diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 20e7fa253a5b760265f57161dad7ef5c5240bcdf..209daad2cf8211815ed338108973b88dfb217af1 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -52,7 +52,7 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Action(StateTransforms.Representation.ExplodeStructureRepresentation3D),
PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3DFromScript),
- PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3D),
+ PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3DFromScript),
PluginSpec.Action(StateTransforms.Volume.VolumeFromCcp4),
PluginSpec.Action(StateTransforms.Representation.VolumeRepresentation3D),
diff --git a/src/mol-plugin/state/transforms/helpers.ts b/src/mol-plugin/state/transforms/helpers.ts
index c777529b70e17883f545566d6142167b8e9d85ad..6d2bbf3cec44b65e5adbf61f5ee883ab8298d215 100644
--- a/src/mol-plugin/state/transforms/helpers.ts
+++ b/src/mol-plugin/state/transforms/helpers.ts
@@ -4,50 +4,9 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-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';
-import { transpileMolScript } from '../../../mol-script/script/mol-script/symbols';
-import { compile } from '../../../mol-script/runtime/query/compiler';
-import { Transparency } from '../../../mol-theme/transparency';
+import { Structure } from '../../../mol-model/structure';
import { ComputedSecondaryStructure } from '../../../mol-model-props/computed/secondary-structure';
-type Script = { language: string, expression: string }
-
-function scriptToLoci(structure: Structure, script: Script) {
- const parsed = parseMolScript(script.expression)
- if (parsed.length === 0) throw new Error('No query')
- const query = transpileMolScript(parsed[0])
-
- const compiled = compile<StructureSelection>(query)
- const result = compiled(new QueryContext(structure))
- return StructureSelection.toLoci2(result)
-}
-
-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]
- layers.push({ loci: scriptToLoci(structure, script), color, clear })
- }
- 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 }
-}
-
/**
* Attaches ComputedSecondaryStructure property when unavailable in sourceData
*/
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index cdc5e19320cf10585a244b03d56cb3fd5f8d1be8..84be0e176ab66d8d095cb1ea2977d91832bf2918 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -29,8 +29,8 @@ import { unwindStructureAssembly, explodeStructure } from '../animation/helpers'
import { Color } from '../../../mol-util/color';
import { Overpaint } from '../../../mol-theme/overpaint';
import { Transparency } from '../../../mol-theme/transparency';
-import { getStructureOverpaintFromScript, getStructureOverpaintFromBundle, getStructureTransparency } from './helpers';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
+import { Script } from '../../../mol-script/script';
export { StructureRepresentation3D }
export { StructureRepresentation3DHelpers }
@@ -39,7 +39,8 @@ export { ExplodeStructureRepresentation3D }
export { UnwindStructureAssemblyRepresentation3D }
export { OverpaintStructureRepresentation3DFromScript }
export { OverpaintStructureRepresentation3DFromBundle }
-export { TransparencyStructureRepresentation3D }
+export { TransparencyStructureRepresentation3DFromScript }
+export { TransparencyStructureRepresentation3DFromBundle }
export { VolumeRepresentation3D }
namespace StructureRepresentation3DHelpers {
@@ -334,12 +335,12 @@ const OverpaintStructureRepresentation3DFromScript = PluginStateTransform.BuiltI
to: SO.Molecule.Structure.Representation3DState,
params: {
layers: PD.ObjectList({
- script: PD.ScriptExpression({ language: 'mol-script', expression: '(sel.atom.all)' }),
+ script: PD.Script(Script('(sel.atom.all)', 'mol-script')),
color: PD.Color(ColorNames.blueviolet),
clear: PD.Boolean(false)
}, e => `${e.clear ? 'Clear' : Color.toRgbString(e.color)}`, {
defaultValue: [{
- script: { language: 'mol-script', expression: '(sel.atom.all)' },
+ script: Script('(sel.atom.all)', 'mol-script'),
color: ColorNames.blueviolet,
clear: false
}]
@@ -352,7 +353,7 @@ const OverpaintStructureRepresentation3DFromScript = PluginStateTransform.BuiltI
},
apply({ a, params }) {
const structure = a.data.source.data
- const overpaint = getStructureOverpaintFromScript(structure, params.layers, params.alpha)
+ const overpaint = Overpaint.ofScript(params.layers, params.alpha, structure)
return new SO.Molecule.Structure.Representation3DState({
state: { overpaint },
@@ -366,7 +367,7 @@ const OverpaintStructureRepresentation3DFromScript = PluginStateTransform.BuiltI
const newStructure = a.data.source.data
if (newStructure !== oldStructure) return StateTransformer.UpdateResult.Recreate
const oldOverpaint = b.data.state.overpaint!
