wip, assembly symmetry

src/mol-model-props/rcsb/representations/assembly-symmetry-axes.ts

@@ -0,0 +1,136 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { RepresentationParamsGetter, RepresentationContext, VisualContext } from 'mol-repr/representation';
+import { ThemeRegistryContext, Theme } from 'mol-theme/theme';
+import { Structure } from 'mol-model/structure';
+import { StructureRepresentationProvider, StructureRepresentation, ComplexRepresentation, ComplexVisual } from 'mol-repr/structure/representation';
+import { AssemblySymmetry } from '../assembly-symmetry';
+import { Table } from 'mol-data/db';
+import { MeshBuilder } from 'mol-geo/geometry/mesh/mesh-builder';
+import { Tensor } from 'mol-math/linear-algebra';
+import { addSphere } from 'mol-geo/geometry/mesh/builder/sphere';
+import { addCylinder } from 'mol-geo/geometry/mesh/builder/cylinder';
+import { VisualUpdateState } from 'mol-repr/util';
+import { ComplexMeshVisual, ComplexMeshParams } from 'mol-repr/structure/complex-visual';
+import { Mesh } from 'mol-geo/geometry/mesh/mesh';
+import { EmptyLoci } from 'mol-model/loci';
+import { LocationIterator } from 'mol-geo/util/location-iterator';
+import { NullLocation } from 'mol-model/location';
+
+export const AssemblySymmetryAxesParams = {
+    ...ComplexMeshParams,
+    sizeFactor: PD.Numeric(0.4, { min: 0, max: 3, step: 0.01 }),
+    radialSegments: PD.Numeric(16, { min: 3, max: 56, step: 1 }),
+    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+    symmetryId: PD.Select<number>(-1, []),
+}
+export type AssemblySymmetryAxesParams = typeof AssemblySymmetryAxesParams
+export function getAssemblySymmetryAxesParams(ctx: ThemeRegistryContext, structure: Structure) {
+    const params = PD.clone(AssemblySymmetryAxesParams)
+
+    if (structure.models[0].customProperties.has(AssemblySymmetry.Descriptor)) {
+        const assemblySymmetry = AssemblySymmetry.get(structure.models[0])!
+        const assemblyName = structure.assemblyName
+        const s = assemblySymmetry.db.rcsb_assembly_symmetry
+        if (s._rowCount) {
+            params.symmetryId.options = []
+            for (let i = 0, il = s._rowCount; i < il; ++i) {
+                if (s.assembly_id.value(i) === assemblyName) {
+                    params.symmetryId.options.push([
+                        s.id.value(i), `${s.symbol.value(i)} ${s.kind.value(i)}`
+                    ])
+                }
+            }
+            params.symmetryId.defaultValue = params.symmetryId.options[0][0]
+        }
+    }
+
+    return params
+}
+
+export type AssemblySymmetryAxesRepresentation = StructureRepresentation<AssemblySymmetryAxesParams>
+export function AssemblySymmetryAxesRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, AssemblySymmetryAxesParams>): AssemblySymmetryAxesRepresentation {
+    return ComplexRepresentation('RCSB Assembly Symmetry Axes', ctx, getParams, AssemblySymmetryAxesVisual)
+}
+
+export const AssemblySymmetryAxesRepresentationProvider: StructureRepresentationProvider<AssemblySymmetryAxesParams> = {
+    label: 'RCSB Assembly Symmetry Axes',
+    description: 'Displays assembly symmetry axes.',
