From 7b55ef85e1ef26cc4ab40b4d75034fa2eee5b38c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Mal=C3=BD?= <michal.maly@ibt.cas.cz>
Date: Tue, 15 Mar 2022 19:10:30 +0100
Subject: [PATCH] DNATCO extension: Fix missing Confal pyramids in some
structures
---
.../dnatco/confal-pyramids/property.ts | 4 +-
src/extensions/dnatco/confal-pyramids/util.ts | 42 +++++++++----------
2 files changed, 20 insertions(+), 26 deletions(-)
diff --git a/src/extensions/dnatco/confal-pyramids/property.ts b/src/extensions/dnatco/confal-pyramids/property.ts
index 2fe28220e..4417ebbc1 100644
--- a/src/extensions/dnatco/confal-pyramids/property.ts
+++ b/src/extensions/dnatco/confal-pyramids/property.ts
@@ -123,10 +123,8 @@ function createPyramidsFromCif(model: Model,
for (let i = 0; i < _rowCount; i++) {
const model_num = PDB_model_number.value(i);
- if (model_num !== model.modelNum) {
+ if (model_num !== model.modelNum)
hasMultipleModels = true;
- continue; // We are only interested in data for the current model
- }
const { _NtC, _confal_score } = getNtCAndConfalScore(id.value(i), i, stepsSummary);
diff --git a/src/extensions/dnatco/confal-pyramids/util.ts b/src/extensions/dnatco/confal-pyramids/util.ts
index e84f84efe..467734af4 100644
--- a/src/extensions/dnatco/confal-pyramids/util.ts
+++ b/src/extensions/dnatco/confal-pyramids/util.ts
@@ -7,7 +7,7 @@
import { ConfalPyramidsProvider } from './property';
import { ConfalPyramidsTypes as CPT } from './types';
-import { OrderedSet, Segmentation } from '../../../mol-data/int';
+import { Segmentation } from '../../../mol-data/int';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, StructureProperties, Unit } from '../../../mol-model/structure';
@@ -63,15 +63,12 @@ export namespace ConfalPyramidsUtil {
return prop.data.hasMultipleModels;
}
- function getPossibleAltIdsIndices(eIFirst: ElementIndex, eILast: ElementIndex, structure: Structure, unit: Unit.Atomic): string[] {
- const loc = StructureElement.Location.create(structure, unit, -1 as ElementIndex);
-
- const uIFirst = OrderedSet.indexOf(unit.elements, eIFirst);
- const uILast = OrderedSet.indexOf(unit.elements, eILast);
-
+ function getPossibleAltIds(residue: Residue, structure: Structure, unit: Unit.Atomic): string[] {
const possibleAltIds: string[] = [];
- for (let uI = uIFirst; uI <= uILast; uI++) {
- loc.element = unit.elements[uI];
+
+ const loc = StructureElement.Location.create(structure, unit, -1 as ElementIndex);
+ for (let rI = residue.start; rI <= residue.end - 1; rI++) {
+ loc.element = unit.elements[rI];
const altId = StructureProperties.atom.label_alt_id(loc);
if (altId !== '' && !possibleAltIds.includes(altId)) possibleAltIds.push(altId);
}
@@ -79,10 +76,6 @@ export namespace ConfalPyramidsUtil {
return possibleAltIds;
}
- function getPossibleAltIdsResidue(residue: Residue, structure: Structure, unit: Unit.Atomic): string[] {
- return getPossibleAltIdsIndices(unit.elements[residue.start], unit.elements[residue.end - 1], structure, unit);
- }
-
class Utility {
protected getPyramidByName(name: string): { pyramid: CPT.Pyramid | undefined, index: number } {
const index = this.data.names.get(name);
@@ -122,19 +115,22 @@ export namespace ConfalPyramidsUtil {
export class UnitWalker extends Utility {
private getAtomIndices(names: string[], residue: Residue): ElementIndex[] {
- let rI = residue.start;
- const rILast = residue.end - 1;
const indices: ElementIndex[] = [];
- for (; rI !== rILast; rI++) {
- const eI = this.unit.elements[rI];
- const loc = StructureElement.Location.create(this.structure, this.unit, eI);
+ const loc = StructureElement.Location.create(this.structure, this.unit, -1 as ElementIndex);
+ for (let rI = residue.start; rI <= residue.end - 1; rI++) {
+ loc.element = this.unit.elements[rI];
const thisName = StructureProperties.atom.label_atom_id(loc);
- if (names.includes(thisName)) indices.push(eI);
+ if (names.includes(thisName)) indices.push(loc.element);
}
- if (indices.length === 0)
- throw new Error(`Element ${name} not found on residue ${residue.index}`);
+ if (indices.length === 0) {
+ let namesStr = '';
+ for (const n of names)
+ namesStr += `${n} `;
+
+ throw new Error(`Element [${namesStr}] not found on residue ${residue.index}`);
+ }
return indices;
}
@@ -257,12 +253,12 @@ export namespace ConfalPyramidsUtil {
}
private step(residue: Residue): { firstAtoms: FirstResidueAtoms[], secondAtoms: SecondResidueAtoms[] } {
- const firstPossibleAltIds = getPossibleAltIdsResidue(residue, this.structure, this.unit);
+ const firstPossibleAltIds = getPossibleAltIds(residue, this.structure, this.unit);
const firstAtoms = this.processFirstResidue(residue, firstPossibleAltIds);
residue = this.residueIt.move();
- const secondPossibleAltIds = getPossibleAltIdsResidue(residue, this.structure, this.unit);
+ const secondPossibleAltIds = getPossibleAltIds(residue, this.structure, this.unit);
const secondAtoms = this.processSecondResidue(residue, secondPossibleAltIds);
return { firstAtoms, secondAtoms };
--
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