diff --git a/src/apps/rednatco/step.ts b/src/apps/rednatco/step.ts
index a988acfad6ba227bbb428fe59a9a9db5d86905fd..2bc7766179c82150ee2171180bcc15098a2ddfb7 100644
--- a/src/apps/rednatco/step.ts
+++ b/src/apps/rednatco/step.ts
@@ -3,25 +3,44 @@ import { StructureElement, StructureProperties } from '../../mol-model/structure
import { Location } from '../../mol-model/structure/structure/element/location';
export namespace Step {
- export type Description = {
+ export interface Description {
+ name: string;
model: number;
entryId: string;
chain: string;
resNo1: number;
- comp1: string;
+ compId1: string;
altId1?: string;
- insCode1?: string;
+ insCode1: string;
resNo2: number;
- comp2: string;
+ compId2: string;
altId2?: string;
- insCode2?: string;
+ insCode2: string;
};
- function nameResidue(seqId: number, compId: string, altId?: string, insCode?: string) {
- return `${compId}${altId ? `.${altId}` : ''}_${seqId}${insCode ? `.${insCode}` : '' }`;
+ export interface ExtendedDescription extends Description{
+ assignedNtC: string;
+ closestNtC: string;
+ };
+
+ function nameResidue(seqId: number, compId: string, altId: string|undefined, insCode: string) {
+ return `${compId}${altId ? `.${altId}` : ''}_${seqId}${insCode !== '' ? `.${insCode}` : '' }`;
+ }
+
+ function nameStep(
+ entryId: string,
+ modelNum: number, asymId: string,
+ seqId1: number, compId1: string, altId1: string|undefined, insCode1: string,
+ seqId2: number, compId2: string, altId2: string|undefined, insCode2: string,
+ multipleModels: boolean
+ ) {
+ const res1 = nameResidue(seqId1, compId1, altId1, insCode1);
+ const res2 = nameResidue(seqId2, compId2, altId2, insCode2);
+
+ return `${entryId}${multipleModels ? `-m${modelNum}` : ''}_${asymId}_${res1}_${res2}`;
}
- function residueDescription(a: string, b: string): { comp: string, altId?: string, resNo: number, insCode?: string }|undefined {
+ function residueDescription(a: string, b: string): { comp: string, altId?: string, resNo: number, insCode: string }|undefined {
const toksA = a.split('.');
const toksB = b.split('.');
@@ -36,35 +55,37 @@ export namespace Step {
comp: toksA[0],
altId: toksA.length === 2 ? toksA[1] : void 0,
resNo,
- insCode: toksB.length === 2 ? toksB[1] : void 0,
+ insCode: toksB.length === 2 ? toksB[1] : '',
};
}
- export function describe(loci: StructureElement.Loci) {
+ export function describe(loci: StructureElement.Loci, multipleModels: boolean) {
const es = loci.elements[0]; // Ignore multiple selections
const loc = Location.create(loci.structure, es.unit);
loc.element = es.unit.elements[OrderedSet.getAt(es.indices, 0)]; // We're assuming a non-empty set
const description: Description = {
+ name: '',
model: es.unit.model.modelNum,
entryId: loci.structure.model.entryId.toLowerCase(),
chain: StructureProperties.chain.auth_asym_id(loc),
resNo1: StructureProperties.residue.auth_seq_id(loc),
- comp1: StructureProperties.atom.auth_comp_id(loc),
- altId1: StructureProperties.atom.label_alt_id(loc),
+ compId1: StructureProperties.atom.auth_comp_id(loc),
+ altId1: StructureProperties.atom.label_alt_id(loc) === '' ? void 0 : StructureProperties.atom.label_alt_id(loc),
insCode1: StructureProperties.residue.pdbx_PDB_ins_code(loc),
resNo2: -1,
- comp2: '',
+ compId2: '',
altId2: void 0,
- insCode2: void 0,
+ insCode2: '',
};
let found = false;
const len = OrderedSet.size(es.indices);
+ const labelResNo = StructureProperties.residue.label_seq_id(loc);
for (let idx = 1; idx < len; idx++) {
loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
- if (StructureProperties.residue.auth_seq_id(loc) !== description.resNo1) {
+ if (StructureProperties.residue.label_seq_id(loc) !== labelResNo) {
found = true;
break;
}
@@ -74,26 +95,34 @@ export namespace Step {
return void 0;
description.resNo2 = StructureProperties.residue.auth_seq_id(loc);
- description.comp2 = StructureProperties.atom.auth_comp_id(loc);
- description.altId2 = StructureProperties.atom.label_alt_id(loc);
+ description.compId2 = StructureProperties.atom.auth_comp_id(loc);
