diff --git a/src/apps/rednatco/api.ts b/src/apps/rednatco/api.ts
index 1010c70981aa32435d3a3529e7fcb3d70dc1bec5..073937f047dab5169e034a1045ddad216d98f5e3 100644
--- a/src/apps/rednatco/api.ts
+++ b/src/apps/rednatco/api.ts
@@ -1,6 +1,19 @@
import { Filters } from './filters';
export namespace ReDNATCOMspApi {
+ export namespace Payloads {
+ export type StepSelection = {
+ name: string;
+ reference?: {
+ NtC: string,
+ color: number,
+ };
+ }
+ function StepSelection(name: string, reference?: StepSelection['reference']): StepSelection {
+ return { name, reference };
+ }
+ }
+
export namespace Commands {
export type Type = 'deselect-step'|'filter'|'redraw'|'select-step'|'switch-model';
@@ -19,21 +32,12 @@ export namespace ReDNATCOMspApi {
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')[],
- };
+ step: Payloads.StepSelection
+ prev?: Payloads.StepSelection;
+ next?: Payloads.StepSelection
+ }
+ export function SelectStep(step: Payloads.StepSelection, prev: Payloads.StepSelection|undefined, next: Payloads.StepSelection|undefined): SelectStep {
+ return { type: 'select-step', step, prev, next };
}
export type SwitchModel = { type: 'switch-model', model: number };
@@ -71,9 +75,9 @@ export namespace ReDNATCOMspApi {
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 type StepSelected = { type: 'step-selected', success: boolean, name: string }
+ export function StepSelectedOk(name: string): StepSelected {
+ return { type: 'step-selected', success: true, name };
}
export function StepSelectedFail(): StepSelected {
return { type: 'step-selected', success: false, name: '' };
@@ -105,9 +109,9 @@ export namespace ReDNATCOMspApi {
return { type: 'current-model-number', num };
}
- 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 SelectedStep = { type: 'selected-step', selected?: Payloads.StepSelection }
+ export function SelectedStep(selected?: Payloads.StepSelection): SelectedStep {
+ return { type: 'selected-step', selected };
}
}
export type Response = Queries.CurrentFilter|Queries.CurrentModelNumber|Queries.SelectedStep;
diff --git a/src/apps/rednatco/index.tsx b/src/apps/rednatco/index.tsx
index 37342bbd618a181a8d252cc4ffbe06a72f5a391b..9216dc3c1984cabfc8764e8be188f101b547690d 100644
--- a/src/apps/rednatco/index.tsx
+++ b/src/apps/rednatco/index.tsx
@@ -9,6 +9,7 @@ import { ColorPicker } from './color-picker';
import { CollapsibleVertical, PushButton, ToggleButton } from './controls';
import { luminance } from './util';
import { Color } from '../../mol-util/color';
+import { assertUnreachable } from '../../mol-util/type-helpers';
import './index.html';
const ConformersByClass = {
@@ -77,7 +78,7 @@ 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: { name: string, rmsd?: number }|undefined;
+ private selectedStep: Api.Payloads.StepSelection|undefined = undefined;
constructor(props: ReDNATCOMsp.Props) {
super(props);
@@ -148,19 +149,18 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
this.setState({ ...this.state, display });
}
- apiQuery(type: Api.Queries.Type): Api.Response {
+ apiQuery(type: Api.Queries.Type) {
if (type === 'current-filter') {
return Api.Queries.CurrentFilter(this.currentFilter);
} else if (type === 'current-model-number') {
return Api.Queries.CurrentModelNumber(this.viewer!.currentModelNumber());
} else if (type === 'selected-step') {
if (this.selectedStep)
- return Api.Queries.SelectedStep(this.selectedStep.name, this.selectedStep.rmsd);
- return Api.Queries.SelectedStep('');
+ return Api.Queries.SelectedStep(this.selectedStep);
+ return Api.Queries.SelectedStep();
}
- // TODO: This cannot happen - figure out how to assert on this
- return Api.Queries.SelectedStep('');
+ assertUnreachable(type);
}
async command(cmd: Api.Command) {
@@ -181,16 +181,16 @@ export class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
this.currentFilter = cmd.filter;
ReDNATCOMspApi.event(Api.Events.FilterApplied());
} 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);
+ const ret = await this.viewer.actionSelectStep(cmd.step, cmd.prev, cmd.next, this.state.display);
