diff --git a/package-lock.json b/package-lock.json
index 7abd6eeb33cb576c79906f6d1926c2bb5aa6f5bc..827a99ea20dff3ef1aae28cd7b173933e62aa801 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index 8d149012463de799160e12c086b3f8724f97eb26..7157fd480347ed9f35d5e7f5b82f10d92a4c2d0e 100644
--- a/package.json
+++ b/package.json
@@ -75,7 +75,7 @@
"@types/benchmark": "^1.0.31",
"@types/compression": "0.0.36",
"@types/express": "^4.16.0",
- "@types/jest": "^23.3.1",
+ "@types/jest": "^23.3.2",
"@types/node": "^10.9.4",
"@types/node-fetch": "^2.1.2",
"@types/react": "^16.4.13",
@@ -95,7 +95,7 @@
"mini-css-extract-plugin": "^0.4.2",
"node-sass": "^4.9.3",
"raw-loader": "^0.5.1",
- "resolve-url-loader": "^2.3.0",
+ "resolve-url-loader": "^2.3.1",
"sass-loader": "^7.1.0",
"style-loader": "^0.23.0",
"ts-jest": "^23.1.4",
@@ -103,7 +103,7 @@
"typescript": "^3.0.3",
"uglify-js": "^3.4.9",
"util.promisify": "^1.0.0",
- "webpack": "^4.17.1",
+ "webpack": "^4.17.2",
"webpack-cli": "^3.1.0"
},
"dependencies": {
@@ -114,8 +114,8 @@
"graphql-request": "^1.8.2",
"immutable": "^4.0.0-rc.9",
"node-fetch": "^2.2.0",
- "react": "^16.4.2",
- "react-dom": "^16.4.2",
- "rxjs": "^6.3.1"
+ "react": "^16.5.0",
+ "react-dom": "^16.5.0",
+ "rxjs": "^6.3.2"
}
}
diff --git a/src/apps/canvas/component/app.tsx b/src/apps/canvas/component/app.tsx
index 6fe5f0872a62a8a5d552767872e1798c8c845426..c1d099b6a7e3e5d77e38a14040e21dbce3ebb4d8 100644
--- a/src/apps/canvas/component/app.tsx
+++ b/src/apps/canvas/component/app.tsx
@@ -9,17 +9,7 @@ import { StructureView } from '../structure-view';
import { App } from '../app';
import { Viewport } from './viewport';
import { StructureViewComponent } from './structure-view';
-
-// export function FileInput (props: {
-// accept: string
-// onChange: (v: FileList | null) => void,
-// }) {
-// return <input
-// accept={props.accept || '*.*'}
-// type='file'
-// onChange={e => props.onChange.call(null, e.target.files)}
-// />
-// }
+import { Examples } from '../examples';
export interface AppProps {
app: App
@@ -75,6 +65,20 @@ export class AppComponent extends React.Component<AppProps, AppState> {
}}
/>
</div>
+ <div>
+ <span>Load example </span>
+ <select
+ style={{width: '200px'}}
+ onChange={e => {
+ this.props.app.loadPdbId(e.target.value)
+ }}
+ >
+ <option value=''></option>
+ {Examples.map(({pdbId, description}, i) => {
+ return <option key={i} value={pdbId}>{`${pdbId} - ${description}`}</option>
+ })}
+ </select>
+ </div>
<hr/>
<div style={{marginBottom: '10px'}}>
{structureView ? <StructureViewComponent structureView={structureView} /> : ''}
diff --git a/src/apps/canvas/component/structure-representation.tsx b/src/apps/canvas/component/structure-representation.tsx
index 25eb022ae279bbae55b8af05fc50cfc8a369d901..bdc194b701b259a28ff093d15372dcc861b75672 100644
--- a/src/apps/canvas/component/structure-representation.tsx
+++ b/src/apps/canvas/component/structure-representation.tsx
@@ -19,6 +19,7 @@ export interface StructureRepresentationComponentProps {
export interface StructureRepresentationComponentState {
label: string
