From 4b323a670fccbb352cbb595436c69602e91913f2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Mal=C3=BD?= <michal.maly@ibt.cas.cz>
Date: Tue, 4 Aug 2020 11:23:28 +0200
Subject: [PATCH] Allow interactive selection of two consecutive residues
---
src/mol-model/loci.ts | 9 +++++++--
src/mol-model/structure/structure/element/loci.ts | 12 ++++++++----
src/mol-plugin-ui/structure/focus.tsx | 15 +++++++++++----
.../selection/structure-focus-representation.ts | 2 +-
.../behavior/dynamic/volume-streaming/behavior.ts | 2 +-
src/mol-theme/label.ts | 2 +-
6 files changed, 29 insertions(+), 13 deletions(-)
diff --git a/src/mol-model/loci.ts b/src/mol-model/loci.ts
index 5e2b27773..f6b55d333 100644
--- a/src/mol-model/loci.ts
+++ b/src/mol-model/loci.ts
@@ -222,7 +222,12 @@ namespace Loci {
'element': (loci: Loci) => loci,
'residue': (loci: Loci) => {
return StructureElement.Loci.is(loci)
- ? StructureElement.Loci.extendToWholeResidues(loci, true)
+ ? StructureElement.Loci.extendToWholeResidues(loci, 1, true)
+ : loci;
+ },
+ 'two-residues': (loci: Loci) => {
+ return StructureElement.Loci.is(loci)
+ ? StructureElement.Loci.extendToWholeResidues(loci, 2, true)
: loci;
},
'chain': (loci: Loci) => {
@@ -261,7 +266,7 @@ namespace Loci {
},
'residueInstances': (loci: Loci) => {
return StructureElement.Loci.is(loci)
- ? StructureElement.Loci.extendToAllInstances(StructureElement.Loci.extendToWholeResidues(loci, true))
+ ? StructureElement.Loci.extendToAllInstances(StructureElement.Loci.extendToWholeResidues(loci, 1, true))
: loci;
},
'chainInstances': (loci: Loci) => {
diff --git a/src/mol-model/structure/structure/element/loci.ts b/src/mol-model/structure/structure/element/loci.ts
index 9fefd8d8f..455d0a3bd 100644
--- a/src/mol-model/structure/structure/element/loci.ts
+++ b/src/mol-model/structure/structure/element/loci.ts
@@ -124,7 +124,7 @@ export namespace Loci {
export function firstResidue(loci: Loci): Loci {
if (isEmpty(loci)) return loci;
- return extendToWholeResidues(firstElement(loci));
+ return extendToWholeResidues(firstElement(loci), 1);
}
export function firstChain(loci: Loci): Loci {
@@ -281,7 +281,7 @@ export namespace Loci {
}
}
- export function extendToWholeResidues(loci: Loci, restrictToConformation?: boolean): Loci {
+ export function extendToWholeResidues(loci: Loci, count: number, restrictToConformation?: boolean): Loci {
const elements: Loci['elements'][0][] = [];
const residueAltIds = new Set<string>();
@@ -305,16 +305,20 @@ export namespace Loci {
residueAltIds.clear();
const eI = unitElements[OrderedSet.getAt(indices, i)];
const rI = residueIndex[eI];
+ const rIEnd = rI + count >= residueIndex.length ? residueIndex.length - 1 : rI + count;
residueAltIds.add(label_alt_id.value(eI));
i++;
while (i < len) {
const eI = unitElements[OrderedSet.getAt(indices, i)];
- if (residueIndex[eI] !== rI) break;
+ const _rI = residueIndex[eI];
+ if (_rI < rI || _rI > rIEnd) {
+ break;
+ }
residueAltIds.add(label_alt_id.value(eI));
i++;
}
const hasSharedAltId = residueAltIds.has('');
- for (let j = residueOffsets[rI], _j = residueOffsets[rI + 1]; j < _j; j++) {
+ for (let j = residueOffsets[rI], _j = residueOffsets[rIEnd]; j < _j; j++) {
const idx = OrderedSet.indexOf(unitElements, j);
if (idx >= 0) {
const altId = label_alt_id.value(j);
diff --git a/src/mol-plugin-ui/structure/focus.tsx b/src/mol-plugin-ui/structure/focus.tsx
index f64af65c6..db4c8b7f4 100644