+    factory: AssemblySymmetryAxesRepresentation,
+    getParams: getAssemblySymmetryAxesParams,
+    defaultValues: PD.getDefaultValues(AssemblySymmetryAxesParams),
+    defaultColorTheme: 'uniform',
+    defaultSizeTheme: 'uniform'
+}
+
+//
+
+export function AssemblySymmetryAxesVisual(): ComplexVisual<AssemblySymmetryAxesParams> {
+    return ComplexMeshVisual<AssemblySymmetryAxesParams>({
+        defaultProps: PD.getDefaultValues(AssemblySymmetryAxesParams),
+        createGeometry: createAssemblySymmetryAxesMesh,
+        createLocationIterator,
+        getLoci: () => EmptyLoci,
+        mark: () => false,
+        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<AssemblySymmetryAxesParams>, currentProps: PD.Values<AssemblySymmetryAxesParams>) => {
+            state.createGeometry = (
+                newProps.sizeFactor !== currentProps.sizeFactor ||
+                newProps.detail !== currentProps.detail ||
+                newProps.symmetryId !== currentProps.symmetryId
+            )
+        }
+    })
+}
+
+function createLocationIterator(structure: Structure) {
+    let groupCount = 0
+
+    const assemblySymmetry = AssemblySymmetry.get(structure.models[0])
+    if (assemblySymmetry) {
+        const axis = assemblySymmetry.db.rcsb_assembly_symmetry_axis
+        groupCount = axis._rowCount
+    }
+
+    return LocationIterator(groupCount, 1, () => NullLocation)
+}
+
+export function createAssemblySymmetryAxesMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<AssemblySymmetryAxesParams>, mesh?: Mesh) {
+
+    const { symmetryId, sizeFactor } = props
+
+    const assemblySymmetry = AssemblySymmetry.get(structure.models[0])
+    if (!assemblySymmetry) return Mesh.createEmpty(mesh)
+
+    const s = assemblySymmetry.db.rcsb_assembly_symmetry
+    const symmetry = Table.pickRow(s, i => s.id.value(i) === symmetryId)
+    if (!symmetry) return Mesh.createEmpty(mesh)
+
+    // symmetry.assembly_id not available for structure.assemblyName
+    if (symmetry.assembly_id !== structure.assemblyName) return Mesh.createEmpty(mesh)
+
+    const axes = assemblySymmetry.getAxes(symmetryId)
+    if (!axes._rowCount) return Mesh.createEmpty(mesh)
+
+    const vectorSpace = AssemblySymmetry.Schema.rcsb_assembly_symmetry_axis.start.space;
+    // const colors: Color[] = []
+    // const labels: string[] = []
+    const radius = 1 * sizeFactor
+    const cylinderProps = { radiusTop: radius, radiusBottom: radius }
+    const builderState = MeshBuilder.createState(256, 128, mesh)
+     for (let i = 0, il = axes._rowCount; i < il; ++i) {
+        const start = Tensor.toVec3(vectorSpace, axes.start.value(i))
+        const end = Tensor.toVec3(vectorSpace, axes.end.value(i))
+        builderState.currentGroup = i
+        addSphere(builderState, start, radius, 2)
+        addSphere(builderState, end, radius, 2)
+        addCylinder(builderState, start, end, 1, cylinderProps)
+        // colors.push(Color(0xCCEE11))
+        // labels.push(`Axis ${i + 1} for ${symmetry.kind} ${symmetry.type.toLowerCase()} symmetry`)
+    }
+    return MeshBuilder.getMesh(builderState)
+}

