diff --git a/src/mol-model-formats/structure/mmcif/secondary-structure.ts b/src/mol-model-formats/structure/mmcif/secondary-structure.ts
index 0ba80546f6aa6d92d472d0a541f4dd7aed16671b..5d83fad54b63c7200e1cb8278d3edb11ec0beb3a 100644
--- a/src/mol-model-formats/structure/mmcif/secondary-structure.ts
+++ b/src/mol-model-formats/structure/mmcif/secondary-structure.ts
@@ -11,12 +11,12 @@ import { AtomicHierarchy, AtomicConformation } from 'mol-model/structure/model/p
import { SecondaryStructure } from 'mol-model/structure/model/properties/seconday-structure';
import { Column } from 'mol-data/db';
import { ChainIndex, ResidueIndex } from 'mol-model/structure/model/indexing';
-import { computeSecondaryStructure } from 'mol-model/structure/model/properties/utils/secondary-structure';
+import { computeModelDSSP } from 'mol-model-props/computed/secondary-structure/dssp';
// TODO add parameter to allow forcing computation
export function getSecondaryStructure(data: mmCIF_Database, hierarchy: AtomicHierarchy, conformation: AtomicConformation): SecondaryStructure {
if (!data.struct_conf._rowCount && !data.struct_sheet_range._rowCount) {
- return computeSecondaryStructure(hierarchy, conformation)
+ return computeModelDSSP(hierarchy, conformation)
} else {
return getSecondaryStructureMmCif(data, hierarchy)
}
@@ -36,7 +36,7 @@ export function getSecondaryStructureMmCif(data: mmCIF_Database, hierarchy: Atom
};
if (map.size > 0) assignSecondaryStructureRanges(hierarchy, map, secStruct);
- return secStruct;
+ return SecondaryStructure(secStruct.type, secStruct.key, secStruct.elements);
}
type SecondaryStructureEntry = {
diff --git a/src/mol-model-props/computed/secondary-structure.ts b/src/mol-model-props/computed/secondary-structure.ts
index 82cb45c68cf5b62276e691445e90003f58385490..48fe6ee221b06f4a29e9b35e032c9736328fc03a 100644
--- a/src/mol-model-props/computed/secondary-structure.ts
+++ b/src/mol-model-props/computed/secondary-structure.ts
@@ -6,21 +6,24 @@
import { CustomPropertyDescriptor, Structure } from 'mol-model/structure';
import { Task } from 'mol-task';
+import { DSSPComputationParams, computeModelDSSP } from './secondary-structure/dssp';
+import { SecondaryStructure } from 'mol-model/structure/model/properties/seconday-structure';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
export namespace ComputedSecondaryStructure {
- export type Property = {} // TODO
+ export type Property = SecondaryStructure
export function get(structure: Structure): Property | undefined {
- return structure.currentPropertyData.__ComputedSecondaryStructure__;
+ return structure.inheritedPropertyData.__ComputedSecondaryStructure__;
}
function set(structure: Structure, prop: Property) {
- (structure.currentPropertyData.__ComputedSecondaryStructure__ as Property) = prop;
+ (structure.inheritedPropertyData.__ComputedSecondaryStructure__ as Property) = prop;
}
- export function createAttachTask() {
+ export function createAttachTask(params: Partial<SecondaryStructureComputationProps> = {}) {
return (structure: Structure) => Task.create('Compute Secondary Structure', async ctx => {
if (get(structure)) return true;
- return await attachFromCifOrCompute(structure, ctx)
+ return await attachFromCifOrCompute(structure, params)
});
}
@@ -30,12 +33,10 @@ export namespace ComputedSecondaryStructure {
// TODO `cifExport` and `symbol`
});
- export async function attachFromCifOrCompute(structure: Structure, params: {
- // TODO params
- }) {
+ export async function attachFromCifOrCompute(structure: Structure, params: Partial<SecondaryStructureComputationProps> = {}) {
if (structure.customPropertyDescriptors.has(Descriptor)) return true;
- const compSecStruc = computeSecondaryStructure(structure)
+ const compSecStruc = computeSecondaryStructure(structure, params)
structure.customPropertyDescriptors.add(Descriptor);
set(structure, compSecStruc);
@@ -43,14 +44,15 @@ export namespace ComputedSecondaryStructure {
}
}
-// export const SecondaryStructureComputationParams = {
-// oldDefinition: PD.Boolean(true, { description: 'Whether to use the old DSSP convention for the annotation of turns and helices, causes them to be two residues shorter' }),
-// oldOrdering: PD.Boolean(true, { description: 'Alpha-helices are preferred over 3-10 helices' })
-// }
-// export type SecondaryStructureComputationParams = typeof SecondaryStructureComputationParams
-
-function computeSecondaryStructure(structure: Structure): ComputedSecondaryStructure.Property {
- // TODO
- console.log('TODO calc secondary structure')
- return {}
+export const SecondaryStructureComputationParams = {
+ ...DSSPComputationParams
+}
+export type SecondaryStructureComputationParams = typeof SecondaryStructureComputationParams
+export type SecondaryStructureComputationProps = PD.Values<SecondaryStructureComputationParams>
+
+function computeSecondaryStructure(structure: Structure, params: Partial<SecondaryStructureComputationProps>): ComputedSecondaryStructure.Property {
+ // TODO compute from structure not from model
+ // TODO use Zhang-Skolnik for CA alpha only parts or for coarse parts with per-residue elements
+ const { atomicHierarchy, atomicConformation } = structure.model
+ return computeModelDSSP(atomicHierarchy, atomicConformation, params)
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/utils/secondary-structure.ts b/src/mol-model-props/computed/secondary-structure/dssp.ts
similarity index 97%
rename from src/mol-model/structure/model/properties/utils/secondary-structure.ts
rename to src/mol-model-props/computed/secondary-structure/dssp.ts
index 7dcd761b8942c66e2815f857dd1401524b68e64b..af16b2814453134390c499866da863af5b7dad33 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.ts
+++ b/src/mol-model-props/computed/secondary-structure/dssp.ts
@@ -14,9 +14,9 @@ import { SortedArray } from 'mol-data/int';
import { IntAdjacencyGraph } from 'mol-math/graph';
import { BitFlags } from 'mol-util';
import { ElementIndex } from 'mol-model/structure/model/indexing';
-import { AtomicHierarchy, AtomicConformation } from '../atomic';
import { ParamDefinition as PD } from 'mol-util/param-definition'
import { radToDeg } from 'mol-math/misc';
+import { AtomicHierarchy, AtomicConformation } from 'mol-model/structure/model/properties/atomic';
/**
* TODO bugs to fix:
@@ -47,7 +47,7 @@ const hbondEnergyCutoff = -0.5
const hbondEnergyMinimal = -9.9
interface DSSPContext {
- params: Partial<PD.Values<SecondaryStructureComputationParams>>,
+ params: Partial<PD.Values<DSSPComputationParams>>,
getResidueFlag: (f: DSSPType) => SecondaryStructureType,
getFlagName: (f: DSSPType) => String,
@@ -113,22 +113,17 @@ namespace DSSPType {
}
}
-export const SecondaryStructureComputationParams = {
+export const DSSPComputationParams = {
oldDefinition: PD.Boolean(true, { description: 'Whether to use the old DSSP convention for the annotation of turns and helices, causes them to be two residues shorter' }),
oldOrdering: PD.Boolean(true, { description: 'Alpha-helices are preferred over 3-10 helices' })
}
-export type SecondaryStructureComputationParams = typeof SecondaryStructureComputationParams
-
-export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
- conformation: AtomicConformation) {
- // TODO use Zhang-Skolnik for CA alpha only parts or for coarse parts with per-residue elements
- return computeModelDSSP(hierarchy, conformation)
-}
+export type DSSPComputationParams = typeof DSSPComputationParams
+export type DSSPComputationProps = PD.Values<DSSPComputationParams>
export function computeModelDSSP(hierarchy: AtomicHierarchy,
conformation: AtomicConformation,
- params: Partial<PD.Values<SecondaryStructureComputationParams>> = {}): SecondaryStructure {
- params = { ...PD.getDefaultValues(SecondaryStructureComputationParams), ...params };
+ params: Partial<DSSPComputationProps> = {}): SecondaryStructure {
+ params = { ...PD.getDefaultValues(DSSPComputationParams), ...params };
const { lookup3d, proteinResidues } = calcAtomicTraceLookup3D(hierarchy, conformation)
const backboneIndices = calcBackboneAtomIndices(hierarchy, proteinResidues)
@@ -187,13 +182,7 @@ export function computeModelDSSP(hierarchy: AtomicHierarchy,
keys[i] = elements.length - 1
}
- const secondaryStructure: SecondaryStructure = {
- type,
- key: keys,
- elements: elements
- }
-
- return secondaryStructure
+ return SecondaryStructure(type, keys, elements)
}
function createElement(kind: string, flag: DSSPType.Flag, getResidueFlag: (f: DSSPType) => SecondaryStructureType): SecondaryStructure.Element {
diff --git a/src/mol-model/structure/model/properties/utils/secondary-structure.validation b/src/mol-model-props/computed/secondary-structure/dssp.validation
similarity index 100%
rename from src/mol-model/structure/model/properties/utils/secondary-structure.validation
rename to src/mol-model-props/computed/secondary-structure/dssp.validation
diff --git a/src/mol-model-props/computed/secondary-structure/zhang-skolnik.ts b/src/mol-model-props/computed/secondary-structure/zhang-skolnik.ts
new file mode 100644
index 0000000000000000000000000000000000000000..0ffdd02fcbce683e436c0030ffe0517135c6ceda
--- /dev/null
+++ b/src/mol-model-props/computed/secondary-structure/zhang-skolnik.ts
@@ -0,0 +1 @@
+// TODO
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/seconday-structure.ts b/src/mol-model/structure/model/properties/seconday-structure.ts
index 9434507ebc9ae1a11b2fc02f4cb9e00d0d4c4d0c..ce78f5589acaf7356d46469e9dc2f063a14550e9 100644
--- a/src/mol-model/structure/model/properties/seconday-structure.ts
+++ b/src/mol-model/structure/model/properties/seconday-structure.ts
@@ -5,17 +5,24 @@
*/
import { SecondaryStructureType } from '../types';
+import { idFactory } from 'mol-util/id-factory';
+
+const getNextSecondaryStructureId = idFactory()
/** Secondary structure "indexed" by residues. */
interface SecondaryStructure {
+ readonly id: number
readonly type: ArrayLike<SecondaryStructureType>,
-
/** index into the elements array */
readonly key: ArrayLike<number>,
/** indexed by key */
readonly elements: ReadonlyArray<SecondaryStructure.Element>
}
+function SecondaryStructure(type: SecondaryStructure['type'], key: SecondaryStructure['key'], elements: SecondaryStructure['elements']) {
+ return { id: getNextSecondaryStructureId(), type, key, elements }
+}
+
namespace SecondaryStructure {
export type Element = None | Turn | Helix | Sheet
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts b/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
index eb401d9cd247118420b04c02a06d3ac1eb975020..f4bf9307cf4b9d0dfbe115e08856a514505d40be 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
@@ -53,6 +53,7 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
}
unregister() {
+ console.log('unregister')
this.ctx.customModelProperties.unregister(StructureQualityReport.Descriptor.name);
this.ctx.lociLabels.removeProvider(labelPDBeValidation);
this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.remove('pdbe-structure-quality-report')
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index 0cc0bf9274c6ba4484e871bcc87300770119b993..f42df562b0d99b868cb49759faf5c633082dfd96 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/src/mol-repr/structure/complex-visual.ts
@@ -106,8 +106,13 @@ export function ComplexVisual<G extends Geometry, P extends ComplexParams & Geom
updateState.createGeometry = true
}
- if (!ColorTheme.areEqual(theme.color, currentTheme.color)) updateState.updateColor = true
- if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) updateState.createGeometry = true
+ if (!ColorTheme.areEqual(theme.color, currentTheme.color)) {
+ updateState.updateColor = true
+ }
+
+ if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) {
+ updateState.createGeometry = true
+ }
if (updateState.createGeometry) {
updateState.updateColor = true
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index bad9e645c3e32c8137c6ef0438b9bdc2219b06ae..f622140015e3bf5e579fb3026f326e9abea19cf0 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -53,7 +53,7 @@ interface UnitsVisualBuilder<P extends UnitsParams, G extends Geometry> {
createLocationIterator(group: Unit.SymmetryGroup): LocationIterator
getLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Loci
eachLocation(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean
- setUpdateState(state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme): void
+ setUpdateState(state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup): void