+ description.altId2 = StructureProperties.atom.label_alt_id(loc) === '' ? void 0 : StructureProperties.atom.label_alt_id(loc);
description.insCode2 = StructureProperties.residue.pdbx_PDB_ins_code(loc);
+ description.name = nameStep(
+ description.entryId,
+ description.model, description.chain,
+ description.resNo1, description.compId1, description.altId1, description.insCode1,
+ description.resNo2, description.compId2, description.altId2, description.insCode2,
+ multipleModels
+ );
return description;
}
export function fromName(name: string) {
const description: Description = {
+ name: '',
model: -1,
entryId: '',
chain: '',
resNo1: -1,
- comp1: '',
+ compId1: '',
altId1: void 0,
- insCode1: void 0,
+ insCode1: '',
resNo2: -1,
- comp2: '',
+ compId2: '',
altId2: void 0,
- insCode2: void 0,
+ insCode2: '',
};
const toks = name.split('_');
@@ -140,13 +169,14 @@ export namespace Step {
}
description.resNo1 = res1.resNo;
- description.comp1 = res1.comp;
+ description.compId1 = res1.comp;
description.altId1 = res1.altId;
description.insCode1 = res1.insCode;
description.resNo2 = res2.resNo;
- description.comp2 = res2.comp;
+ description.compId2 = res2.comp;
description.altId2 = res2.altId;
description.insCode2 = res2.insCode;
+ description.name = name;
return description;
}
@@ -170,11 +200,4 @@ export namespace Step {
return false;
}
-
- export function name(description: Description, multipleModels: boolean) {
- const res1 = nameResidue(description.resNo1, description.comp1, description.altId1, description.insCode1);
- const res2 = nameResidue(description.resNo2, description.comp2, description.altId2, description.insCode2);
-
- return `${description.entryId}${multipleModels ? `-m${description.model}` : ''}_${description.chain}_${res1}_${res2}`;
- }
}
diff --git a/src/apps/rednatco/viewer.ts b/src/apps/rednatco/viewer.ts
index 8540db32c74cd3f96b45ce793febe8b7f4cf4c5f..2edc54ee3cc5651f70479612f8e1159cebbdcac5 100644
--- a/src/apps/rednatco/viewer.ts
+++ b/src/apps/rednatco/viewer.ts
@@ -55,22 +55,6 @@ const NtCSupSel = 'ntc-sup-sel';
const NtCSupNext = 'ntc-sup-next';
const SphereBoundaryHelper = new BoundaryHelper('98');
-type StepInfo = {
- name: string;
- assignedNtC: string;
- closestNtC: string;
- chain: string;
- resNo1: number;
- resNo2: number;
- compId1: string;
- compId2: string;
- altId1?: string;
- altId2?: string;
- insCode1: string;
- insCode2: string;
- model: number;
-}
-
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)]);
@@ -249,7 +233,7 @@ const ReDNATCOLociSelectionProvider = PluginBehavior.create({
export class ReDNATCOMspViewer {
private haveMultipleModels = false;
- private steps: StepInfo[] = [];
+ private steps: Step.ExtendedDescription[] = [];
private stepNames: Map<string, number> = new Map();
private app: ReDNATCOMsp;
@@ -671,12 +655,12 @@ export class ReDNATCOMspViewer {
this.focusOnLoci(focusOn);
}
- gatherStepInfo(): { steps: StepInfo[], stepNames: Map<string, number> }|undefined {
+ gatherStepInfo(): { steps: Step.ExtendedDescription[], 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;
+ const struModel = (obj as StateObject<Model>);
+ const sourceData = struModel.data.sourceData;
if (!MmcifFormat.is(sourceData))
return void 0;
@@ -709,7 +693,7 @@ export class ReDNATCOMspViewer {
const len = _ids.length;
const stepNames = new Map<string, number>();
- const steps = new Array<StepInfo>(len);
+ const steps = new Array<Step.ExtendedDescription>(len);
for (let idx = 0; idx < len; idx++) {
const id = _ids[idx];
@@ -732,6 +716,8 @@ export class ReDNATCOMspViewer {
// We're assuming that steps are ID'd with a contigious, monotonic sequence starting from 1
steps[id - 1] = {
name,
+ model,
+ entryId: struModel.data.entryId,
assignedNtC,
closestNtC,
chain,
@@ -743,7 +729,6 @@ export class ReDNATCOMspViewer {
altId2,
insCode1,
insCode2,
- model
};
stepNames.set(name, id - 1);
break;
@@ -941,11 +926,9 @@ export class ReDNATCOMspViewer {
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);
- }
+ const stepDesc = Step.describe(loci, this.haveMultipleModels);
+ if (stepDesc && this.stepNames.has(stepDesc.name))
+ this.app.viewerStepSelected(stepDesc.name);
}
}