if (!ret) {
ReDNATCOMspApi.event(Api.Events.StepSelectedFail());
return;
}
this.viewer.focusOnSelectedStep();
- this.selectedStep = { name: cmd.stepName, rmsd: ret.rmsd };
+ this.selectedStep = cmd.step;
- ReDNATCOMspApi.event(Api.Events.StepSelectedOk(this.selectedStep.name, this.selectedStep.rmsd));
+ ReDNATCOMspApi.event(Api.Events.StepSelectedOk(this.selectedStep.name));
} else if (cmd.type === 'switch-model') {
if (cmd.model < 1 || cmd.model > this.viewer.getModelCount())
return;
diff --git a/src/apps/rednatco/reference-conformers.ts b/src/apps/rednatco/reference-conformers.ts
index 32505c6c31665c77bfc5ddc94f12a261a0c422fc..9de0cdcb2dd2a36a4ea24bb924ecf0bdb607ce25 100644
--- a/src/apps/rednatco/reference-conformers.ts
+++ b/src/apps/rednatco/reference-conformers.ts
@@ -1,6 +1,6 @@
/* eslint-disable array-bracket-spacing, no-multi-spaces, indent */
-export type Ring = 'purine'|'pyrimidine';
+export type Ring = 'purine'|'pyrimidine'|'PSU';
export const ReferenceCompounds: Record<string, [string, string]> = {
AA00: [ 'A', 'G'],
@@ -102,7 +102,7 @@ export const ReferenceCompounds: Record<string, [string, string]> = {
};
export type ReferenceCompounds = typeof ReferenceCompounds;
-export const CompoundRings: Record<string, Ring> = {
+export const BaseAtomsKinds: Record<string, Ring> = {
'0AD': 'purine',
'0AV': 'purine',
'0SP': 'purine',
@@ -427,14 +427,23 @@ export const CompoundRings: Record<string, Ring> = {
'U': 'pyrimidine',
'UMP': 'pyrimidine',
'2DT': 'pyrimidine',
- 'CFZ': 'pyrimidine'
+ 'CFZ': 'pyrimidine',
+
+ 'PSU': 'PSU'
};
-export type CompoundRings = typeof CompoundRings;
export const BackboneAtoms = {
first: ["C5'", "C4'", "O4'", "C3'", "O3'", "C1'"],
/* eslint-disable @typescript-eslint/quotes */
second: ["P", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C1'"],
+};
+
+export const BaseAtoms: Record<keyof typeof BaseAtomsKinds, string[]> = {
purine: ['N9', 'C4'],
pyrimidine: ['N1', 'C2'],
+ PSU: ['C5', 'C4'],
};
+
+export function referenceAtoms(compId: keyof typeof BaseAtomsKinds, order: 'first'|'second') {
+ return [...BackboneAtoms[order], ...BaseAtoms[compId]];
+}
diff --git a/src/apps/rednatco/traverse.ts b/src/apps/rednatco/traverse.ts
index 913b679694f8c8affc7d5a751c056ca9e0aa3eb3..547a81d758deed809eba5d53e4d5b2f27c99e7c5 100644
--- a/src/apps/rednatco/traverse.ts
+++ b/src/apps/rednatco/traverse.ts
@@ -1,7 +1,8 @@
import { Segmentation } from '../../mol-data/int';
import { OrderedSet } from '../../mol-data/int/ordered-set';
-import { EmptyLoci, Loci } from '../../mol-model/loci';
+import { EmptyLoci } from '../../mol-model/loci';
import { ResidueIndex, Structure, StructureElement, StructureProperties, Unit } from '../../mol-model/structure';
+import { structureUnion } from '../../mol-model/structure/query/utils/structure-set';
import { Location } from '../../mol-model/structure/structure/element/location';
export namespace Traverse {
@@ -20,9 +21,12 @@ export namespace Traverse {
return altIds;
}
- export function findResidue(asymId: string, seqId: number, altId: string|undefined, loci: StructureElement.Loci, source: 'label'|'auth') {
+ // 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') {
+ _loc.structure = loci.structure;
for (const e of loci.elements) {
- const loc = Location.create(loci.structure, e.unit);
+ _loc.unit = e.unit;
const getAsymId = source === 'label' ? StructureProperties.chain.label_asym_id : StructureProperties.chain.auth_asym_id;
const getSeqId = source === 'label' ? StructureProperties.residue.label_seq_id : StructureProperties.residue.auth_seq_id;
@@ -34,18 +38,22 @@ export namespace Traverse {
const elemIndex = (idx: number) => OrderedSet.getAt(e.unit.elements, idx);
while (chainIt.hasNext) {
const chain = chainIt.move();
- loc.element = elemIndex(chain.start);
- const _asymId = getAsymId(loc);
+ _loc.element = elemIndex(chain.start);
+ const _asymId = getAsymId(_loc);
if (_asymId !== asymId)
continue; // Wrong chain, skip it
residueIt.setSegment(chain);