- const newOverpaint = getStructureOverpaintFromScript(newStructure, newParams.layers, newParams.alpha)
+ const newOverpaint = Overpaint.ofScript(newParams.layers, newParams.alpha, newStructure)
if (oldParams.alpha === newParams.alpha && Overpaint.areEqual(oldOverpaint, newOverpaint)) return StateTransformer.UpdateResult.Unchanged
b.data.state.overpaint = newOverpaint
@@ -403,7 +404,7 @@ const OverpaintStructureRepresentation3DFromBundle = PluginStateTransform.BuiltI
},
apply({ a, params }) {
const structure = a.data.source.data
- const overpaint = getStructureOverpaintFromBundle(structure, params.layers, params.alpha)
+ const overpaint = Overpaint.ofBundle(params.layers, params.alpha, structure)
return new SO.Molecule.Structure.Representation3DState({
state: { overpaint },
@@ -417,7 +418,7 @@ const OverpaintStructureRepresentation3DFromBundle = PluginStateTransform.BuiltI
const newStructure = a.data.source.data
if (newStructure !== oldStructure) return StateTransformer.UpdateResult.Recreate
const oldOverpaint = b.data.state.overpaint!
- const newOverpaint = getStructureOverpaintFromBundle(newStructure, newParams.layers, newParams.alpha)
+ const newOverpaint = Overpaint.ofBundle(newParams.layers, newParams.alpha, newStructure)
if (oldParams.alpha === newParams.alpha && Overpaint.areEqual(oldOverpaint, newOverpaint)) return StateTransformer.UpdateResult.Unchanged
b.data.state.overpaint = newOverpaint
@@ -427,14 +428,14 @@ const OverpaintStructureRepresentation3DFromBundle = PluginStateTransform.BuiltI
}
});
-type TransparencyStructureRepresentation3D = typeof TransparencyStructureRepresentation3D
-const TransparencyStructureRepresentation3D = PluginStateTransform.BuiltIn({
- name: 'transparency-structure-representation-3d',
+type TransparencyStructureRepresentation3DFromScript = typeof TransparencyStructureRepresentation3DFromScript
+const TransparencyStructureRepresentation3DFromScript = PluginStateTransform.BuiltIn({
+ name: 'transparency-structure-representation-3d-from-script',
display: 'Transparency 3D Representation',
from: SO.Molecule.Structure.Representation3D,
to: SO.Molecule.Structure.Representation3DState,
params: {
- script: PD.ScriptExpression({ language: 'mol-script', expression: '(sel.atom.all)' }),
+ script: PD.Script(Script('(sel.atom.all)', 'mol-script')),
value: PD.Numeric(0.75, { min: 0, max: 1, step: 0.01 }, { label: 'Transparency' }),
variant: PD.Select('single', [['single', 'Single-layer'], ['multi', 'Multi-layer']])
}
@@ -444,7 +445,7 @@ const TransparencyStructureRepresentation3D = PluginStateTransform.BuiltIn({
},
apply({ a, params }) {
const structure = a.data.source.data
- const transparency = getStructureTransparency(structure, params.script, params.value, params.variant)
+ const transparency = Transparency.ofScript(params.script, params.value, params.variant, structure)
return new SO.Molecule.Structure.Representation3DState({
state: { transparency },
@@ -457,7 +458,47 @@ const TransparencyStructureRepresentation3D = PluginStateTransform.BuiltIn({
const structure = b.data.info as Structure
if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate
const oldTransparency = b.data.state.transparency!
