From 09c7edce885514a0a70f2abbdc5bf61c9408d67e Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 24 Sep 2019 10:11:42 -0700
Subject: [PATCH] smaller terminal links and dashed terminal links to metals
---
.../carbohydrate-terminal-link-cylinder.ts | 18 ++++++++++++------
1 file changed, 12 insertions(+), 6 deletions(-)
diff --git a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
index 0dbb6c91b..25c86190f 100644
--- a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -20,10 +20,11 @@ import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { OrderedSet, Interval } from '../../../mol-data/int';
import { PickingId } from '../../../mol-geo/geometry/picking';
import { EmptyLoci, Loci } from '../../../mol-model/loci';
+import { getElementIdx, MetalsSet } from '../../../mol-model/structure/structure/unit/links/common';
function createCarbohydrateTerminalLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateTerminalLinkParams>, mesh?: Mesh) {
const { terminalLinks, elements } = structure.carbohydrates
- const { linkSizeFactor } = props
+ const { terminalLinkSizeFactor } = props
const location = StructureElement.Location.create()
@@ -41,7 +42,12 @@ function createCarbohydrateTerminalLinkCylinderMesh(ctx: VisualContext, structur
}
},
order: (edgeIndex: number) => 1,
- flags: (edgeIndex: number) => BitFlags.create(LinkType.Flag.None),
+ flags: (edgeIndex: number) => {
+ const l = terminalLinks[edgeIndex]
+ const eI = l.elementUnit.elements[l.elementIndex]
+ const beI = getElementIdx(l.elementUnit.model.atomicHierarchy.atoms.type_symbol.value(eI));
+ return BitFlags.create(MetalsSet.has(beI) ? LinkType.Flag.MetallicCoordination : LinkType.Flag.None);
+ },
radius: (edgeIndex: number) => {
const l = terminalLinks[edgeIndex]
if (l.fromCarbohydrate) {
@@ -51,7 +57,7 @@ function createCarbohydrateTerminalLinkCylinderMesh(ctx: VisualContext, structur
location.unit = l.elementUnit
location.element = l.elementUnit.elements[l.elementIndex]
}
- return theme.size.size(location) * linkSizeFactor
+ return theme.size.size(location) * terminalLinkSizeFactor
},
ignore: (edgeIndex: number) => false
}
@@ -62,7 +68,7 @@ function createCarbohydrateTerminalLinkCylinderMesh(ctx: VisualContext, structur
export const CarbohydrateTerminalLinkParams = {
...UnitsMeshParams,
...LinkCylinderParams,
- linkSizeFactor: PD.Numeric(0.3, { min: 0, max: 3, step: 0.01 }),
+ terminalLinkSizeFactor: PD.Numeric(0.2, { min: 0, max: 3, step: 0.01 }),
}
export type CarbohydrateTerminalLinkParams = typeof CarbohydrateTerminalLinkParams
@@ -75,7 +81,7 @@ export function CarbohydrateTerminalLinkVisual(materialId: number): ComplexVisua
eachLocation: eachTerminalLink,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<CarbohydrateTerminalLinkParams>, currentProps: PD.Values<CarbohydrateTerminalLinkParams>) => {
state.createGeometry = (
- newProps.linkSizeFactor !== currentProps.linkSizeFactor ||
+ newProps.terminalLinkSizeFactor !== currentProps.terminalLinkSizeFactor ||
newProps.radialSegments !== currentProps.radialSegments
)
}
--
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