diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8f4fe35f873a06fed51681d0bf9b0712dfb7b22b..f3016fe910dd92cc61dbe3938d9d727f72d85860 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,9 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
+- Improve aromatic bond visuals (add ``aromaticScale``, ``aromaticSpacing``, ``aromaticDashCount`` params)
+- [Breaking] Change ``adjustCylinderLength`` default to ``false`` (set to true for focus representation)
+
## [v2.3.5] - 2021-10-19
- Fix sequence viewer for PDB files with COMPND record and multichain entities.
@@ -153,29 +156,22 @@ Note that since we don't clearly distinguish between a public and private interf
- Fixed Measurements UI labels (#166)
## [v2.0.3] - 2021-04-09
-### Added
-- Support for ``ColorTheme.palette`` designed for providing gradient-like coloring.
-### Changed
+- Add support for ``ColorTheme.palette`` designed for providing gradient-like coloring.
- [Breaking] The ``zip`` function is now asynchronous and expects a ``RuntimeContext``. Also added ``Zip()`` returning a ``Task``.
- [Breaking] Add ``CubeGridFormat`` in ``alpha-orbitals`` extension.
## [v2.0.2] - 2021-03-29
-### Added
-- ``Canvas3D.getRenderObjects``.
-- [WIP] Animate state interpolating, including model trajectories
-### Changed
+- Add ``Canvas3D.getRenderObjects``.
+- [WIP] Animate state interpolating, including model trajectories
- Recognise MSE, SEP, TPO, PTR and PCA as non-standard amino-acids.
-
-### Fixed
-- VolumeFromDensityServerCif transform label
-
+- Fix VolumeFromDensityServerCif transform label
## [v2.0.1] - 2021-03-23
-### Fixed
-- Exclude tsconfig.commonjs.tsbuildinfo from npm bundle
+- Exclude tsconfig.commonjs.tsbuildinfo from npm bundle
## [v2.0.0] - 2021-03-23
+
Too many changes to list as this is the start of the changelog... Notably, default exports are now forbidden.
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 43ad81abd070d9b3d51ec70d004b6bc6ce6ff664..fbd8fa87c570f069641eacf95c3e36b46badd536 100644
--- a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
+++ b/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
@@ -25,7 +25,7 @@ const StructureFocusRepresentationParams = (plugin: PluginContext) => {
expandRadius: PD.Numeric(5, { min: 1, max: 10, step: 1 }),
targetParams: PD.Group(reprParams, {
label: 'Target',
- customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.26, alpha: 0.51 } })
+ customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.26, alpha: 0.51, adjustCylinderLength: true } })
}),
surroundingsParams: PD.Group(reprParams, {
label: 'Surroundings',
diff --git a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
index c735dbeaeac4b67371671abddc47e9aa9a1398a5..5385bac813dbc3f0b461d149c8d9d3a116de447f 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
@@ -215,6 +215,9 @@ export function InterUnitBondCylinderImpostorVisual(materialId: number): Complex
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.linkCap !== currentProps.linkCap ||
+ newProps.aromaticScale !== currentProps.aromaticScale ||
+ newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.dashScale !== currentProps.dashScale ||
newProps.dashCap !== currentProps.dashCap ||
@@ -254,6 +257,9 @@ export function InterUnitBondCylinderMeshVisual(materialId: number): ComplexVisu
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.linkCap !== currentProps.linkCap ||
+ newProps.aromaticScale !== currentProps.aromaticScale ||
+ newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.dashScale !== currentProps.dashScale ||
newProps.dashCap !== currentProps.dashCap ||
diff --git a/src/mol-repr/structure/visual/bond-inter-unit-line.ts b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
index 62c030b93f5533c4ee499c60c4a126ef66329e12..1fb4b9784d8fe7cfbb7a56fa27a9243d96ab69f0 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
@@ -131,6 +131,7 @@ export function InterUnitBondLineVisual(materialId: number): ComplexVisual<Inter
newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
index 3e42f0cc066fa5b14bad7a9f83b35b5e1363d01b..abd5d82a7282c0f403faec6fbb92597030c134f5 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
@@ -228,6 +228,9 @@ export function IntraUnitBondCylinderImpostorVisual(materialId: number): UnitsVi
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.linkCap !== currentProps.linkCap ||
+ newProps.aromaticScale !== currentProps.aromaticScale ||
+ newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.dashScale !== currentProps.dashScale ||
newProps.dashCap !== currentProps.dashCap ||
@@ -272,6 +275,9 @@ export function IntraUnitBondCylinderMeshVisual(materialId: number): UnitsVisual
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.linkCap !== currentProps.linkCap ||
+ newProps.aromaticScale !== currentProps.aromaticScale ||
+ newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.dashScale !== currentProps.dashScale ||
newProps.dashCap !== currentProps.dashCap ||
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-line.ts b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
index 10708af2f9f5b6e92df1ccf9afc6a761e66efd6d..1ad1fa45f7bbbad9eda44e63e311bd0e995925a4 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
