Skip to content
Snippets Groups Projects
Commit 1b79d349 authored by Alexander Rose's avatar Alexander Rose
Browse files

fix marking of carbohydrate visuals

parent fc52e29c
No related branches found
No related tags found
No related merge requests found
......@@ -14,6 +14,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Add Model Export extension
- Bugfix: Automatically treat empty string as "non-present" value in BinaryCIF writer.
- Fix coarse model support in entity-id color theme
- Fix marking of carbohydrate visuals (whole chain could get marked instead of single residue)
## [v3.0.0-dev.10] - 2022-01-17
......
/**
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
......@@ -101,6 +101,8 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
return EmptyLoci;
}
const __linkIndicesSet = new Set<number>();
function eachCarbohydrateLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
let changed = false;
if (!StructureElement.Loci.is(loci)) return false;
......@@ -110,12 +112,15 @@ function eachCarbohydrateLink(loci: Loci, structure: Structure, apply: (interval
for (const { unit, indices } of loci.elements) {
if (!Unit.isAtomic(unit)) continue;
__linkIndicesSet.clear();
OrderedSet.forEach(indices, v => {
// TODO avoid duplicate calls to apply
const linkIndices = getLinkIndices(unit, unit.elements[v]);
for (let i = 0, il = linkIndices.length; i < il; ++i) {
if (!__linkIndicesSet.has(linkIndices[i])) {
__linkIndicesSet.add(linkIndices[i]);
if (apply(Interval.ofSingleton(linkIndices[i]))) changed = true;
}
}
});
}
return changed;
......
/**
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
......@@ -29,8 +29,8 @@ import { getAltResidueLociFromId } from './util/common';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
const t = Mat4.identity();
const sVec = Vec3.zero();
const pd = Vec3.zero();
const sVec = Vec3();
const pd = Vec3();
const SideFactor = 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4)
......@@ -212,6 +212,8 @@ function getCarbohydrateLoci(pickingId: PickingId, structure: Structure, id: num
return EmptyLoci;
}
const __elementIndicesSet = new Set<number>();
/** For each carbohydrate (usually a monosaccharide) when all its residue's elements are in a loci. */
function eachCarbohydrate(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
const { getElementIndices } = structure.carbohydrates;
......@@ -222,12 +224,15 @@ function eachCarbohydrate(loci: Loci, structure: Structure, apply: (interval: In
for (const { unit, indices } of loci.elements) {
if (!Unit.isAtomic(unit)) continue;
__elementIndicesSet.clear();
OrderedSet.forEach(indices, v => {
// TODO avoid duplicate calls to apply
const elementIndices = getElementIndices(unit, unit.elements[v]);
for (let i = 0, il = elementIndices.length; i < il; ++i) {
if (!__elementIndicesSet.has(elementIndices[i])) {
__elementIndicesSet.add(elementIndices[i]);
if (apply(Interval.ofSingleton(elementIndices[i] * 2))) changed = true;
}
}
});
}
return changed;
......
/**
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
......@@ -123,6 +123,8 @@ function getTerminalLinkLoci(pickingId: PickingId, structure: Structure, id: num
return EmptyLoci;
}
const __linkIndicesSet = new Set<number>();
function eachTerminalLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
let changed = false;
if (!StructureElement.Loci.is(loci)) return false;
......@@ -132,12 +134,15 @@ function eachTerminalLink(loci: Loci, structure: Structure, apply: (interval: In
for (const { unit, indices } of loci.elements) {
if (!Unit.isAtomic(unit)) continue;
__linkIndicesSet.clear();
OrderedSet.forEach(indices, v => {
// TODO avoid duplicate calls to apply
const linkIndices = getTerminalLinkIndices(unit, unit.elements[v]);
for (let i = 0, il = linkIndices.length; i < il; ++i) {
if (!__linkIndicesSet.has(linkIndices[i])) {
__linkIndicesSet.add(linkIndices[i]);
if (apply(Interval.ofSingleton(linkIndices[i]))) changed = true;
}
}
});
}
return changed;
......
/**
* Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
......@@ -88,6 +88,7 @@ namespace Visual {
const currentStatus = markerStatus.ref.value as MarkerInfo['status'];
if (!isEveryLoci(loci)) {
// assume that all interval are non-overlapping
let intervalSize = 0;
lociApply(loci, interval => {
intervalSize += Interval.size(interval);
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment