From 3083c7d9e06745deb6d9d5b584a3b7f4ed09bd9c Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 28 Aug 2019 12:04:47 -0700
Subject: [PATCH] overpaint improvements
---
src/mol-plugin/index.ts | 2 +-
src/mol-plugin/state/transforms/helpers.ts | 14 ++++++-
.../util/structure-overpaint-helper.ts | 38 +++++++------------
.../structure/complex-representation.ts | 7 +++-
.../structure/units-representation.ts | 7 +++-
src/mol-theme/overpaint.ts | 10 +++++
6 files changed, 49 insertions(+), 29 deletions(-)
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index a6360d01c..20e7fa253 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -51,7 +51,7 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Action(StateTransforms.Representation.StructureLabels3D),
PluginSpec.Action(StateTransforms.Representation.ExplodeStructureRepresentation3D),
PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
- PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3D),
+ PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3DFromScript),
PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3D),
PluginSpec.Action(StateTransforms.Volume.VolumeFromCcp4),
diff --git a/src/mol-plugin/state/transforms/helpers.ts b/src/mol-plugin/state/transforms/helpers.ts
index 793336dbe..c777529b7 100644
--- a/src/mol-plugin/state/transforms/helpers.ts
+++ b/src/mol-plugin/state/transforms/helpers.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Structure, StructureSelection, QueryContext } from '../../../mol-model/structure';
+import { Structure, StructureSelection, QueryContext, StructureElement } from '../../../mol-model/structure';
import { Color } from '../../../mol-util/color';
import { Overpaint } from '../../../mol-theme/overpaint';
import { parseMolScript } from '../../../mol-script/language/parser';
@@ -25,7 +25,7 @@ function scriptToLoci(structure: Structure, script: Script) {
return StructureSelection.toLoci2(result)
}
-export function getStructureOverpaint(structure: Structure, scriptLayers: { script: Script, color: Color, clear: boolean }[], alpha: number): Overpaint {
+export function getStructureOverpaintFromScript(structure: Structure, scriptLayers: { script: Script, color: Color, clear: boolean }[], alpha: number): Overpaint {
const layers: Overpaint.Layer[] = []
for (let i = 0, il = scriptLayers.length; i < il; ++i) {
const { script, color, clear } = scriptLayers[i]
@@ -34,6 +34,16 @@ export function getStructureOverpaint(structure: Structure, scriptLayers: { scri
return { layers, alpha }
}
+export function getStructureOverpaintFromBundle(structure: Structure, bundleLayers: { bundle: StructureElement.Bundle, color: Color, clear: boolean }[], alpha: number): Overpaint {
+ const layers: Overpaint.Layer[] = []
+ for (let i = 0, il = bundleLayers.length; i < il; ++i) {
+ const { bundle, color, clear } = bundleLayers[i]
+ const loci = StructureElement.Bundle.toLoci(bundle, structure.root)
+ layers.push({ loci, color, clear })
+ }
+ return { layers, alpha }
+}
+
export function getStructureTransparency(structure: Structure, script: Script, value: number, variant: Transparency.Variant): Transparency {
return { loci: scriptToLoci(structure, script), value, variant }
}
diff --git a/src/mol-plugin/util/structure-overpaint-helper.ts b/src/mol-plugin/util/structure-overpaint-helper.ts
index 47b3399f8..43169738b 100644
--- a/src/mol-plugin/util/structure-overpaint-helper.ts
+++ b/src/mol-plugin/util/structure-overpaint-helper.ts
@@ -8,22 +8,12 @@ import { PluginStateObject } from '../../mol-plugin/state/objects';
import { StateTransforms } from '../../mol-plugin/state/transforms';
import { StateSelection, StateObjectCell, StateTransform, StateBuilder } from '../../mol-state';
import { Structure, StructureElement } from '../../mol-model/structure';
-import { isEmptyLoci, EmptyLoci } from '../../mol-model/loci';
import { PluginContext } from '../context';
import { Color } from '../../mol-util/color';
-import { MolScriptBuilder } from '../../mol-script/language/builder';
-import { formatMolScript } from '../../mol-script/language/expression-formatter';
-type OverpaintEachReprCallback = (update: StateBuilder.Root, repr: StateObjectCell<PluginStateObject.Molecule.Structure.Representation3D, StateTransform<typeof StateTransforms.Representation.StructureRepresentation3D>>, rootStructure: Structure, overpaint?: StateObjectCell<any, StateTransform<typeof StateTransforms.Representation.OverpaintStructureRepresentation3D>>) => void
+type OverpaintEachReprCallback = (update: StateBuilder.Root, repr: StateObjectCell<PluginStateObject.Molecule.Structure.Representation3D, StateTransform<typeof StateTransforms.Representation.StructureRepresentation3D>>, overpaint?: StateObjectCell<any, StateTransform<typeof StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle>>) => void
const OverpaintManagerTag = 'overpaint-controls'
-export function getExpression(loci: StructureElement.Loci | EmptyLoci) {
- const scriptExpression = isEmptyLoci(loci)
- ? MolScriptBuilder.struct.generator.empty()
- : StructureElement.Loci.toScriptExpression(loci)
- return formatMolScript(scriptExpression)
-}
-
export class StructureOverpaintHelper {
private async eachRepr(callback: OverpaintEachReprCallback) {
const state = this.plugin.state.dataState;
@@ -31,29 +21,29 @@ export class StructureOverpaintHelper {
const update = state.build();
for (const r of reprs) {
- const overpaint = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Representation.OverpaintStructureRepresentation3D, r.transform.ref).withTag(OverpaintManagerTag));
-
- const structure = r.obj!.data.source.data
-
- callback(update, r, structure.root, overpaint[0])
+ const overpaint = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, r.transform.ref).withTag(OverpaintManagerTag))
+ callback(update, r, overpaint[0])
}
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
}
async set(color: Color | -1, lociGetter: (structure: Structure) => StructureElement.Loci, types?: string[]) {
- await this.eachRepr((update, repr, rootStructure, overpaint) => {
+ await this.eachRepr((update, repr, overpaint) => {
+ console.log(types, repr.params!.values.type.name)
if (types && !types.includes(repr.params!.values.type.name)) return
- // TODO cleanup when loci is full structure or empty
- // TODO add & use QueryOverpaintStructureRepresentation3D
+ // TODO merge overpaint layers, delete shadowed ones
+ // TODO filter overpaint layers for given structure
- const loci = lociGetter(rootStructure)
- if (loci.elements.length === 0) return
- const expression = getExpression(loci)
+ const structure = repr.obj!.data.source.data
+ // always use the root structure to get the loci so the overpaint
+ // stays applicable as long as the root structure does not change
+ const loci = lociGetter(structure.root)
+ if (StructureElement.Loci.isEmpty(loci)) return
const layer = {
- script: { language: 'mol-script', expression },
+ bundle: StructureElement.Bundle.fromLoci(loci),
color: color === -1 ? Color(0) : color,
clear: color === -1
}
@@ -62,7 +52,7 @@ export class StructureOverpaintHelper {
update.to(overpaint).update({ layers: [ ...overpaint.params!.values.layers, layer ], alpha: 1 })
} else {
update.to(repr.transform.ref)
- .apply(StateTransforms.Representation.OverpaintStructureRepresentation3D, { layers: [ layer ], alpha: 1 }, { tags: OverpaintManagerTag });
+ .apply(StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, { layers: [ layer ], alpha: 1 }, { tags: OverpaintManagerTag });
}
})
}
diff --git a/src/mol-repr/structure/complex-representation.ts b/src/mol-repr/structure/complex-representation.ts
index eae6db967..cfe563c8c 100644
--- a/src/mol-repr/structure/complex-representation.ts
+++ b/src/mol-repr/structure/complex-representation.ts
@@ -16,6 +16,7 @@ import { Task } from '../../mol-task';
import { PickingId } from '../../mol-geo/geometry/picking';
import { EmptyLoci, Loci } from '../../mol-model/loci';
import { MarkerAction } from '../../mol-util/marker-action';
+import { Overpaint } from '../../mol-theme/overpaint';
export function ComplexRepresentation<P extends StructureParams>(label: string, ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, P>, visualCtor: (materialId: number) => ComplexVisual<P>): StructureRepresentation<P> {
let version = 0
@@ -73,7 +74,11 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
}
if (state.alphaFactor !== undefined && visual) visual.setAlphaFactor(state.alphaFactor)
if (state.pickable !== undefined && visual) visual.setPickable(state.pickable)
- if (state.overpaint !== undefined && visual) visual.setOverpaint(state.overpaint)
+ if (state.overpaint !== undefined && visual) {
+ // Remap loci from equivalent structure to the current structure
+ const remappedOverpaint = Overpaint.remap(state.overpaint, _structure)
+ visual.setOverpaint(remappedOverpaint)
+ }
if (state.transparency !== undefined && visual) visual.setTransparency(state.transparency)
if (state.transform !== undefined && visual) visual.setTransform(state.transform)
if (state.unitTransforms !== undefined && visual) {
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index 5ae02a3d0..c7a98b433 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -19,6 +19,7 @@ import { Task } from '../../mol-task';
import { PickingId } from '../../mol-geo/geometry/picking';
import { Loci, EmptyLoci, isEmptyLoci } from '../../mol-model/loci';
import { MarkerAction } from '../../mol-util/marker-action';
+import { Overpaint } from '../../mol-theme/overpaint';
export const UnitsParams = {
...StructureParams,
@@ -181,7 +182,11 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, ctx: R
if (visible !== undefined) visuals.forEach(({ visual }) => visual.setVisibility(visible))
if (alphaFactor !== undefined) visuals.forEach(({ visual }) => visual.setAlphaFactor(alphaFactor))
if (pickable !== undefined) visuals.forEach(({ visual }) => visual.setPickable(pickable))
- if (overpaint !== undefined) visuals.forEach(({ visual }) => visual.setOverpaint(overpaint))
+ if (overpaint !== undefined) {
+ // Remap loci from equivalent structure to the current `_structure`
+ const remappedOverpaint = Overpaint.remap(overpaint, _structure)
+ visuals.forEach(({ visual }) => visual.setOverpaint(remappedOverpaint))
+ }
if (transparency !== undefined) visuals.forEach(({ visual }) => visual.setTransparency(transparency))
if (transform !== undefined) visuals.forEach(({ visual }) => visual.setTransform(transform))
if (unitTransforms !== undefined) {
diff --git a/src/mol-theme/overpaint.ts b/src/mol-theme/overpaint.ts
index d885a5de8..2d80d6154 100644
--- a/src/mol-theme/overpaint.ts
+++ b/src/mol-theme/overpaint.ts
@@ -6,6 +6,7 @@
import { Loci } from '../mol-model/loci';
import { Color } from '../mol-util/color';
+import { Structure } from '../mol-model/structure';
export { Overpaint }
@@ -26,4 +27,13 @@ namespace Overpaint {
}
return true
}
+
+ export function remap(overpaint: Overpaint, structure: Structure) {
+ const layers: Overpaint.Layer[] = []
+ for (const layer of overpaint.layers) {
+ const { loci, color, clear } = layer
+ layers.push({ loci: Loci.remap(loci, structure), color, clear })
+ }
+ return { layers, alpha: overpaint.alpha }
+ }
}
\ No newline at end of file
--
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