src/mol-model-props/rcsb/themes/assembly-symmetry.ts → src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts

@@ -32,7 +32,7 @@ function clusterMemberKey (asym_id: string, oper_list_ids: string[]) {
 
 export const AssemblySymmetryClusterColorThemeParams = {
     list: PD.Select<ColorListName>('Viridis', ColorListOptions),
-    symmetryId: PD.Select<number>(0, []),
+    symmetryId: PD.Select<number>(-1, []),
 }
 export type AssemblySymmetryClusterColorThemeParams = typeof AssemblySymmetryClusterColorThemeParams
 export function getAssemblySymmetryClusterColorThemeParams(ctx: ThemeDataContext) {
@@ -51,7 +51,7 @@ export function getAssemblySymmetryClusterColorThemeParams(ctx: ThemeDataContext
                     ])
                 }
             }
-            params.symmetryId.defaultValue = s.id.value(0)
+            params.symmetryId.defaultValue = params.symmetryId.options[0][0]
         }
     }
 

src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts

@@ -8,7 +8,8 @@ import { PluginBehavior } from 'mol-plugin/behavior';
 import { ParamDefinition as PD } from 'mol-util/param-definition'
 import { AssemblySymmetry } from 'mol-model-props/rcsb/assembly-symmetry';
 import { CustomPropertyRegistry } from 'mol-plugin/util/custom-prop-registry';
-import { AssemblySymmetryClusterColorThemeProvider } from 'mol-model-props/rcsb/themes/assembly-symmetry';
+import { AssemblySymmetryClusterColorThemeProvider } from 'mol-model-props/rcsb/themes/assembly-symmetry-cluster';
+import { AssemblySymmetryAxesRepresentationProvider } from 'mol-model-props/rcsb/representations/assembly-symmetry-axes';
 
 export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean }>({
     name: 'rcsb-assembly-symmetry-prop',
@@ -27,9 +28,10 @@ export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean
         register(): void {
             this.ctx.customModelProperties.register(this.provider);
 
-            // TODO: support filtering of themes based on the input structure
+            // TODO: support filtering of themes and representations based on the input structure
             // in this case, it would check structure.models[0].customProperties.has(AssemblySymmetry.Descriptor)
             this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.add('rcsb-assembly-symmetry-cluster', AssemblySymmetryClusterColorThemeProvider)
+            this.ctx.structureRepresentation.registry.add('rcsb-assembly-symmetry-axes', AssemblySymmetryAxesRepresentationProvider)
         }
 
         update(p: { autoAttach: boolean }) {
@@ -42,6 +44,7 @@ export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean
         unregister() {
             this.ctx.customModelProperties.unregister(AssemblySymmetry.Descriptor.name);
             this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.remove('rcsb-assembly-symmetry-cluster')
+            this.ctx.structureRepresentation.registry.remove('rcsb-assembly-symmetry-axes')
         }
     },
     params: () => ({

src/mol-repr/structure/representation/ball-and-stick.ts

@@ -43,7 +43,7 @@ export function BallAndStickRepresentation(ctx: RepresentationContext, getParams
     return Representation.createMulti('Ball & Stick', ctx, getParams, BallAndStickVisuals as unknown as Representation.Def<Structure, BallAndStickParams>)
 }
 
-export const BallAndStickRepresentationProvider: StructureRepresentationProvider<typeof BallAndStickParams> = {
+export const BallAndStickRepresentationProvider: StructureRepresentationProvider<BallAndStickParams> = {
     label: 'Ball & Stick',
     description: 'Displays atoms as spheres and bonds as cylinders.',
     factory: BallAndStickRepresentation,

src/mol-repr/structure/representation/distance-restraint.ts

@@ -31,7 +31,7 @@ export function DistanceRestraintRepresentation(ctx: RepresentationContext, getP
     return Representation.createMulti('DistanceRestraint', ctx, getParams, DistanceRestraintVisuals as unknown as Representation.Def<Structure, DistanceRestraintParams>)
 }
 
-export const DistanceRestraintRepresentationProvider: StructureRepresentationProvider<typeof DistanceRestraintParams> = {
+export const DistanceRestraintRepresentationProvider: StructureRepresentationProvider<DistanceRestraintParams> = {
     label: 'Distance Restraint',
     description: 'Displays cross-link distance restraints.',
     factory: DistanceRestraintRepresentation,

src/mol-repr/structure/representation/spacefill.ts

@@ -31,7 +31,7 @@ export function SpacefillRepresentation(ctx: RepresentationContext, getParams: R
     return Representation.createMulti('Spacefill', ctx, getParams, SpacefillVisuals as unknown as Representation.Def<Structure, SpacefillParams>)
 }
 
-export const SpacefillRepresentationProvider: StructureRepresentationProvider<typeof SpacefillParams> = {
+export const SpacefillRepresentationProvider: StructureRepresentationProvider<SpacefillParams> = {
     label: 'Spacefill',
     description: 'Displays atoms as spheres.',
     factory: SpacefillRepresentation,