- const newTransparency = getStructureTransparency(structure, newParams.script, newParams.value, newParams.variant)
+ const newTransparency = Transparency.ofScript(newParams.script, newParams.value, newParams.variant, structure)
+ if (Transparency.areEqual(oldTransparency, newTransparency)) return StateTransformer.UpdateResult.Unchanged
+
+ b.data.state.transparency = newTransparency
+ b.data.source = a
+ b.label = `Transparency (${newTransparency.value})`
+ return StateTransformer.UpdateResult.Updated
+ }
+});
+
+type TransparencyStructureRepresentation3DFromBundle = typeof TransparencyStructureRepresentation3DFromBundle
+const TransparencyStructureRepresentation3DFromBundle = PluginStateTransform.BuiltIn({
+ name: 'transparency-structure-representation-3d-from-bundle',
+ display: 'Transparency 3D Representation',
+ from: SO.Molecule.Structure.Representation3D,
+ to: SO.Molecule.Structure.Representation3DState,
+ params: {
+ bundle: PD.Value<StructureElement.Bundle>(StructureElement.Bundle.Empty),
+ value: PD.Numeric(0.75, { min: 0, max: 1, step: 0.01 }, { label: 'Transparency' }),
+ variant: PD.Select('single', [['single', 'Single-layer'], ['multi', 'Multi-layer']])
+ }
+})({
+ canAutoUpdate() {
+ return true;
+ },
+ apply({ a, params }) {
+ const structure = a.data.source.data
+ const transparency = Transparency.ofBundle(params.bundle, params.value, params.variant, structure)
+
+ return new SO.Molecule.Structure.Representation3DState({
+ state: { transparency },
+ initialState: { transparency: Transparency.Empty },
+ info: structure,
+ source: a
+ }, { label: `Transparency (${transparency.value})` })
+ },
+ update({ a, b, newParams, oldParams }) {
+ const structure = b.data.info as Structure
+ if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate
+ const oldTransparency = b.data.state.transparency!
+ const newTransparency = Transparency.ofBundle(newParams.bundle, newParams.value, newParams.variant, structure)
if (Transparency.areEqual(oldTransparency, newTransparency)) return StateTransformer.UpdateResult.Unchanged
b.data.state.transparency = newTransparency
diff --git a/src/mol-theme/overpaint.ts b/src/mol-theme/overpaint.ts
index 2d80d6154f99cea09537034782e0c1130a8bafb5..b7de9494417c0c5c7044a681a846331f250b9683 100644
--- a/src/mol-theme/overpaint.ts
+++ b/src/mol-theme/overpaint.ts
@@ -6,7 +6,8 @@
import { Loci } from '../mol-model/loci';
import { Color } from '../mol-util/color';
-import { Structure } from '../mol-model/structure';
+import { Structure, StructureElement } from '../mol-model/structure';
+import { Script } from '../mol-script/script';
export { Overpaint }
@@ -36,4 +37,23 @@ namespace Overpaint {
}
return { layers, alpha: overpaint.alpha }
}
+
+ export function ofScript(scriptLayers: { script: Script, color: Color, clear: boolean }[], alpha: number, structure: Structure): Overpaint {
+ const layers: Overpaint.Layer[] = []
+ for (let i = 0, il = scriptLayers.length; i < il; ++i) {
+ const { script, color, clear } = scriptLayers[i]
+ layers.push({ loci: Script.toLoci(script, structure), color, clear })
+ }
+ return { layers, alpha }
+ }
+
+ export function ofBundle(bundleLayers: { bundle: StructureElement.Bundle, color: Color, clear: boolean }[], alpha: number, structure: Structure): 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 }
+ }
}
\ No newline at end of file
diff --git a/src/mol-theme/transparency.ts b/src/mol-theme/transparency.ts
index acb152aed3311a3c259076f569b4adf48e65625b..8bf1032ca3c6946db889b2fc406d7c0efb63941a 100644
--- a/src/mol-theme/transparency.ts
+++ b/src/mol-theme/transparency.ts
@@ -5,6 +5,8 @@
*/
import { Loci, EmptyLoci } from '../mol-model/loci';
+import { StructureElement, Structure } from '../mol-model/structure';
+import { Script } from '../mol-script/script';
export { Transparency }
@@ -24,4 +26,12 @@ namespace Transparency {
if (!Loci.areEqual(tA.loci, tB.loci)) return false
return true
}
+
+ export function ofScript(script: Script, value: number, variant: Transparency.Variant, structure: Structure): Transparency {
+ return { loci: Script.toLoci(script, structure), value, variant }
+ }
+
+ export function ofBundle(bundle: StructureElement.Bundle, value: number, variant: Transparency.Variant, structure: Structure): Transparency {
+ return { loci: StructureElement.Bundle.toLoci(bundle, structure), value, variant }
+ }
}
\ No newline at end of file