}
interface UnitsVisualGeometryBuilder<P extends UnitsParams, G extends Geometry> extends UnitsVisualBuilder<P, G> {
@@ -100,12 +100,13 @@ export function UnitsVisual<G extends Geometry, P extends UnitsParams & Geometry
return
}
- setUpdateState(updateState, newProps, currentProps, theme, currentTheme)
+ setUpdateState(updateState, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup)
- if (!ColorTheme.areEqual(theme.color, currentTheme.color)) {
+ if (!ColorTheme.areEqual(newTheme.color, currentTheme.color)) {
// console.log('new colorTheme')
updateState.updateColor = true
}
+
if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) {
// console.log('new unitKinds')
updateState.createGeometry = true
@@ -121,10 +122,12 @@ export function UnitsVisual<G extends Geometry, P extends UnitsParams & Geometry
}
// check if the conformation of unit.model has changed
- // if (Unit.conformationId(newStructureGroup.group.units[0]) !== Unit.conformationId(currentStructureGroup.group.units[0])) {
- if (Unit.conformationId(newStructureGroup.group.units[0]) !== Unit.conformationId(currentStructureGroup.group.units[0])
+ const newUnit = newStructureGroup.group.units[0]
+ const currentUnit = currentStructureGroup.group.units[0]
+ // if (Unit.conformationId(newUnit) !== Unit.conformationId(currentUnit)) {
+ if (Unit.conformationId(newUnit) !== Unit.conformationId(currentUnit)
// TODO: this needs more attention
- || newStructureGroup.group.units[0].conformation !== currentStructureGroup.group.units[0].conformation) {
+ || newUnit.conformation !== currentUnit.conformation) {
// console.log('new conformation')
updateState.updateTransform = true;
updateState.createGeometry = true
@@ -270,8 +273,8 @@ export interface UnitsMeshVisualBuilder<P extends UnitsMeshParams> extends Units
export function UnitsMeshVisual<P extends UnitsMeshParams>(builder: UnitsMeshVisualBuilder<P>, materialId: number): UnitsVisual<P> {
return UnitsVisual<Mesh, StructureMeshParams & UnitsParams>({
...builder,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
- builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
+ builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup)
if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.createGeometry = true
},
geometryUtils: Mesh.Utils
@@ -287,8 +290,8 @@ export interface UnitsSpheresVisualBuilder<P extends UnitsSpheresParams> extends
export function UnitsSpheresVisual<P extends UnitsSpheresParams>(builder: UnitsSpheresVisualBuilder<P>, materialId: number): UnitsVisual<P> {
return UnitsVisual<Spheres, StructureSpheresParams & UnitsParams>({
...builder,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
- builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
+ builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup)
if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.updateSize = true
},
geometryUtils: Spheres.Utils
@@ -304,8 +307,8 @@ export interface UnitsPointVisualBuilder<P extends UnitsPointsParams> extends Un
export function UnitsPointsVisual<P extends UnitsPointsParams>(builder: UnitsPointVisualBuilder<P>, materialId: number): UnitsVisual<P> {
return UnitsVisual<Points, StructurePointsParams & UnitsParams>({
...builder,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
- builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
+ builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup)
if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.updateSize = true
},
geometryUtils: Points.Utils
@@ -321,8 +324,8 @@ export interface UnitsLinesVisualBuilder<P extends UnitsLinesParams> extends Uni
export function UnitsLinesVisual<P extends UnitsLinesParams>(builder: UnitsLinesVisualBuilder<P>, materialId: number): UnitsVisual<P> {
return UnitsVisual<Lines, StructureLinesParams & UnitsParams>({
...builder,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
- builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
+ builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup)
if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.updateSize = true
},
geometryUtils: Lines.Utils