while (residueIt.hasNext) {
const residue = residueIt.move();
- loc.element = elemIndex(residue.start);
+ _loc.element = elemIndex(residue.start);
- const _seqId = getSeqId(loc);
+ const _seqId = getSeqId(_loc);
if (_seqId === seqId) {
+ const _insCode = StructureProperties.residue.pdbx_PDB_ins_code(_loc);
+ if (_insCode !== insCode)
+ continue;
+
if (altId) {
const _altIds = residueAltIds(loci.structure, e.unit, residue);
if (!_altIds.includes(altId))
@@ -66,36 +74,21 @@ 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];
- const loc = Location.create(cursor.structure, e.unit);
-
- loc.element = e.unit.elements[OrderedSet.getAt(e.indices, 0)];
- const asymId = StructureProperties.chain.label_asym_id(loc);
- const seqId = StructureProperties.residue.label_seq_id(loc);
-
- const from = 0 as StructureElement.UnitIndex;
- const to = entireUnit.elements.length as StructureElement.UnitIndex;
-
- const loci = findResidue(
- asymId,
- seqId + shift,
- altId,
- StructureElement.Loci(cursor.structure, [{ unit: entireUnit, indices: OrderedSet.ofBounds(from, to) }]),
- 'label'
- );
- if (!Loci.isEmpty(loci))
- return loci;
- }
- return EmptyLoci;
+ 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'
+ ) {
+ const first = findResidue(asymId, seqId1, altId1, insCode1, loci, source);
+ if (first.kind === 'empty-loci')
+ return EmptyLoci;
+
+ const second = findResidue(asymId, seqId2, altId2, insCode2, loci, source);
+ if (second.kind === 'empty-loci')
+ return EmptyLoci;
+
+ const union = structureUnion(loci.structure, [StructureElement.Loci.toStructure(first), StructureElement.Loci.toStructure(second)]);
+ return Structure.toStructureElementLoci(union);
}
}
diff --git a/src/apps/rednatco/viewer.ts b/src/apps/rednatco/viewer.ts
index c54638ddf2b211eeefe05d8319605019079eff95..32007e713e99a8af1c5811c31885bc986d1207ee 100644
--- a/src/apps/rednatco/viewer.ts
+++ b/src/apps/rednatco/viewer.ts
@@ -1,5 +1,6 @@
import * as IDs from './idents';
import * as RefCfmr from './reference-conformers';
+import { ReDNATCOMspApi as Api } from './api';
import { ReDNATCOMsp, Display, VisualRepresentations } from './index';
import { NtCColors } from './colors';
import { Filters } from './filters';
@@ -57,39 +58,32 @@ const SphereBoundaryHelper = new BoundaryHelper('98');
type StepInfo = {
name: string;
assignedNtC: string;
- closestNtC: string; // Fallback for cases where assignedNtC is NANT
+ closestNtC: string;
chain: string;
resNo1: number;
resNo2: number;
+ compId1: string;
+ compId2: string;
altId1?: string;
altId2?: string;
+ insCode1: string;
+ insCode2: string;
model: number;
}
-type StepWithStructure = {
- step: StepInfo;
- loci: StructureElement.Loci;
-}
-
-function dinucleotideBackbone(loci: StructureElement.Loci, altId1?: string, altId2?: string) {
+function dinucleotideBackbone(loci: StructureElement.Loci) {
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) => {
+ const gather = (atoms: string[], start: number, end: number) => {
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;
}
@@ -117,23 +111,18 @@ function dinucleotideBackbone(loci: StructureElement.Loci, altId1?: string, altI
if (secondIdx === -1)
return [];
- // Gather ElementIndices for backbone atoms of the first residue
+ // Gather element indices for 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))
+ const compId1 = StructureProperties.atom.label_comp_id(loc);
+ const atoms1 = RefCfmr.referenceAtoms(compId1.toUpperCase(), 'first');
+ if (!gather(atoms1, 0, secondIdx))
return [];
+ // Gather element indices for the second residue
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))
+ const compId2 = StructureProperties.atom.label_comp_id(loc);
+ const atoms2 = RefCfmr.referenceAtoms(compId2.toUpperCase(), 'second');
+ if (!gather(atoms2, secondIdx, len))
return [];
return indices;
@@ -307,8 +296,8 @@ export class ReDNATCOMspViewer {
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 ntcRef(ntc: string, where: 'sel'|'prev'|'next') {
+ return rcref(ntc, where);
}