visible: boolean
+ alpha: number
quality: VisualQuality
colorTheme: ColorThemeProps
}
@@ -27,6 +28,7 @@ export class StructureRepresentationComponent extends React.Component<StructureR
state = {
label: this.props.representation.label,
visible: this.props.representation.props.visible,
+ alpha: this.props.representation.props.alpha,
quality: this.props.representation.props.quality,
colorTheme: this.props.representation.props.colorTheme,
}
@@ -38,6 +40,7 @@ export class StructureRepresentationComponent extends React.Component<StructureR
...this.state,
label: repr.label,
visible: repr.props.visible,
+ alpha: repr.props.alpha,
quality: repr.props.quality,
colorTheme: repr.props.colorTheme,
})
@@ -49,6 +52,7 @@ export class StructureRepresentationComponent extends React.Component<StructureR
if (state.visible !== undefined) props.visible = state.visible
if (state.quality !== undefined) props.quality = state.quality
+ if (state.alpha !== undefined) props.alpha = state.alpha
if (state.colorTheme !== undefined) props.colorTheme = state.colorTheme
await repr.createOrUpdate(props).run()
@@ -60,13 +64,14 @@ export class StructureRepresentationComponent extends React.Component<StructureR
...this.state,
visible: repr.props.visible,
quality: repr.props.quality,
+ alpha: repr.props.alpha,
colorTheme: repr.props.colorTheme,
}
this.setState(newState)
}
render() {
- const { label, visible, quality, colorTheme } = this.state
+ const { label, visible, quality, alpha, colorTheme } = this.state
const ct = ColorTheme(colorTheme)
@@ -91,6 +96,17 @@ export class StructureRepresentationComponent extends React.Component<StructureR
{VisualQualityNames.map(name => <option key={name} value={name}>{name}</option>)}
</select>
</div>
+ <div>
+ <span>Opacity </span>
+ <input type='range'
+ defaultValue={alpha.toString()}
+ min='0'
+ max='1'
+ step='0.05'
+ onInput={(e) => this.update({ alpha: parseFloat(e.currentTarget.value) })}
+ >
+ </input>
+ </div>
<div>
<span>Color Theme </span>
<select value={colorTheme.name} onChange={(e) => this.update({ colorTheme: { name: e.target.value as ColorThemeName } }) }>
diff --git a/src/apps/canvas/examples.ts b/src/apps/canvas/examples.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7fefc15700eaa03921e809617ff396e5873e458a
--- /dev/null
+++ b/src/apps/canvas/examples.ts
@@ -0,0 +1,169 @@
+
+
+export interface Example {
+ pdbId: string
+ description: string
+}
+
+export const Examples: Example[] = [
+ {
+ pdbId: '1jj2',
+ description: 'ribosome'
+ },
+ {
+ pdbId: '1grm',
+ description: 'helix-like sheets'
+ },
+ {
+ pdbId: '4umt',
+ description: 'ligand has bond with order 3'
+ },
+ {
+ pdbId: '1crn',
+ description: 'small'
+ },
+ {
+ pdbId: '1hrv',
+ description: 'viral assembly'
+ },
+ {
+ pdbId: '1rb8',
+ description: 'virus'
+ },
+ {
+ pdbId: '1blu',
+ description: 'metal coordination'
+ },
+ {
+ pdbId: '3pqr',
+ description: 'inter unit bonds, two polymer chains, ligands, water, carbohydrates linked to protein'
+ },
+ {
+ pdbId: '4v5a',
+ description: 'ribosome'
+ },
+ {
+ pdbId: '3j3q',
+ description: '...'