@@ -153,6 +153,7 @@ export function IntraUnitBondLineVisual(materialId: number): UnitsVisual<IntraUn
newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
diff --git a/src/mol-repr/structure/visual/util/bond.ts b/src/mol-repr/structure/visual/util/bond.ts
index 11fd2cf27adf49274b85e6fab523a4e7ce936d33..d2fb94a7769d27880135d6008e0c46c724ae1ef4 100644
--- a/src/mol-repr/structure/visual/util/bond.ts
+++ b/src/mol-repr/structure/visual/util/bond.ts
@@ -28,7 +28,7 @@ export type BondProps = typeof DefaultBondProps
export const BondCylinderParams = {
...LinkCylinderParams,
...BondParams,
- adjustCylinderLength: PD.Boolean(true, { description: 'Shorten cylinders to reduce overlap with spheres.' })
+ adjustCylinderLength: PD.Boolean(false, { description: 'Shorten cylinders to reduce overlap with spheres. Useful for for transparent bonds. Not working well with aromatic bonds.' })
};
export const DefaultBondCylinderProps = PD.getDefaultValues(BondCylinderParams);
export type BondCylinderProps = typeof DefaultBondCylinderProps
diff --git a/src/mol-repr/structure/visual/util/link.ts b/src/mol-repr/structure/visual/util/link.ts
index f28aef6918560ea4c199a515931d3222292252b6..c62aea5d0a496badcf2924404c35ce6153cf9c3f 100644
--- a/src/mol-repr/structure/visual/util/link.ts
+++ b/src/mol-repr/structure/visual/util/link.ts
@@ -21,6 +21,9 @@ export const LinkCylinderParams = {
linkScale: PD.Numeric(0.45, { min: 0, max: 1, step: 0.01 }),
linkSpacing: PD.Numeric(1, { min: 0, max: 2, step: 0.01 }),
linkCap: PD.Boolean(false),
+ aromaticScale: PD.Numeric(0.3, { min: 0, max: 1, step: 0.01 }),
+ aromaticSpacing: PD.Numeric(1.5, { min: 0, max: 3, step: 0.01 }),
+ aromaticDashCount: PD.Numeric(2, { min: 2, max: 6, step: 2 }),
dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
dashScale: PD.Numeric(0.8, { min: 0, max: 2, step: 0.1 }),
dashCap: PD.Boolean(true),
@@ -33,6 +36,7 @@ export type LinkCylinderProps = typeof DefaultLinkCylinderProps
export const LinkLineParams = {
linkScale: PD.Numeric(0.5, { min: 0, max: 1, step: 0.1 }),
linkSpacing: PD.Numeric(0.1, { min: 0, max: 2, step: 0.01 }),
+ aromaticDashCount: PD.Numeric(2, { min: 2, max: 6, step: 2 }),
dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
};
export const DefaultLinkLineProps = PD.getDefaultValues(LinkLineParams);
@@ -107,7 +111,7 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
if (!linkCount) return Mesh.createEmpty(mesh);
- const { linkScale, linkSpacing, radialSegments, linkCap, dashCount, dashScale, dashCap, stubCap } = props;
+ const { linkScale, linkSpacing, radialSegments, linkCap, aromaticScale, aromaticSpacing, aromaticDashCount, dashCount, dashScale, dashCap, stubCap } = props;
const vertexCountEstimate = radialSegments * 2 * linkCount * 2;
const builderState = MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 4, mesh);
@@ -138,8 +142,7 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
const [topCap, bottomCap] = dirFlag ? [linkStub, linkCap] : [linkCap, linkStub];
builderState.currentGroup = edgeIndex;
- const aromaticOffsetFactor = 5.5;
- const multipleOffsetFactor = 4;
+ const aromaticSegmentCount = aromaticDashCount + 1;
if (linkStyle === LinkStyle.Solid) {
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
@@ -153,8 +156,8 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
addFixedCountDashedCylinder(builderState, va, vb, 0.5, segmentCount, cylinderProps);
} else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
- const order = linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble ? 2 :
- linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple ? 3 : 1.5;
+ const order = (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble) ? 2 :
+ (linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple) ? 3 : 1.5;
const multiRadius = linkRadius * (linkScale / (0.5 * order));
const absOffset = (linkRadius - multiRadius) * linkSpacing;
@@ -167,21 +170,28 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
addCylinder(builderState, va, vb, 0.5, cylinderProps);
- cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * linkScale;
+ const aromaticOffset = linkRadius + aromaticScale * linkRadius + aromaticScale * linkRadius * aromaticSpacing;
+
+ v3setMagnitude(tmpV12, v3sub(tmpV12, vb, va), linkRadius * 0.5);
+ v3add(va, va, tmpV12);
+ v3sub(vb, vb, tmpV12);
+
+ cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * aromaticScale;
cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
- v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
+ v3setMagnitude(vShift, vShift, aromaticOffset);
v3sub(va, va, vShift);
v3sub(vb, vb, vShift);
- addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
+ addFixedCountDashedCylinder(builderState, va, vb, 0.5, aromaticSegmentCount, cylinderProps);
if (linkStyle === LinkStyle.MirroredAromatic) {
- v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+ v3setMagnitude(vShift, vShift, aromaticOffset * 2);
v3add(va, va, vShift);
v3add(vb, vb, vShift);
- addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
+ addFixedCountDashedCylinder(builderState, va, vb, 0.5, aromaticSegmentCount, cylinderProps);
}
} else if (linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.OffsetTriple) {
