From 5c4a44fc99823713304eab986f531b717a936513 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 6 Mar 2019 15:33:39 -0800
Subject: [PATCH] fixed intra link referencePosition
---
.../structure/visual/intra-unit-link-cylinder.ts | 10 ++++++++--
src/mol-repr/structure/visual/util/link.ts | 1 -
2 files changed, 8 insertions(+), 3 deletions(-)
diff --git a/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts b/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
index 116ef8cf1..9f86c6700 100644
--- a/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
@@ -40,12 +40,18 @@ function createIntraUnitLinkCylinderMesh(ctx: VisualContext, unit: Unit, structu
linkCount: edgeCount * 2,
referencePosition: (edgeIndex: number) => {
let aI = a[edgeIndex], bI = b[edgeIndex];
+
if (aI > bI) [aI, bI] = [bI, aI]
+ if (offset[aI + 1] - offset[aI] === 1) [aI, bI] = [bI, aI]
+ // TODO prefer reference atoms in rings
+
for (let i = offset[aI], il = offset[aI + 1]; i < il; ++i) {
- if (b[i] !== bI) return pos(elements[b[i]], vRef)
+ const _bI = b[i]
+ if (_bI !== bI && _bI !== aI) return pos(elements[_bI], vRef)
}
for (let i = offset[bI], il = offset[bI + 1]; i < il; ++i) {
- if (a[i] !== aI) return pos(elements[a[i]], vRef)
+ const _aI = a[i]
+ if (_aI !== aI && _aI !== bI) return pos(elements[_aI], vRef)
}
return null
},
diff --git a/src/mol-repr/structure/visual/util/link.ts b/src/mol-repr/structure/visual/util/link.ts
index 956f61728..ab5ddbd8f 100644
--- a/src/mol-repr/structure/visual/util/link.ts
+++ b/src/mol-repr/structure/visual/util/link.ts
@@ -29,7 +29,6 @@ const tmpShiftV13 = Vec3.zero()
/** Calculate 'shift' direction that is perpendiculat to v1 - v2 and goes through v3 */
export function calculateShiftDir (out: Vec3, v1: Vec3, v2: Vec3, v3: Vec3 | null) {
Vec3.normalize(tmpShiftV12, Vec3.sub(tmpShiftV12, v1, v2))
-
if (v3 !== null) {
Vec3.sub(tmpShiftV13, v1, v3)
} else {
--
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