+ },
+ {
+ pdbId: '2np2',
+ description: 'dna'
+ },
+ {
+ pdbId: '1d66',
+ description: 'dna'
+ },
+ {
+ pdbId: '9dna',
+ description: 'A form dna'
+ },
+ {
+ pdbId: '1bna',
+ description: 'B form dna'
+ },
+ {
+ pdbId: '199d',
+ description: 'C form dna'
+ },
+ {
+ pdbId: '4lb6',
+ description: 'Z form dna'
+ },
+ {
+ pdbId: '1egk',
+ description: '4-way dna-rna junction'
+ },
+ {
+ pdbId: '1y26',
+ description: 'rna'
+ },
+ {
+ pdbId: '1xv6',
+ description: 'rna, modified nucleotides'
+ },
+ {
+ pdbId: '3bbm',
+ description: 'rna with linker'
+ },
+ {
+ pdbId: '1euq',
+ description: 't-rna'
+ },
+ {
+ pdbId: '2e2i',
+ description: 'rna, dna, protein'
+ },
+ {
+ pdbId: '1gfl',
+ description: 'GFP, flourophore has carbonyl oxygen removed'
+ },
+ {
+ pdbId: '1sfi',
+ description: 'contains cyclic peptid'
+ },
+ {
+ pdbId: '3sn6',
+ description: 'discontinuous chains'
+ },
+ {
+ pdbId: '2zex',
+ description: 'contains carbohydrate polymer'
+ },
+ {
+ pdbId: '3sgj',
+ description: 'contains carbohydrate polymer'
+ },
+ {
+ pdbId: '3ina',
+ description: 'contains GlcN and IdoA'
+ },
+ {
+ pdbId: '1umz',
+ description: 'contains Xyl (Xyloglucan)'
+ },
+ {
+ pdbId: '1mfb',
+ description: 'contains Abe'
+ },
+ {
+ pdbId: '2gdu',
+ description: 'contains sucrose'
+ },
+ {
+ pdbId: '2fnc',
+ description: 'contains maltotriose'
+ },
+ {
+ pdbId: '4zs9',
+ description: 'contains raffinose'
+ },
+ {
+ pdbId: '2yft',
+ description: 'contains kestose'
+ },
+ {
+ pdbId: '2b5t',
+ description: 'contains large carbohydrate polymer'
+ },
+ {
+ pdbId: '1b5f',
+ description: 'contains carbohydrate with alternate locations'
+ },
+ {
+ pdbId: '5u0q',
+ description: 'mixed dna/rna in same polymer'
+ },
+ {
+ pdbId: '1xj9',
+ description: 'PNA (peptide nucleic acid)'
+ },
+ {
+ pdbId: '5eme',
+ description: 'PNA (peptide nucleic acid) and RNA'
+ },
+ {
+ pdbId: '2X3T',
+ description: 'temp'
+ },
+]
\ No newline at end of file
diff --git a/src/apps/canvas/structure-view.ts b/src/apps/canvas/structure-view.ts
index b381ab2f082e2918092e7e695c1de8b82a8ffd45..c5674578f27d99dae9056db73f63464279da2c44 100644
--- a/src/apps/canvas/structure-view.ts
+++ b/src/apps/canvas/structure-view.ts
@@ -24,6 +24,7 @@ import { StructureRepresentation } from 'mol-geo/representation/structure';
import { BehaviorSubject } from 'rxjs';
import { SpacefillRepresentation } from 'mol-geo/representation/structure/representation/spacefill';
import { DistanceRestraintRepresentation } from 'mol-geo/representation/structure/representation/distance-restraint';
+import { SurfaceRepresentation } from 'mol-geo/representation/structure/representation/surface';
export interface StructureView {
readonly viewer: Viewer
@@ -66,6 +67,7 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
const active: { [k: string]: boolean } = {
cartoon: true,
point: false,
+ surface: true,
ballAndStick: false,
carbohydrate: false,
spacefill: false,
@@ -76,6 +78,7 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
const structureRepresentations: { [k: string]: StructureRepresentation<any> } = {
cartoon: CartoonRepresentation(),
+ surface: SurfaceRepresentation(),
point: PointRepresentation(),
ballAndStick: BallAndStickRepresentation(),
carbohydrate: CarbohydrateRepresentation(),
diff --git a/src/mol-geo/representation/structure/representation/surface.ts b/src/mol-geo/representation/structure/representation/surface.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7e95466e6ffa51421b7973b8436b2a5ef1e9a6d8
--- /dev/null
+++ b/src/mol-geo/representation/structure/representation/surface.ts
@@ -0,0 +1,47 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { UnitsRepresentation } from '..';
+import { GaussianSurfaceVisual, DefaultGaussianSurfaceProps } from '../visual/gaussian-surface-mesh';
+import { StructureRepresentation } from '../units-representation';
+import { Structure } from 'mol-model/structure';
+import { MarkerAction } from '../../../util/marker-data';
+import { Loci } from 'mol-model/loci';
