diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 3fce9342c9409b2ce783bb4559a0f3b8de0aa507..7650a7447a7f29aa2a4330aa3107b440fc019772 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -46,7 +46,8 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Action(StateTransforms.Representation.StructureLabels3D),
PluginSpec.Action(StateTransforms.Representation.ExplodeStructureRepresentation3D),
PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
- PluginSpec.Action(StateTransforms.Representation.ColorStructureRepresentation3D),
+ PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3D),
+ PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3D),
PluginSpec.Action(StateTransforms.Representation.VolumeRepresentation3D),
PluginSpec.Action(StateActions.Structure.StructureFromSelection),
diff --git a/src/mol-plugin/state/animation/helpers.ts b/src/mol-plugin/state/animation/helpers.ts
index df6bfb962bbc35bfe78088aed47fc39df1d854f2..d86448d5fedb44a6d39f2e87c4c3a895e112d238 100644
--- a/src/mol-plugin/state/animation/helpers.ts
+++ b/src/mol-plugin/state/animation/helpers.ts
@@ -4,16 +4,10 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-
import { SymmetryOperator } from 'mol-math/geometry';
import { Mat4, Vec3 } from 'mol-math/linear-algebra';
-import { Structure, StructureSelection, QueryContext } from 'mol-model/structure';
+import { Structure } from 'mol-model/structure';
import { StructureUnitTransforms } from 'mol-model/structure/structure/util/unit-transforms';
-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';
const _unwindMatrix = Mat4.zero();
export function unwindStructureAssembly(structure: Structure, unitTransforms: StructureUnitTransforms, t: number) {
@@ -38,22 +32,4 @@ export function explodeStructure(structure: Structure, unitTransforms: Structure
unitTransforms.setTransform(_transMat, u);
}
-}
-
-type ScriptLayers = { script: { language: string, expression: string }, color: Color }[]
-export function getStructureOverpaint(structure: Structure, scriptLayers: ScriptLayers, alpha: number): Overpaint {
- const layers: Overpaint.Layer[] = []
- for (let i = 0, il = scriptLayers.length; i < il; ++i) {
- const { script, color } = scriptLayers[i]
- 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))
- const loci = StructureSelection.toLoci2(result)
-
- layers.push({ loci, color })
- }
- return { layers, alpha }
}
\ No newline at end of file
diff --git a/src/mol-plugin/state/transforms/helpers.ts b/src/mol-plugin/state/transforms/helpers.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e5a55427d9b51d3cd90bf47b60be79acd78cf873
--- /dev/null
+++ b/src/mol-plugin/state/transforms/helpers.ts
@@ -0,0 +1,49 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Structure, StructureSelection, QueryContext } 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';
+
+type Script = { language: string, expression: string }
+
+export function getStructureOverpaint(structure: Structure, scriptLayers: { script: Script, color: Color }[], alpha: number): Overpaint {
+ const layers: Overpaint.Layer[] = []
+ for (let i = 0, il = scriptLayers.length; i < il; ++i) {
+ const { script, color } = scriptLayers[i]
+ 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))
+ const loci = StructureSelection.toLoci2(result)
+
+ layers.push({ loci, color })
+ }
+ return { layers, alpha }
+}
+
+export function getStructureTransparency(structure: Structure, scriptLayers: { script: Script, value: number }[]): Transparency {
+ const layers: Transparency.Layer[] = []
+ for (let i = 0, il = scriptLayers.length; i < il; ++i) {
+ const { script, value } = scriptLayers[i]
+ 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))
+ const loci = StructureSelection.toLoci2(result)
+
+ layers.push({ loci, value })
+ }
+ return { layers }
+}
\ No newline at end of file
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index b5c9e1a8257281547faf30b096c49b42558d1816..79af0ae63b5b0b93f2ce91643cfb4f77542839df 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -25,16 +25,19 @@ import { ColorNames } from 'mol-util/color/tables';
import { getLabelRepresentation } from 'mol-plugin/util/structure-labels';
import { ShapeRepresentation } from 'mol-repr/shape/representation';
import { StructureUnitTransforms } from 'mol-model/structure/structure/util/unit-transforms';
-import { unwindStructureAssembly, explodeStructure, getStructureOverpaint } from '../animation/helpers';
+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 { getStructureOverpaint, getStructureTransparency } from './helpers';
export { StructureRepresentation3D }
export { StructureRepresentation3DHelpers }
export { StructureLabels3D}
export { ExplodeStructureRepresentation3D }
export { UnwindStructureAssemblyRepresentation3D }
-export { OverpaintStructureRepresentation3D as ColorStructureRepresentation3D }
+export { OverpaintStructureRepresentation3D }
+export { TransparencyStructureRepresentation3D }
export { VolumeRepresentation3D }
namespace StructureRepresentation3DHelpers {
@@ -366,6 +369,57 @@ const OverpaintStructureRepresentation3D = PluginStateTransform.BuiltIn({
}
});
+type TransparencyStructureRepresentation3D = typeof TransparencyStructureRepresentation3D
+const TransparencyStructureRepresentation3D = PluginStateTransform.BuiltIn({
+ name: 'transparency-structure-representation-3d',
+ display: 'Transparency 3D Representation',
+ from: SO.Molecule.Structure.Representation3D,
+ to: SO.Molecule.Structure.Representation3DState,
+ params: {
+ layers: PD.ObjectList({
+ script: PD.ScriptExpression({ language: 'mol-script', expression: '(sel.atom.atom-groups :chain-test (= atom.label_asym_id A))' }),
+ value: PD.Numeric(0.5)
+ }, e => `Transparency ${e.value}`, {
+ defaultValue: [
+ {
+ script: {
+ language: 'mol-script',
+ expression: '(sel.atom.atom-groups :chain-test (= atom.label_asym_id A))'
+ },
+ value: 0.5
+ }
+ ]
+ }),
+ }
+})({
+ canAutoUpdate() {
+ return true;
+ },
+ apply({ a, params }) {
+ const structure = a.data.source.data
+ const transparency = getStructureTransparency(structure, params.layers)
+
+ return new SO.Molecule.Structure.Representation3DState({
+ state: { transparency },
+ initialState: { transparency: Transparency.Empty },
+ info: structure,
+ source: a
+ }, { label: `Transparency (${transparency.layers.length} Layers)` })
+ },
+ 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 = getStructureTransparency(structure, newParams.layers)
+ if (Transparency.areEqual(oldTransparency, newTransparency)) return StateTransformer.UpdateResult.Unchanged
+
+ b.data.state.transparency = newTransparency
+ b.data.source = a
+ b.label = `Transparency (${newTransparency.layers.length} Layers)`
+ return StateTransformer.UpdateResult.Updated
+ }
+});
+
//
export namespace VolumeRepresentation3DHelpers {