diff --git a/src/apps/rednatco/index.tsx b/src/apps/rednatco/index.tsx
index 9216dc3c1984cabfc8764e8be188f101b547690d..560639472edd520d7521e47ad5da2693e98a7d44 100644
--- a/src/apps/rednatco/index.tsx
+++ b/src/apps/rednatco/index.tsx
@@ -181,14 +181,14 @@ 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.step, cmd.prev, cmd.next, this.state.display);
- if (!ret) {
+ const success = await this.viewer.actionSelectStep(cmd.step, cmd.prev, cmd.next, this.state.display);
+ if (!success) {
ReDNATCOMspApi.event(Api.Events.StepSelectedFail());
return;
}
- this.viewer.focusOnSelectedStep();
this.selectedStep = cmd.step;
+ this.viewer.focusOnSelectedStep();
ReDNATCOMspApi.event(Api.Events.StepSelectedOk(this.selectedStep.name));
} else if (cmd.type === 'switch-model') {
diff --git a/src/apps/rednatco/reference-conformers.ts b/src/apps/rednatco/reference-conformers.ts
index 9de0cdcb2dd2a36a4ea24bb924ecf0bdb607ce25..47eeb698076398194929b3752917ba0dbcde55f8 100644
--- a/src/apps/rednatco/reference-conformers.ts
+++ b/src/apps/rednatco/reference-conformers.ts
@@ -1,5 +1,7 @@
/* eslint-disable array-bracket-spacing, no-multi-spaces, indent */
+import {ObjectKeys} from "../../mol-util/type-helpers";
+
export type Ring = 'purine'|'pyrimidine'|'PSU';
export const ReferenceCompounds: Record<string, [string, string]> = {
@@ -432,18 +434,30 @@ export const BaseAtomsKinds: Record<string, Ring> = {
'PSU': 'PSU'
};
+const _BaseAtomKindKeys = ObjectKeys(BaseAtomsKinds);
+function isKnownResidue(compId: string): compId is keyof typeof BaseAtomsKinds {
+ return _BaseAtomKindKeys.includes(compId);
+}
+
+
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[]> = {
+export const BaseAtoms: Record<Ring, 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]];
+export function referenceAtoms(compId: string, order: keyof typeof BackboneAtoms) {
+ if (!isKnownResidue(compId))
+ return [];
+
+ return [
+ ...BackboneAtoms[order],
+ ...BaseAtoms[BaseAtomsKinds[compId]]
+ ];
}
diff --git a/src/apps/rednatco/viewer.ts b/src/apps/rednatco/viewer.ts
index 32007e713e99a8af1c5811c31885bc986d1207ee..8540db32c74cd3f96b45ce793febe8b7f4cf4c5f 100644
--- a/src/apps/rednatco/viewer.ts
+++ b/src/apps/rednatco/viewer.ts
@@ -71,7 +71,7 @@ type StepInfo = {
model: number;
}
-function dinucleotideBackbone(loci: StructureElement.Loci) {
+function superpositionAtomsIndices(loci: StructureElement.Loci) {
const es = loci.elements[0];
const loc = Location.create(loci.structure, es.unit, es.unit.elements[OrderedSet.getAt(es.indices, 0)]);
const len = OrderedSet.size(es.indices);
@@ -98,32 +98,38 @@ function dinucleotideBackbone(loci: StructureElement.Loci) {
};
// Find split between first and second residue
- const resNo1 = StructureProperties.residue.auth_seq_id(loc);
+ const resNo1 = StructureProperties.residue.label_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);
+ const resNo = StructureProperties.residue.label_seq_id(loc);
if (resNo !== resNo1) {
secondIdx = idx;
break;
}
}
- if (secondIdx === -1)
+ if (secondIdx === -1) {
+ console.log('No first/second residue split');
return [];
+ }
// Gather element indices for the first residue
loc.element = es.unit.elements[OrderedSet.getAt(es.indices, 0)];
const compId1 = StructureProperties.atom.label_comp_id(loc);
const atoms1 = RefCfmr.referenceAtoms(compId1.toUpperCase(), 'first');
- if (!gather(atoms1, 0, secondIdx))
+ if (!gather(atoms1, 0, secondIdx)) {
+ console.log('No ref atoms for first');
return [];
+ }
// Gather element indices for the second residue
loc.element = es.unit.elements[OrderedSet.getAt(es.indices, secondIdx)];
const compId2 = StructureProperties.atom.label_comp_id(loc);
const atoms2 = RefCfmr.referenceAtoms(compId2.toUpperCase(), 'second');
- if (!gather(atoms2, secondIdx, len))
+ if (!gather(atoms2, secondIdx, len)) {
+ console.log('No ref atoms for second');
return [];
+ }
return indices;
}
@@ -270,13 +276,6 @@ export class ReDNATCOMspViewer {
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;
@@ -390,8 +389,8 @@ export class ReDNATCOMspViewer {
}
private superpose(reference: StructureElement.Loci, stru: StructureElement.Loci) {
- const refElems = dinucleotideBackbone(reference);
- const struElems = dinucleotideBackbone(stru);
+ const refElems = superpositionAtomsIndices(reference);
+ const struElems = superpositionAtomsIndices(stru);
return Superpose.superposition(
{ elements: refElems, conformation: reference.elements[0].unit.conformation },
@@ -654,7 +653,6 @@ export class ReDNATCOMspViewer {
}
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));
@@ -1004,10 +1002,10 @@ export class ReDNATCOMspViewer {
this.resetCameraRadius();
}
- async actionSelectStep(stepSel: Api.Payloads.StepSelection, prevSel: Api.Payloads.StepSelection|undefined, nextSel: Api.Payloads.StepSelection|undefined, display: Display): Promise<{ rmsd: number }|undefined> {
+ async actionSelectStep(stepSel: Api.Payloads.StepSelection, prevSel: Api.Payloads.StepSelection|undefined, nextSel: Api.Payloads.StepSelection|undefined, display: Display) {
const step = this.stepFromName(stepSel.name);
if (!step)
- return;
+ return false;
// Switch to a different model if the selected step is from a different model
// This is the first thing we need to do
@@ -1016,7 +1014,7 @@ export class ReDNATCOMspViewer {
const entireStruCell = this.plugin.state.data.cells.get(IDs.ID('structure', 'nucleic', BaseRef));
if (!entireStruCell)
- return void 0;
+ return false;
const stru = entireStruCell.obj!.data!;
const struLoci = StructureSelection.toLociWithSourceUnits(StructureSelection.Singletons(stru, stru));
@@ -1027,7 +1025,7 @@ export class ReDNATCOMspViewer {
struLoci, 'auth'
);
if (stepLoci.kind !== 'element-loci')
- return;
+ return false;
const prevLoci = prevSel ? this.toStepLoci(prevSel.name, struLoci) : EmptyLoci;
const nextLoci = nextSel ? this.toStepLoci(nextSel.name, struLoci) : EmptyLoci;
@@ -1083,6 +1081,7 @@ export class ReDNATCOMspViewer {
);
await b.commit();
+ return true;
}
async switchModel(display: Partial<Display>) {