+import { PickingId } from '../../../util/picking';
+
+export const DefaultSurfaceProps = {
+ ...DefaultGaussianSurfaceProps,
+}
+export type SurfaceProps = typeof DefaultSurfaceProps
+
+export type SurfaceRepresentation = StructureRepresentation<SurfaceProps>
+
+export function SurfaceRepresentation(): SurfaceRepresentation {
+ let currentProps: SurfaceProps
+ const gaussianRepr = UnitsRepresentation('Gaussian surface', GaussianSurfaceVisual)
+ return {
+ label: 'Surface',
+ get renderObjects() {
+ return [ ...gaussianRepr.renderObjects ]
+ },
+ get props() {
+ return { ...gaussianRepr.props }
+ },
+ createOrUpdate: (props: Partial<SurfaceProps> = {}, structure?: Structure) => {
+ currentProps = Object.assign({}, DefaultSurfaceProps, currentProps, props)
+ return gaussianRepr.createOrUpdate(currentProps, structure)
+ },
+ getLoci: (pickingId: PickingId) => {
+ return gaussianRepr.getLoci(pickingId)
+ },
+ mark: (loci: Loci, action: MarkerAction) => {
+ return gaussianRepr.mark(loci, action)
+ },
+ destroy() {
+ gaussianRepr.destroy()
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/units-visual.ts b/src/mol-geo/representation/structure/units-visual.ts
index 534764f3d57028e1ad33103d4e90125d3c69d4fe..a98620a7f37577c8370be896af55bbbc0213c6a0 100644
--- a/src/mol-geo/representation/structure/units-visual.ts
+++ b/src/mol-geo/representation/structure/units-visual.ts
@@ -32,7 +32,7 @@ export type UnitsMeshProps = typeof DefaultUnitsMeshProps
export interface UnitsMeshVisualBuilder<P extends UnitsMeshProps> {
defaultProps: P
- createMesh(ctx: RuntimeContext, unit: Unit, props: P, mesh?: Mesh): Promise<Mesh>
+ createMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: P, mesh?: Mesh): Promise<Mesh>
createLocationIterator(group: Unit.SymmetryGroup): LocationIterator
getLoci(pickingId: PickingId, group: Unit.SymmetryGroup, id: number): Loci
mark(loci: Loci, group: Unit.SymmetryGroup, apply: (interval: Interval) => boolean): boolean
@@ -59,7 +59,7 @@ export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisu
const unit = group.units[0]
currentConformationId = Unit.conformationId(unit)
mesh = currentProps.unitKinds.includes(unit.kind)
- ? await createMesh(ctx, unit, currentProps, mesh)
+ ? await createMesh(ctx, unit, currentStructure, currentProps, mesh)
: Mesh.createEmpty(mesh)
// TODO create empty location iterator when not in unitKinds
@@ -102,7 +102,7 @@ export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisu
if (updateState.createMesh) {
mesh = newProps.unitKinds.includes(unit.kind)
- ? await createMesh(ctx, unit, newProps, mesh)
+ ? await createMesh(ctx, unit, currentStructure, newProps, mesh)
: Mesh.createEmpty(mesh)
ValueCell.update(renderObject.values.drawCount, mesh.triangleCount * 3)
updateState.updateColor = true
diff --git a/src/mol-geo/representation/structure/visual/element-point.ts b/src/mol-geo/representation/structure/visual/element-point.ts
index d0b74c089e9f37c81a817f653f54702e4574fabf..eac5fb80226aad8dc30f67570d11f9c7469cdfe2 100644
--- a/src/mol-geo/representation/structure/visual/element-point.ts
+++ b/src/mol-geo/representation/structure/visual/element-point.ts
@@ -23,7 +23,7 @@ import { SizeThemeProps } from 'mol-view/theme/size';
import { LocationIterator } from '../../../util/location-iterator';
import { createTransforms } from '../../../util/transform-data';
import { StructureGroup } from '../units-visual';
-import { updateRenderableState } from '../../util';
+import { updateRenderableState, updateBaseValues } from '../../util';
export const DefaultElementPointProps = {
...DefaultStructureProps,
@@ -130,6 +130,7 @@ export function ElementPointVisual(): UnitsVisual<ElementPointProps> {
await createSizes(ctx, locationIt, newProps.sizeTheme, renderObject.values)
}
+ updateBaseValues(renderObject.values, newProps)
updateRenderableState(renderObject.state, newProps)
currentProps = newProps
diff --git a/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
new file mode 100644