@@ -338,8 +341,8 @@ export interface UnitsDirectVolumeVisualBuilder<P extends UnitsDirectVolumeParam
export function UnitsDirectVolumeVisual<P extends UnitsDirectVolumeParams>(builder: UnitsDirectVolumeVisualBuilder<P>, materialId: number): UnitsVisual<P> {
return UnitsVisual<DirectVolume, StructureDirectVolumeParams & UnitsParams>({
...builder,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
- builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
+ builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup)
if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.createGeometry = true
},
geometryUtils: DirectVolume.Utils
@@ -355,8 +358,8 @@ export interface UnitsTextureMeshVisualBuilder<P extends UnitsTextureMeshParams>
export function UnitsTextureMeshVisual<P extends UnitsTextureMeshParams>(builder: UnitsTextureMeshVisualBuilder<P>, materialId: number): UnitsVisual<P> {
return UnitsVisual<TextureMesh, StructureTextureMeshParams & UnitsParams>({
...builder,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
- builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
+ builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup)
if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.createGeometry = true
},
geometryUtils: TextureMesh.Utils
diff --git a/src/mol-repr/structure/visual/polymer-direction-wedge.ts b/src/mol-repr/structure/visual/polymer-direction-wedge.ts
index 43712a89d45b50cd00ffd9e810b4d11220c31d45..46523a359151140fdd2acd8b1a2e2b179a3fbea7 100644
--- a/src/mol-repr/structure/visual/polymer-direction-wedge.ts
+++ b/src/mol-repr/structure/visual/polymer-direction-wedge.ts
@@ -50,7 +50,7 @@ function createPolymerDirectionWedgeMesh(ctx: VisualContext, unit: Unit, structu
const { normalVectors, binormalVectors } = state
let i = 0
- const polymerTraceIt = PolymerTraceIterator(unit)
+ const polymerTraceIt = PolymerTraceIterator(unit, structure)
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move()
builderState.currentGroup = i
diff --git a/src/mol-repr/structure/visual/polymer-trace-mesh.ts b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
index 8f4f73616d44174479907ca2157e6efadb761475..fd8716ee9399b6f3b9f5b1ff59dea59d7611c48c 100644
--- a/src/mol-repr/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-trace-mesh.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>
*/
@@ -9,7 +9,7 @@ import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator, getPolymerElementLoci, eachPolymerElement, interpolateSizes } from './util/polymer';
import { SecondaryStructureType, isNucleic } from 'mol-model/structure/model/types';
-import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
+import { UnitsMeshVisual, UnitsMeshParams, StructureGroup } from '../units-visual';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { Mesh } from 'mol-geo/geometry/mesh/mesh';
import { MeshBuilder } from 'mol-geo/geometry/mesh/mesh-builder';
@@ -17,6 +17,8 @@ import { addSheet } from 'mol-geo/geometry/mesh/builder/sheet';
import { addTube } from 'mol-geo/geometry/mesh/builder/tube';
import { VisualContext } from 'mol-repr/visual';
import { Theme } from 'mol-theme/theme';
+import { ComputedSecondaryStructure } from 'mol-model-props/computed/secondary-structure';
+import { SecondaryStructure } from 'mol-model/structure/model/properties/seconday-structure';
export const PolymerTraceMeshParams = {
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
@@ -44,7 +46,7 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
const { curvePoints, normalVectors, binormalVectors, widthValues, heightValues } = state
let i = 0
- const polymerTraceIt = PolymerTraceIterator(unit)
+ const polymerTraceIt = PolymerTraceIterator(unit, structure)
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move()
builderState.currentGroup = i
@@ -111,7 +113,7 @@ export function PolymerTraceVisual(materialId: number): UnitsVisual<PolymerTrace
createLocationIterator: PolymerLocationIterator.fromGroup,
getLoci: getPolymerElementLoci,
eachLocation: eachPolymerElement,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerTraceParams>, currentProps: PD.Values<PolymerTraceParams>) => {
