wip, transparency

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),

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) {
@@ -39,21 +33,3 @@ export function explodeStructure(structure: Structure, unitTransforms: Structure
         unitTransforms.setTransform(_transMat, u);
     }
 }
\ No newline at end of file
-
-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

src/mol-plugin/state/transforms/helpers.ts

+/**
+ * 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

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 {