index 0000000000000000000000000000000000000000..6b894f5a573b51e7f975fa8e5f64cf4340c04caf
--- /dev/null
+++ b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
@@ -0,0 +1,153 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Unit, Structure } from 'mol-model/structure';
+import { UnitsVisual, MeshUpdateState } from '..';
+import { RuntimeContext } from 'mol-task'
+import { Mesh } from '../../../mesh/mesh';
+import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
+import { StructureElementIterator, getElementLoci, markElement } from './util/element';
+import { computeMarchingCubes } from '../../../util/marching-cubes/algorithm';
+import { Tensor, Vec3, Mat4 } from 'mol-math/linear-algebra';
+import { Box3D } from 'mol-math/geometry';
+import { ValueCell } from 'mol-util';
+import { smoothstep } from 'mol-math/interpolate';
+
+export interface GaussianSurfaceMeshProps {
+
+}
+
+function getDelta(box: Box3D) {
+ const extent = Vec3.sub(Vec3.zero(), box.max, box.min)
+
+ const n = Math.pow(128, 3)
+ const f = (extent[0] * extent[1] * extent[2]) / n
+ const s = Math.pow(f, 1 / 3)
+ const size = Vec3.zero()
+ // Vec3.scale(size, extent, s)
+ Vec3.ceil(size, Vec3.scale(size, extent, s))
+ const delta = Vec3.div(Vec3.zero(), extent, size)
+ return delta
+}
+
+async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianSurfaceMeshProps, mesh?: Mesh): Promise<Mesh> {
+
+ const { elements } = unit;
+ const elementCount = elements.length;
+
+ const r = 2.5;
+
+ const v = Vec3.zero()
+ const p = Vec3.zero()
+ const pos = unit.conformation.invariantPosition
+ const box = unit.lookup3d.boundary.box
+ const expandedBox = Box3D.expand(Box3D.empty(), box, Vec3.create(r*3, r*3, r*3));
+ const extent = Vec3.sub(Vec3.zero(), expandedBox.max, expandedBox.min)
+ const min = expandedBox.min
+
+ // const n = Math.pow(128, 3)
+ // const f = (extent[0] * extent[1] * extent[2]) / n
+ // const s = Math.pow(f, 1 / 3)
+ // const size = Vec3.zero()
+ // // Vec3.scale(size, extent, s)
+ // Vec3.ceil(size, Vec3.scale(size, extent, s))
+ // const delta = Vec3.div(Vec3.zero(), extent, size)
+
+ // console.log('extent', extent)
+ // console.log('n', n)
+ // console.log('f', f)
+ // console.log('s', s)
+ // console.log('size', size)
+ // console.log('delta', delta)
+ const delta = getDelta(Box3D.expand(Box3D.empty(), structure.boundary.box, Vec3.create(r*3, r*3, r*3)))
+ const dim = Vec3.zero()
+ Vec3.ceil(dim, Vec3.mul(dim, extent, delta))
+ // console.log('dim', dim, dim[0] * dim[1] * dim[2])
+
+ const space = Tensor.Space(dim, [0, 1, 2], Float32Array)
+ const data = space.create()
+ const field = Tensor.create(space, data)
+
+ for (let i = 0; i < elementCount; i++) {
+ pos(elements[i], v)
+
+ Vec3.mul(v, Vec3.sub(v, v, min), delta)
+
+ const size = r
+ const radius = size * delta[0]
+
+ const minX = Math.floor(v[0] - radius)
+ const minY = Math.floor(v[1] - radius)
+ const minZ = Math.floor(v[2] - radius)
+ const maxX = Math.floor(v[0] + radius)
+ const maxY = Math.floor(v[1] + radius)
+ const maxZ = Math.floor(v[2] + radius)
+
+ for (let x = minX; x <= maxX; ++x) {
+ for (let y = minY; y <= maxY; ++y) {
+ for (let z = minZ; z <= maxZ; ++z) {
+ const dist = Vec3.distance(Vec3.set(p, x, y, z), v)
+ if (dist <= radius) {
+ const density = 1.0 - smoothstep(0.0, radius * 1.0, dist)
+ space.set(data, x, y, z, space.get(data, x, y, z) + density)
+ }
+ }
+ }
+ }
+
+ if (i % 10000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'Gaussian surface', current: i, max: elementCount });
+ }
+ }
+
+ // console.log('data', data)
+
+ const surface = await computeMarchingCubes({
+ isoLevel: 0.1,
+ scalarField: field,
+ oldSurface: mesh
+
+ }).runAsChild(ctx);
+
+ const t = Mat4.identity()
+ Mat4.fromUniformScaling(t, 1 / delta[0])
+ Mat4.setTranslation(t, expandedBox.min)
+
+ ValueCell.update(surface.groupBuffer, new Float32Array(surface.vertexCount))
+ Mesh.transformImmediate(surface, t)
+ await Mesh.computeNormals(surface).runAsChild(ctx)
+
+ // console.log('surface', surface)
+