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerTraceParams>, currentProps: PD.Values<PolymerTraceParams>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.linearSegments !== currentProps.linearSegments ||
@@ -119,6 +121,12 @@ export function PolymerTraceVisual(materialId: number): UnitsVisual<PolymerTrace
newProps.aspectRatio !== currentProps.aspectRatio ||
newProps.arrowFactor !== currentProps.arrowFactor
)
+
+ const computedSecondaryStructure = ComputedSecondaryStructure.get(newStructureGroup.structure)
+ if ((state.info.computedSecondaryStructure as SecondaryStructure) !== computedSecondaryStructure) {
+ state.createGeometry = true;
+ state.info.computedSecondaryStructure = computedSecondaryStructure
+ }
}
}, materialId)
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/polymer-tube-mesh.ts b/src/mol-repr/structure/visual/polymer-tube-mesh.ts
index 8f433bf01a8c4ba16704f1e13601db57148fd33e..4678499c11b606519af8862339a8fc2892aa3502 100644
--- a/src/mol-repr/structure/visual/polymer-tube-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-tube-mesh.ts
@@ -40,7 +40,7 @@ function createPolymerTubeMesh(ctx: VisualContext, unit: Unit, structure: Struct
const { curvePoints, normalVectors, binormalVectors, widthValues, heightValues } = state
let i = 0
- const polymerTraceIt = PolymerTraceIterator(unit)
+ const polymerTraceIt = PolymerTraceIterator(unit, structure)
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move()
builderState.currentGroup = i
diff --git a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
index 6216c5307bf739bda64629d24387b3754b68e94a..9ecccfa49ec77f9f5587d02ef3c7dc3e7e8bb897 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, StructureElement, ElementIndex, ResidueIndex } from 'mol-model/structure';
+import { Unit, StructureElement, ElementIndex, ResidueIndex, Structure } from 'mol-model/structure';
import { Segmentation } from 'mol-data/int';
import { MoleculeType, SecondaryStructureType } from 'mol-model/structure/model/types';
import Iterator from 'mol-data/iterator';
@@ -13,17 +13,18 @@ import SortedRanges from 'mol-data/int/sorted-ranges';
import { CoarseSphereConformation, CoarseGaussianConformation } from 'mol-model/structure/model/properties/coarse';
import { getPolymerRanges } from '../polymer';
import { AtomicConformation } from 'mol-model/structure/model/properties/atomic';
+import { ComputedSecondaryStructure } from 'mol-model-props/computed/secondary-structure';
/**
* Iterates over individual residues/coarse elements in polymers of a unit while
* providing information about the neighbourhood in the underlying model for drawing splines
*/
-export function PolymerTraceIterator(unit: Unit): Iterator<PolymerTraceElement> {
+export function PolymerTraceIterator(unit: Unit, structure: Structure): Iterator<PolymerTraceElement> {
switch (unit.kind) {
- case Unit.Kind.Atomic: return new AtomicPolymerTraceIterator(unit)
+ case Unit.Kind.Atomic: return new AtomicPolymerTraceIterator(unit, structure)
case Unit.Kind.Spheres:
case Unit.Kind.Gaussians:
- return new CoarsePolymerTraceIterator(unit)
+ return new CoarsePolymerTraceIterator(unit, structure)
}
}
@@ -236,18 +237,20 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
return this.value;
}
- constructor(private unit: Unit.Atomic) {
+ constructor(private unit: Unit.Atomic, structure: Structure) {
this.atomicConformation = unit.model.atomicConformation
this.residueAtomSegments = unit.model.atomicHierarchy.residueAtomSegments
this.traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex as ArrayLike<ElementIndex> // can assume it won't be -1 for polymer residues
this.directionElementIndex = unit.model.atomicHierarchy.derived.residue.directionElementIndex
this.moleculeType = unit.model.atomicHierarchy.derived.residue.moleculeType
this.cyclicPolymerMap = unit.model.atomicHierarchy.cyclicPolymerMap
- this.secondaryStructureType = unit.model.properties.secondaryStructure.type
this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements)
this.residueIt = Segmentation.transientSegments(this.residueAtomSegments, unit.elements);
this.value = createPolymerTraceElement(unit)
this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext
+
+ const computedSecondaryStructure = ComputedSecondaryStructure.get(structure)
+ this.secondaryStructureType = (computedSecondaryStructure && computedSecondaryStructure.type) || unit.model.properties.secondaryStructure.type
}
}
@@ -316,7 +319,7 @@ export class CoarsePolymerTraceIterator implements Iterator<PolymerTraceElement>
return this.value;
}
- constructor(private unit: Unit.Spheres | Unit.Gaussians) {
+ constructor(private unit: Unit.Spheres | Unit.Gaussians, structure: Structure) {
this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
this.value = createPolymerTraceElement(unit)
switch (unit.kind) {
diff --git a/src/mol-repr/util.ts b/src/mol-repr/util.ts
index d4428fad2a1b15fedbe677377346e0f093156dea..e9e1a5962157dc8d1980230d4bf22a225704d7d4 100644
--- a/src/mol-repr/util.ts
+++ b/src/mol-repr/util.ts
@@ -15,6 +15,9 @@ export interface VisualUpdateState {
updateSize: boolean
createGeometry: boolean
createNew: boolean
+
+ /** holds contextual info, is not reset */
+ info: { [k: string]: unknown }
}
export namespace VisualUpdateState {
export function create(): VisualUpdateState {
@@ -25,6 +28,8 @@ export namespace VisualUpdateState {
updateSize: false,
createGeometry: false,
createNew: false,
+
+ info: {}
}
}
export function reset(state: VisualUpdateState) {
diff --git a/src/mol-theme/color.ts b/src/mol-theme/color.ts
index cab7d59fcd15c3839d33722eed8d6d929908f7ec..a2c2417686935eb95a0ea3385591d38e0f8ba0f5 100644
--- a/src/mol-theme/color.ts
+++ b/src/mol-theme/color.ts
@@ -36,6 +36,7 @@ interface ColorTheme<P extends PD.Params> {
readonly granularity: ColorType
readonly color: LocationColor
readonly props: Readonly<PD.Values<P>>
+ readonly contextHash?: number
readonly description?: string
readonly legend?: Readonly<ScaleLegend | TableLegend>
}
@@ -44,10 +45,15 @@ namespace ColorTheme {
export type Factory<P extends PD.Params> = (ctx: ThemeDataContext, props: PD.Values<P>) => ColorTheme<P>
export const EmptyFactory = () => Empty
const EmptyColor = Color(0xCCCCCC)
- export const Empty: ColorTheme<{}> = { factory: EmptyFactory, granularity: 'uniform', color: () => EmptyColor, props: {} }
+ export const Empty: ColorTheme<{}> = {
+ factory: EmptyFactory,
+ granularity: 'uniform',
+ color: () => EmptyColor,
+ props: {}
+ }
export function areEqual(themeA: ColorTheme<any>, themeB: ColorTheme<any>) {
- return themeA.factory === themeB.factory && deepEqual(themeA.props, themeB.props)
+ return themeA.contextHash === themeB.contextHash && themeA.factory === themeB.factory && deepEqual(themeA.props, themeB.props)
}
export interface Provider<P extends PD.Params> extends ThemeProvider<ColorTheme<P>, P> { }
diff --git a/src/mol-theme/color/secondary-structure.ts b/src/mol-theme/color/secondary-structure.ts
index cb8878f28b77889d830573b5609a3b1c32feed6e..5711250af7834f0bdf688c6817a9d9c323d998d5 100644
--- a/src/mol-theme/color/secondary-structure.ts
+++ b/src/mol-theme/color/secondary-structure.ts
@@ -13,6 +13,8 @@ import { getElementMoleculeType } from 'mol-model/structure/util';
import { ParamDefinition as PD } from 'mol-util/param-definition'
import { ThemeDataContext } from '../theme';
import { TableLegend } from 'mol-util/color/tables';
+import { ComputedSecondaryStructure } from 'mol-model-props/computed/secondary-structure';
+import { SecondaryStructure } from 'mol-model/structure/model/properties/seconday-structure';
// from Jmol http://jmol.sourceforge.net/jscolors/ (shapely)
const SecondaryStructureColors = ColorMap({
@@ -40,10 +42,12 @@ export function getSecondaryStructureColorThemeParams(ctx: ThemeDataContext) {
return SecondaryStructureColorThemeParams // TODO return copy
}
-export function secondaryStructureColor(unit: Unit, element: ElementIndex): Color {
+export function secondaryStructureColor(unit: Unit, element: ElementIndex, computedSecondaryStructure: SecondaryStructure | undefined): Color {
let secStrucType = SecondaryStructureType.create(SecondaryStructureType.Flag.None)
if (Unit.isAtomic(unit)) {
- secStrucType = unit.model.properties.secondaryStructure.type[unit.residueIndex[element]]
+ secStrucType = computedSecondaryStructure ?