private pyramidsParams(colors: NtCColors.Conformers, visible: Map<string, boolean>, transparent: boolean) {
@@ -400,9 +389,9 @@ export class ReDNATCOMspViewer {
}
}
- private superpose(reference: StructureElement.Loci, stru: StructureElement.Loci, altId1?: string, altId2?: string) {
+ private superpose(reference: StructureElement.Loci, stru: StructureElement.Loci) {
const refElems = dinucleotideBackbone(reference);
- const struElems = dinucleotideBackbone(stru, altId1, altId2);
+ const struElems = dinucleotideBackbone(stru);
return Superpose.superposition(
{ elements: refElems, conformation: reference.elements[0].unit.conformation },
@@ -439,22 +428,18 @@ export class ReDNATCOMspViewer {
}
}
- private toStepWithStructure(name: string, struLoci: StructureElement.Loci): StepWithStructure|undefined {
+ private toStepLoci(name: string, struLoci: StructureElement.Loci) {
const step = this.stepFromName(name);
if (!step)
- return void 0;
+ return EmptyLoci;
- const loci = Traverse.findStep(
+ return Traverse.findStep(
step.chain,
- step.resNo1,
- step.altId1,
+ step.resNo1, step.altId1, step.insCode1,
+ step.resNo2, step.altId2, step.insCode2,
struLoci,
'auth'
);
- if (loci.kind === 'element-loci')
- return { step, loci };
-
- return void 0;
}
private waterVisuals(color: Color) {
@@ -704,51 +689,47 @@ export class ReDNATCOMspViewer {
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) {
+ const _ids = tableStep.getField('id')?.toIntArray();
+ const _names = tableStep.getField('name')?.toStringArray();
+ const _chains = tableStep.getField('auth_asym_id_1')?.toStringArray();
+ const _authSeqId1 = tableStep.getField('auth_seq_id_1')?.toIntArray();
+ const _authSeqId2 = tableStep.getField('auth_seq_id_2')?.toIntArray();
+ const _compId1 = tableStep.getField('label_comp_id_1')?.toStringArray();
+ const _compId2 = tableStep.getField('label_comp_id_2')?.toStringArray();
+ const _labelAltId1 = tableStep.getField('label_alt_id_1')?.toStringArray();
+ const _labelAltId2 = tableStep.getField('label_alt_id_2')?.toStringArray();
+ const _PDBinsCode1 = tableStep.getField('PDB_ins_code_1')?.toStringArray();
+ const _PDBinsCode2 = tableStep.getField('PDB_ins_code_2')?.toStringArray();
+ const _stepIds = tableSum.getField('step_id')?.toIntArray();
+ const _assignedNtCs = tableSum.getField('assigned_NtC')?.toStringArray();
+ const _closestNtCs = tableSum.getField('closest_NtC')?.toStringArray();
+ const _models = tableStep.getField('PDB_model_number')?.toIntArray();
+ if (!_ids || !_names || !_chains || !_stepIds || !_assignedNtCs || !_closestNtCs || !_labelAltId1 || !_labelAltId2 || !_authSeqId1 || !_authSeqId2 || !_compId1 || !_compId2 || !_PDBinsCode1 || !_PDBinsCode2 || !_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 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];
+ 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];
+ 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 compId1 = _compId1[jdx];
+ const compId2 = _compId2[jdx];
+ const altId1 = _labelAltId1[jdx] === '' ? void 0 : _labelAltId1[jdx];
+ const altId2 = _labelAltId2[jdx] === '' ? void 0 : _labelAltId2[jdx];
+ const insCode1 = _PDBinsCode1[jdx];
+ const insCode2 = _PDBinsCode2[jdx];
+ const model = _models[jdx];
// We're assuming that steps are ID'd with a contigious, monotonic sequence starting from 1
steps[id - 1] = {
@@ -758,8 +739,12 @@ export class ReDNATCOMspViewer {
chain,
resNo1,
resNo2,
+ compId1,
+ compId2,
altId1,
altId2,
+ insCode1,
+ insCode2,
model
};
stepNames.set(name, id - 1);
@@ -1019,15 +1004,15 @@ export class ReDNATCOMspViewer {
this.resetCameraRadius();
}
- async actionSelectStep(stepName: string, stepNamePrev: string|undefined, stepNameNext: string|undefined, referenceNtc: string, references: ('sel'|'prev'|'next')[], display: Display): Promise<{ rmsd: number }|undefined> {
- const stepCurrent = this.stepFromName(stepName);
- if (!stepCurrent)
- return void 0;
+ async actionSelectStep(stepSel: Api.Payloads.StepSelection, prevSel: Api.Payloads.StepSelection|undefined, nextSel: Api.Payloads.StepSelection|undefined, display: Display): Promise<{ rmsd: number }|undefined> {