+ // const transform = VolumeData.getGridToCartesianTransform(volume);
+ // ctx.update({ message: 'Transforming mesh...' });
+ // Mesh.transformImmediate(surface, transform);
+
+ return surface;
+}
+
+export const DefaultGaussianSurfaceProps = {
+ ...DefaultUnitsMeshProps,
+ linearSegments: 8,
+ radialSegments: 12,
+ aspectRatio: 5,
+ arrowFactor: 1.5,
+
+ flipSided: true,
+ // flatShaded: true,
+}
+export type GaussianSurfaceProps = typeof DefaultGaussianSurfaceProps
+
+export function GaussianSurfaceVisual(): UnitsVisual<GaussianSurfaceProps> {
+ return UnitsMeshVisual<GaussianSurfaceProps>({
+ defaultProps: DefaultGaussianSurfaceProps,
+ createMesh: createGaussianSurfaceMesh,
+ createLocationIterator: StructureElementIterator.fromGroup,
+ getLoci: getElementLoci,
+ mark: markElement,
+ setUpdateState: (state: MeshUpdateState, newProps: GaussianSurfaceProps, currentProps: GaussianSurfaceProps) => {}
+ })
+}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
index 9b9452a4191d579a07837137b34ccb22082261ae..a3d6dd8687bc1624fd75fb2b45c2a96e383af1c8 100644
--- a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Unit, Link, StructureElement } from 'mol-model/structure';
+import { Unit, Link, StructureElement, Structure } from 'mol-model/structure';
import { UnitsVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { DefaultLinkCylinderProps, LinkCylinderProps, createLinkCylinderMesh, LinkIterator } from './util/link';
@@ -18,7 +18,7 @@ import { Interval } from 'mol-data/int';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
import { BitFlags } from 'mol-util';
-async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit, props: LinkCylinderProps, mesh?: Mesh) {
+async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: LinkCylinderProps, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
const sizeTheme = SizeTheme(props.sizeTheme)
diff --git a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
index 8b5d893ef85dc1b6ae8b18ea8a651c3427e8872d..dcf176ba3d1fef8188b3b2886be11e7d46beb4c6 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
+import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
@@ -33,7 +33,7 @@ const sVec = Vec3.zero()
const box = Box()
// TODO define props, should be scalable
-async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, props: {}, mesh?: Mesh) {
+async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: {}, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
// TODO better vertex count estimate
diff --git a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
index d975ae940228601a3fd1a833979d28dc2c0dc96e..cd9ca682c0cab90544d44ab88e7958a4858ef956 100644
--- a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
+import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
@@ -23,7 +23,7 @@ export interface PolymerBackboneCylinderProps {
radialSegments: number
}
-async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit, props: PolymerBackboneCylinderProps, mesh?: Mesh) {
+async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: PolymerBackboneCylinderProps, mesh?: Mesh) {
const polymerElementCount = unit.polymerElements.length
if (!polymerElementCount) return Mesh.createEmpty(mesh)
diff --git a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
index 1e6b8e42a198d66249becde9ff3219b723a659ee..bf6afd3f8f2c21565851435caa2f10bbe60fa8cb 100644
--- a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
+import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
@@ -32,7 +32,7 @@ export interface PolymerDirectionWedgeProps {
sizeTheme: SizeThemeProps
}
-async function createPolymerDirectionWedgeMesh(ctx: RuntimeContext, unit: Unit, props: PolymerDirectionWedgeProps, mesh?: Mesh) {
+async function createPolymerDirectionWedgeMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: PolymerDirectionWedgeProps, mesh?: Mesh) {
const polymerElementCount = unit.polymerElements.length
if (!polymerElementCount) return Mesh.createEmpty(mesh)
