );
+ await b.commit();
+ }
+ } else {
+ await PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.data, ref: IDs.ID('visual', sub, BaseRef) });
+ this.resetCameraRadius();
+ }
+ }
+ }
+}