From 9d0190c11cbfff29803e39034405e19a86fc26b6 Mon Sep 17 00:00:00 2001
From: JonStargaryen <sebastian.bittrich@rcsb.org>
Date: Tue, 9 Jun 2020 11:53:39 -0700
Subject: [PATCH] color
---
.../membrane-orientation/behavior.ts | 8 +--
src/extensions/membrane-orientation/color.ts | 63 +++++++++++++++++++
.../computed/membrane-orientation/ANVIL.ts | 10 +--
3 files changed, 72 insertions(+), 9 deletions(-)
create mode 100644 src/extensions/membrane-orientation/color.ts
diff --git a/src/extensions/membrane-orientation/behavior.ts b/src/extensions/membrane-orientation/behavior.ts
index e7ba82909..216d8c0a7 100644
--- a/src/extensions/membrane-orientation/behavior.ts
+++ b/src/extensions/membrane-orientation/behavior.ts
@@ -10,7 +10,6 @@ import { StructureRepresentationPresetProvider, PresetStructureRepresentations }
import { MembraneOrientationProvider } from '../../mol-model-props/computed/membrane-orientation';
import { StateObjectRef } from '../../mol-state';
import { Task } from '../../mol-task';
-import { AccessibleSurfaceAreaColorThemeProvider } from '../../mol-model-props/computed/themes/accessible-surface-area';
import { PluginBehavior } from '../../mol-plugin/behavior';
import { StructureSelectionQuery, StructureSelectionCategory } from '../../mol-plugin-state/helpers/structure-selection-query';
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
@@ -21,6 +20,7 @@ import Type from '../../mol-script/language/type';
import { isInMembranePlane } from '../../mol-model-props/computed/membrane-orientation/ANVIL';
import { StructureProperties } from '../../mol-model/structure';
import { Vec3 } from '../../mol-math/linear-algebra';
+import { HydrophobicityColorThemeProvider } from '../../mol-theme/color/hydrophobicity';
export const MembraneOrientationData = PluginBehavior.create<{ autoAttach: boolean }>({
name: 'membrane-orientation-prop',
@@ -37,7 +37,7 @@ export const MembraneOrientationData = PluginBehavior.create<{ autoAttach: boole
this.ctx.customStructureProperties.register(this.provider, this.params.autoAttach);
- this.ctx.representation.structure.themes.colorThemeRegistry.add(AccessibleSurfaceAreaColorThemeProvider);
+ this.ctx.representation.structure.themes.colorThemeRegistry.add(HydrophobicityColorThemeProvider);
this.ctx.representation.structure.registry.add(MembraneOrientationRepresentationProvider);
this.ctx.query.structure.registry.add(isTransmembrane);
@@ -56,7 +56,7 @@ export const MembraneOrientationData = PluginBehavior.create<{ autoAttach: boole
DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
- this.ctx.representation.structure.themes.colorThemeRegistry.remove(AccessibleSurfaceAreaColorThemeProvider);
+ this.ctx.representation.structure.themes.colorThemeRegistry.remove(HydrophobicityColorThemeProvider);
this.ctx.representation.structure.registry.remove(MembraneOrientationRepresentationProvider);
this.ctx.query.structure.registry.remove(isTransmembrane);
@@ -118,7 +118,7 @@ export const MembraneOrientationPreset = StructureRepresentationPresetProvider({
await MembraneOrientationProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure);
}));
- const colorTheme = AccessibleSurfaceAreaColorThemeProvider.name as any;
+ const colorTheme = HydrophobicityColorThemeProvider.name as any;
return await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: colorTheme }, plugin);
}
});
diff --git a/src/extensions/membrane-orientation/color.ts b/src/extensions/membrane-orientation/color.ts
new file mode 100644
index 000000000..145010c40
--- /dev/null
+++ b/src/extensions/membrane-orientation/color.ts
@@ -0,0 +1,63 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ */
+
+import { ThemeDataContext } from '../../mol-theme/theme';
+import { ColorTheme, LocationColor } from '../../mol-theme/color';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Color } from '../../mol-util/color';
+import { TableLegend } from '../../mol-util/legend';
+import { StructureElement, Unit, StructureProperties } from '../../mol-model/structure';
+import { isHydrophobic } from '../../mol-model-props/computed/membrane-orientation/ANVIL';
+import { Location } from '../../mol-model/location';
+
+const DefaultColor = Color(0x909090);
+
+const HydrophobicColor = Color(0x2166ac);
+const HydrophilicColor = Color(0xfee08b);
+
+const ColorLegend = TableLegend([
+ ['Data unavailable', DefaultColor],
+ ['Hydrophobic', HydrophobicColor],
+ ['Hydrophilic', HydrophilicColor],
+]);
+
+export function HydrophobicityColorTheme(ctx: ThemeDataContext, props: {}): ColorTheme<{}> {
+ let color: LocationColor = () => DefaultColor;
+ const { label_comp_id } = StructureProperties.residue;
+
+ if (ctx.structure) {
+ color = (location: Location): Color => {
+ if (StructureElement.Location.is(location) && Unit.isAtomic(location.unit)) {
+ if (isHydrophobic(label_comp_id(location))) {
+ return HydrophobicColor;
+ } else {
+ return HydrophilicColor;
+ }
+ }
+ return DefaultColor;
+ };
+ }
+
+ return {
+ factory: HydrophobicityColorTheme,
+ granularity: 'group',
+ color,
+ props,
+ description: 'Assigns residue colors according to their hydrophobicity.',
+ legend: ColorLegend
+ };
+}
+
+export const HydrophobicityColorThemeProvider: ColorTheme.Provider<{}, 'hydrophobicity'> = {
+ name: 'hydrophobicity',
+ label: 'Hydrophobicity',
+ category: ColorTheme.Category.Residue,
+ factory: HydrophobicityColorTheme,
+ getParams: () => ({}),
+ defaultValues: PD.getDefaultValues({}),
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure
+};
\ No newline at end of file
diff --git a/src/mol-model-props/computed/membrane-orientation/ANVIL.ts b/src/mol-model-props/computed/membrane-orientation/ANVIL.ts
index f394d3a6f..b712b4253 100644
--- a/src/mol-model-props/computed/membrane-orientation/ANVIL.ts
+++ b/src/mol-model-props/computed/membrane-orientation/ANVIL.ts
@@ -333,12 +333,12 @@ namespace HphobHphil {
}
return of(hphob, hphil);
}
+}
- // ANVIL-specific (not general) definition of membrane-favoring amino acids
- const HYDROPHOBIC_AMINO_ACIDS = new Set(['ALA', 'CYS', 'GLY', 'HIS', 'ILE', 'LEU', 'MET', 'PHE', 'SER', 'THR', 'VAL']);
- function isHydrophobic(label_comp_id: string): boolean {
- return HYDROPHOBIC_AMINO_ACIDS.has(label_comp_id);
- }
+// ANVIL-specific (not general) definition of membrane-favoring amino acids
+const HYDROPHOBIC_AMINO_ACIDS = new Set(['ALA', 'CYS', 'GLY', 'HIS', 'ILE', 'LEU', 'MET', 'PHE', 'SER', 'THR', 'VAL']);
+export function isHydrophobic(label_comp_id: string): boolean {
+ return HYDROPHOBIC_AMINO_ACIDS.has(label_comp_id);
}
function setLocation(l: StructureElement.Location, structure: Structure, serialIndex: number) {
--
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