diff --git a/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts b/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
index 24038dfc3182746c74d2ae0336a5556ff00cfcde..21ebafc2d3ffd91d4160defa3e9412568df14d86 100644
--- a/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
+import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
@@ -24,7 +24,7 @@ export interface PolymerGapCylinderProps {
radialSegments: number
}
-async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, props: PolymerGapCylinderProps, mesh?: Mesh) {
+async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: PolymerGapCylinderProps, mesh?: Mesh) {
const polymerGapCount = unit.gapElements.length
if (!polymerGapCount) return Mesh.createEmpty(mesh)
diff --git a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
index 1a37e4d9809fa189a779c2dcb2b969ccc382dcba..685b0d3c4f6889f3d55586505053c00cb5aba739 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
+import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
@@ -26,7 +26,7 @@ export interface PolymerTraceMeshProps {
// TODO handle polymer ends properly
-async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, props: PolymerTraceMeshProps, mesh?: Mesh) {
+async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: PolymerTraceMeshProps, mesh?: Mesh) {
const polymerElementCount = unit.polymerElements.length
if (!polymerElementCount) return Mesh.createEmpty(mesh)
diff --git a/src/mol-geo/representation/structure/visual/util/element.ts b/src/mol-geo/representation/structure/visual/util/element.ts
index 0de1861eefddaeac2d28b8d6e8f20790f4eca963..6887addab337f1956adcb4c1645e2586c9bbd4ab 100644
--- a/src/mol-geo/representation/structure/visual/util/element.ts
+++ b/src/mol-geo/representation/structure/visual/util/element.ts
@@ -5,7 +5,7 @@
*/
import { Vec3 } from 'mol-math/linear-algebra';
-import { Unit, StructureElement } from 'mol-model/structure';
+import { Unit, StructureElement, Structure } from 'mol-model/structure';
import { RuntimeContext } from 'mol-task';
import { sphereVertexCount } from '../../../../primitive/sphere';
import { Mesh } from '../../../../mesh/mesh';
@@ -22,7 +22,7 @@ export interface ElementSphereMeshProps {
detail: number,
}
-export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, props: ElementSphereMeshProps, mesh?: Mesh) {
+export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: ElementSphereMeshProps, mesh?: Mesh) {
const { detail } = props
const { elements } = unit;
diff --git a/src/mol-gl/shader/chunks/assign-material-color.glsl b/src/mol-gl/shader/chunks/assign-material-color.glsl
index 11b1779411269ab223e03cbbc42a90865a286d69..bc56340c25f74d749e9c8cc6377ac9ca265b2035 100644
--- a/src/mol-gl/shader/chunks/assign-material-color.glsl
+++ b/src/mol-gl/shader/chunks/assign-material-color.glsl
@@ -1,5 +1,7 @@
#if defined(dColorType_uniform)
vec4 material = vec4(uColor, uAlpha);
-#elif defined(dColorType_attribute) || defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance) || defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+#elif defined(dColorType_attribute) || defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance)
+ vec4 material = vec4(vColor.rgb, uAlpha);
+#elif defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
vec4 material = vColor;
#endif
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/carbohydrates/constants.ts b/src/mol-model/structure/structure/carbohydrates/constants.ts
index ed3949f122fb46a6bd1c7de14cce975daf741952..d68c1f81a0eaddfbdf46a2070605caa12e444723 100644
--- a/src/mol-model/structure/structure/carbohydrates/constants.ts
+++ b/src/mol-model/structure/structure/carbohydrates/constants.ts
@@ -182,7 +182,7 @@ export const MonosaccharidesColorTable: [string, Color][] = [
['Alt-family', SaccharideColors.Pink],
['All-family', SaccharideColors.Purple],
['Tal-family', SaccharideColors.LightBlue],
- ['Ido-family', SaccharideColors.Blue],
+ ['Ido-family', SaccharideColors.Brown],
['Fuc-family', SaccharideColors.Red],
['Generic/Unknown/Secondary', SaccharideColors.Secondary],
]