--- a/src/mol-plugin-ui/structure/focus.tsx
+++ b/src/mol-plugin-ui/structure/focus.tsx
@@ -24,14 +24,21 @@ interface StructureFocusControlsState {
showAction: boolean
}
-function addSymmetryGroupEntries(entries: Map<string, FocusEntry[]>, location: StructureElement.Location, unitSymmetryGroup: Unit.SymmetryGroup, granularity: 'residue' | 'chain') {
+function addSymmetryGroupEntries(entries: Map<string, FocusEntry[]>, location: StructureElement.Location, unitSymmetryGroup: Unit.SymmetryGroup, granularity: 'residue' | 'two-residues' | 'chain') {
const idx = SortedArray.indexOf(location.unit.elements, location.element) as UnitIndex;
const base = StructureElement.Loci(location.structure, [
{ unit: location.unit, indices: OrderedSet.ofSingleton(idx) }
]);
- const extended = granularity === 'residue'
- ? StructureElement.Loci.extendToWholeResidues(base)
- : StructureElement.Loci.extendToWholeChains(base);
+ const extended = (() => {
+ switch (granularity) {
+ case 'residue':
+ return StructureElement.Loci.extendToWholeResidues(base, 1);
+ case 'two-residues':
+ return StructureElement.Loci.extendToWholeResidues(base, 2);
+ default:
+ return StructureElement.Loci.extendToWholeChains(base);
+ }
+ })();
const name = StructureProperties.entity.pdbx_description(location).join(', ');
for (const u of unitSymmetryGroup.units) {
diff --git a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts b/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
index 344b5b1bb..eda773be8 100644
--- a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
+++ b/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
@@ -160,7 +160,7 @@ class StructureFocusRepresentationBehavior extends PluginBehavior.WithSubscriber
this.currentSource = sourceLoci;
const loci = StructureElement.Loci.remap(sourceLoci, parent.obj!.data);
- const residueLoci = StructureElement.Loci.extendToWholeResidues(loci);
+ const residueLoci = StructureElement.Loci.extendToWholeResidues(loci, 1);
const residueBundle = StructureElement.Bundle.fromLoci(residueLoci);
const target = StructureElement.Bundle.toExpression(residueBundle);
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
index 1050783fa..deaff2473 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
@@ -340,7 +340,7 @@ export namespace VolumeStreaming {
const transform = GlobalModelTransformInfo.get(root.obj?.data.models[0]!);
if (transform) Mat4.invert(this._invTransform, transform);
- const extendedLoci = StructureElement.Loci.extendToWholeResidues(loci);
+ const extendedLoci = StructureElement.Loci.extendToWholeResidues(loci, 1);
const box = StructureElement.Loci.getBoundary(extendedLoci, transform && !Number.isNaN(this._invTransform[0]) ? this._invTransform : void 0).box;
if (StructureElement.Loci.size(extendedLoci) === 1) {
diff --git a/src/mol-theme/label.ts b/src/mol-theme/label.ts
index f04c8f658..1eae651ec 100644
--- a/src/mol-theme/label.ts
+++ b/src/mol-theme/label.ts
@@ -14,7 +14,7 @@ import { Vec3 } from '../mol-math/linear-algebra';
import { radToDeg } from '../mol-math/misc';
import { Volume } from '../mol-model/volume';
-export type LabelGranularity = 'element' | 'conformation' | 'residue' | 'chain' | 'structure'
+export type LabelGranularity = 'element' | 'conformation' | 'residue' | 'two-residues' | 'chain' | 'structure'
export const DefaultLabelOptions = {
granularity: 'element' as LabelGranularity,
--
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