+ const step = this.stepFromName(stepSel.name);
+ if (!step)
+ return;
// 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 });
+ if (step.model !== this.currentModelNumber())
+ await this.switchModel({ modelNumber: step.model });
const entireStruCell = this.plugin.state.data.cells.get(IDs.ID('structure', 'nucleic', BaseRef));
if (!entireStruCell)
@@ -1035,29 +1020,23 @@ export class ReDNATCOMspViewer {
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'
+ const stepLoci = Traverse.findStep(
+ step.chain,
+ step.resNo1, step.altId1, step.insCode1,
+ step.resNo2, step.altId2, step.insCode2,
+ struLoci, 'auth'
);
- if (lociCurrent.kind !== 'element-loci')
- return void 0;
-
- const current = {
- step: stepCurrent,
- loci: lociCurrent,
- };
+ if (stepLoci.kind !== 'element-loci')
+ return;
- const prev = stepNamePrev ? this.toStepWithStructure(stepNamePrev, struLoci) : undefined;
- const next = stepNameNext ? this.toStepWithStructure(stepNameNext, struLoci) : undefined;
+ const prevLoci = prevSel ? this.toStepLoci(prevSel.name, struLoci) : EmptyLoci;
+ const nextLoci = nextSel ? this.toStepLoci(nextSel.name, struLoci) : EmptyLoci;
- 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 toUnionize = [stepLoci.structure];
+ if (prevLoci.kind !== 'empty-loci')
+ toUnionize.push(prevLoci.structure);
+ if (nextLoci.kind !== 'empty-loci')
+ toUnionize.push(nextLoci.structure);
const slice = structureUnion(stru, toUnionize);
const stepBundle = StructureElement.Bundle.fromSubStructure(stru, slice);
@@ -1096,13 +1075,14 @@ export class ReDNATCOMspViewer {
.delete(IDs.ID('visual', 'nucleic', BaseRef));
}
- const rmsd = this.superposeReferences(b.toRoot(), current, prev, next, referenceNtc, references);
- if (!rmsd)
- return void 0;
+ this.superposeReferences(
+ b.toRoot(),
+ stepSel.reference ? { loci: stepLoci, reference: stepSel.reference } : void 0,
+ prevSel?.reference && prevLoci.kind === 'element-loci' ? { loci: prevLoci, reference: prevSel.reference } : void 0,
+ nextSel?.reference && nextLoci.kind === 'element-loci' ? { loci: nextLoci, reference: nextSel.reference } : void 0
+ );
await b.commit();
-
- return { rmsd };
}
async switchModel(display: Partial<Display>) {
@@ -1125,7 +1105,12 @@ export class ReDNATCOMspViewer {
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')[]) {
+ superposeReferences<A extends StateObject, T extends StateTransformer>(
+ b: StateBuilder.To<A, T>,
+ step?: { loci: StructureElement.Loci, reference: Api.Payloads.StepSelection['reference'] },
+ prev?: { loci: StructureElement.Loci, reference: Api.Payloads.StepSelection['reference'] },
+ next?: { loci: StructureElement.Loci, reference: Api.Payloads.StepSelection['reference'] }
+ ) {
const ReferenceVisuals = (color: number) => {
return {
type: { name: 'ball-and-stick', params: { sizeFactor: 0.15, aromaticBonds: false } },
@@ -1133,49 +1118,43 @@ export class ReDNATCOMspViewer {
};
};
- 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 addReference = (ntcRef: string, superposRef: string, stepLoci: StructureElement.Loci, 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 { bTransform } = this.superpose(refLoci, stepLoci);
+ 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) }
+ );
};
- 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 (step?.reference) {
+ const ref = this.ntcRef(step.reference.NtC, 'sel');
+ addReference(ref, NtCSupSel, step.loci, step.reference.color);
}
- if (ntcRefNext) {
- const { altId1, altId2 } = next!.step;
- addReference(ntcRefNext, NtCSupNext, next!.loci, altId1, altId2, 0x00FFFF);
+ if (prev?.reference) {
+ const ref = this.ntcRef(prev.reference.NtC, 'prev');
+ addReference(ref, NtCSupPrev, prev.loci, prev.reference.color);
+ }
+ if (next?.reference) {
+ const ref = this.ntcRef(next?.reference.NtC, 'next');
+ addReference(ref, NtCSupNext, next.loci, next.reference.color);
}
-
- return rmsd;
}
async toggleSubstructure(sub: IDs.Substructure, display: Display) {