- v3setMagnitude(vShift, vShift, absOffset);
+ const multipleOffset = linkRadius + multiRadius + linkScale * linkRadius * linkSpacing;
+ v3setMagnitude(vShift, vShift, multipleOffset);
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
addCylinder(builderState, va, vb, 0.5, cylinderProps);
@@ -193,13 +203,13 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
cylinderProps.radiusTop = cylinderProps.radiusBottom = multiRadius;
cylinderProps.topCap = dirFlag ? linkStub : dashCap;
cylinderProps.bottomCap = dirFlag ? dashCap : linkStub;
- v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
+ v3setMagnitude(vShift, vShift, multipleOffset);
v3sub(va, va, vShift);
v3sub(vb, vb, vShift);
addCylinder(builderState, va, vb, 0.5, cylinderProps);
if (order === 3) {
- v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor * 2);
+ v3setMagnitude(vShift, vShift, multipleOffset * 2);
v3add(va, va, vShift);
v3add(vb, vb, vShift);
addCylinder(builderState, va, vb, 0.5, cylinderProps);
@@ -236,7 +246,7 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
if (!linkCount) return Cylinders.createEmpty(cylinders);
- const { linkScale, linkSpacing, linkCap, dashCount, dashScale, dashCap, stubCap } = props;
+ const { linkScale, linkSpacing, linkCap, aromaticScale, aromaticSpacing, aromaticDashCount, dashCount, dashScale, dashCap, stubCap } = props;
const cylindersCountEstimate = linkCount * 2;
const builder = CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
@@ -250,10 +260,8 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
const segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
const lengthScale = 0.5 - (0.5 / 2 / segmentCount);
- const aromaticSegmentCount = 3;
+ const aromaticSegmentCount = aromaticDashCount + 1;
const aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
- const aromaticOffsetFactor = 5.5;
- const multipleOffsetFactor = 4;
for (let edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
if (ignore && ignore(edgeIndex)) continue;
@@ -272,8 +280,8 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
v3sub(vb, vb, tmpV12);
builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
} else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
- const order = linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble ? 2 :
- linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple ? 3 : 1.5;
+ const order = (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble) ? 2 :
+ (linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple) ? 3 : 1.5;
const multiScale = linkScale / (0.5 * order);
const absOffset = (linkRadius - multiScale * linkRadius) * linkSpacing;
@@ -283,26 +291,32 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
if (linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
+ const aromaticOffset = linkRadius + aromaticScale * linkRadius + aromaticScale * linkRadius * aromaticSpacing;
+
v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
v3sub(vb, vb, tmpV12);
- v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
+ v3setMagnitude(tmpV12, v3sub(tmpV12, vb, va), linkRadius * 0.5);
+ v3add(va, va, tmpV12);
+
+ v3setMagnitude(vShift, vShift, aromaticOffset);
v3sub(va, va, vShift);
v3sub(vb, vb, vShift);
- builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
+ builder.addFixedCountDashes(va, vb, aromaticSegmentCount, aromaticScale, dashCap, dashCap, edgeIndex);
if (linkStyle === LinkStyle.MirroredAromatic) {
- v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+ v3setMagnitude(vShift, vShift, aromaticOffset * 2);
v3add(va, va, vShift);
v3add(vb, vb, vShift);
- builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
+ builder.addFixedCountDashes(va, vb, aromaticSegmentCount, aromaticScale, dashCap, dashCap, edgeIndex);
}
} else if (linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.OffsetTriple) {
- v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
+ const multipleOffset = linkRadius + multiScale * linkRadius + linkScale * linkRadius * linkSpacing;
+ v3setMagnitude(vShift, vShift, multipleOffset);
builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
- v3scale(tmpV12, v3sub(tmpV12, va, vb), linkSpacing * linkScale * 0.2);
+ v3setMagnitude(tmpV12, v3sub(tmpV12, va, vb), linkRadius / 1.5);
v3sub(va, va, tmpV12);
if (order === 3) builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
@@ -335,7 +349,7 @@ export function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProp
if (!linkCount) return Lines.createEmpty(lines);
- const { linkScale, linkSpacing, dashCount } = props;
+ const { linkScale, linkSpacing, aromaticDashCount, dashCount } = props;
const linesCountEstimate = linkCount * 2;
const builder = LinesBuilder.create(linesCountEstimate, linesCountEstimate / 4, lines);
@@ -349,7 +363,7 @@ export function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProp
const segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
const lengthScale = 0.5 - (0.5 / 2 / segmentCount);
- const aromaticSegmentCount = 3;
+ const aromaticSegmentCount = aromaticDashCount + 1;
const aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
const aromaticOffsetFactor = 4.5;
const multipleOffsetFactor = 3;