+ computedSecondaryStructure.type[unit.residueIndex[element]] :
+ unit.model.properties.secondaryStructure.type[unit.residueIndex[element]]
}
if (SecondaryStructureType.is(secStrucType, SecondaryStructureType.Flag.Helix)) {
@@ -75,11 +79,16 @@ export function secondaryStructureColor(unit: Unit, element: ElementIndex): Colo
}
export function SecondaryStructureColorTheme(ctx: ThemeDataContext, props: PD.Values<SecondaryStructureColorThemeParams>): ColorTheme<SecondaryStructureColorThemeParams> {
+
+ const computedSecondaryStructure = ctx.structure && ComputedSecondaryStructure.get(ctx.structure)
+ // use `computedSecondaryStructure.id` as context hash, when available
+ const contextHash = computedSecondaryStructure && computedSecondaryStructure.id
+
function color(location: Location): Color {
if (StructureElement.isLocation(location)) {
- return secondaryStructureColor(location.unit, location.element)
+ return secondaryStructureColor(location.unit, location.element, computedSecondaryStructure)
} else if (Link.isLocation(location)) {
- return secondaryStructureColor(location.aUnit, location.aUnit.elements[location.aIndex])
+ return secondaryStructureColor(location.aUnit, location.aUnit.elements[location.aIndex], computedSecondaryStructure)
}
return DefaultSecondaryStructureColor
}
@@ -89,6 +98,7 @@ export function SecondaryStructureColorTheme(ctx: ThemeDataContext, props: PD.Va
granularity: 'group',
color,
props,
+ contextHash,
description: Description,
legend: TableLegend(Object.keys(SecondaryStructureColors).map(name => {
return [name, (SecondaryStructureColors as any)[name] as Color] as [string, Color]
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index 290afa43d6b56c3b607aafcfdf98f8a7ac46724d..7529018f0976d3d9deefa9c5ade68a7867314aa9 100644
--- a/src/tests/browser/render-structure.ts
+++ b/src/tests/browser/render-structure.ts
@@ -12,10 +12,10 @@ import { ColorTheme } from 'mol-theme/color';
import { SizeTheme } from 'mol-theme/size';
import { CartoonRepresentationProvider } from 'mol-repr/structure/representation/cartoon';
import { trajectoryFromMmCIF } from 'mol-model-formats/structure/mmcif';
-import { computeModelDSSP } from 'mol-model/structure/model/properties/utils/secondary-structure';
import { MolecularSurfaceRepresentationProvider } from 'mol-repr/structure/representation/molecular-surface';
import { BallAndStickRepresentationProvider } from 'mol-repr/structure/representation/ball-and-stick';
import { GaussianSurfaceRepresentationProvider } from 'mol-repr/structure/representation/gaussian-surface';
+import { computeModelDSSP } from 'mol-model-props/computed/secondary-structure/dssp';
const parent = document.getElementById('app')!
parent.style.width = '100%'