diff --git a/src/extensions/membrane-orientation/ANVIL.ts b/src/extensions/membrane-orientation/ANVIL.ts
index db0e7250182c725faaef5775df0d13e558c2a63c..db61ee2b8e10cc11c3ba6a5df273aa77ea549a08 100644
--- a/src/extensions/membrane-orientation/ANVIL.ts
+++ b/src/extensions/membrane-orientation/ANVIL.ts
@@ -14,8 +14,8 @@ import { Vec3 } from '../../mol-math/linear-algebra';
import { getElementMoleculeType } from '../../mol-model/structure/util';
import { MoleculeType } from '../../mol-model/structure/model/types';
import { AccessibleSurfaceArea } from '../../mol-model-props/computed/accessible-surface-area/shrake-rupley';
-import { MembraneOrientation } from '../../mol-model/structure/model/properties/membrane-orientation';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { MembraneOrientation } from './membrane-orientation';
export const ANVILParams = {
numberOfSpherePoints: PD.Numeric(120, { min: 35, max: 700, step: 1 }, { description: 'Number of spheres/directions to test for membrane placement. Original value is 350.' }),
@@ -123,7 +123,13 @@ export async function calculate(runtime: RuntimeContext, structure: Structure, p
const membrane = initialMembrane.qmax! > alternativeMembrane.qmax! ? initialMembrane : alternativeMembrane;
- return MembraneOrientation(membrane.planePoint1, membrane.planePoint2, membrane.normalVector!, ctx.extent, ctx.centroid);
+ return {
+ p1: membrane.planePoint1,
+ p2: membrane.planePoint2,
+ normal: membrane.normalVector!,
+ radius: ctx.extent,
+ centroid: ctx.centroid
+ };
}
interface MembraneCandidate {
diff --git a/src/extensions/membrane-orientation/behavior.ts b/src/extensions/membrane-orientation/behavior.ts
index bff75c6b282fbf3de319fb59f132d2438a0e4357..ea097071964839ba4777248bff2ec894acbe3220 100644
--- a/src/extensions/membrane-orientation/behavior.ts
+++ b/src/extensions/membrane-orientation/behavior.ts
@@ -7,19 +7,11 @@
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../mol-plugin-state/builder/structure/representation-preset';
-import { MembraneOrientationProvider } from './membrane-orientation';
+import { MembraneOrientationProvider, MembraneOrientation } from './membrane-orientation';
import { StateObjectRef } from '../../mol-state';
import { Task } from '../../mol-task';
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';
-import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
import { MembraneOrientationRepresentationProvider } from './representation';
-import { CustomPropSymbol } from '../../mol-script/language/symbol';
-import Type from '../../mol-script/language/type';
-import { isInMembranePlane } from './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 }>({
@@ -38,7 +30,7 @@ export const MembraneOrientationData = PluginBehavior.create<{ autoAttach: boole
this.ctx.representation.structure.themes.colorThemeRegistry.add(HydrophobicityColorThemeProvider);
this.ctx.representation.structure.registry.add(MembraneOrientationRepresentationProvider);
- this.ctx.query.structure.registry.add(isTransmembrane);
+ this.ctx.query.structure.registry.add(MembraneOrientation.isTransmembrane);
this.ctx.builders.structure.representation.registerPreset(MembraneOrientationPreset);
}
@@ -56,7 +48,7 @@ export const MembraneOrientationData = PluginBehavior.create<{ autoAttach: boole
this.ctx.representation.structure.themes.colorThemeRegistry.remove(HydrophobicityColorThemeProvider);
this.ctx.representation.structure.registry.remove(MembraneOrientationRepresentationProvider);
- this.ctx.query.structure.registry.remove(isTransmembrane);
+ this.ctx.query.structure.registry.remove(MembraneOrientation.isTransmembrane);
this.ctx.builders.structure.representation.unregisterPreset(MembraneOrientationPreset);
}
@@ -66,36 +58,6 @@ export const MembraneOrientationData = PluginBehavior.create<{ autoAttach: boole
})
});
-const pos = Vec3();
-const isTransmembraneSymbol = QuerySymbolRuntime.Dynamic(CustomPropSymbol('membrane-orientation', 'is-transmembrane', Type.Bool),
- ctx => {
- const structure = ctx.currentStructure;
- const { x, y, z } = StructureProperties.atom;
- if (!structure.isAtomic) return false;
- const membraneOrientation = MembraneOrientationProvider.get(structure).value;
- if (!membraneOrientation) return false;
- Vec3.set(pos, x(ctx.element), y(ctx.element), z(ctx.element));
- const { normal, p1, p2 } = membraneOrientation!;
- return isInMembranePlane(pos, normal, p1, p2);
- });
-
-const isTransmembrane = StructureSelectionQuery('Residues embedded in membrane', MS.struct.modifier.union([
- MS.struct.modifier.wholeResidues([
- MS.struct.modifier.union([
- MS.struct.generator.atomGroups({
- 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
- 'atom-test': isTransmembraneSymbol.symbol(),
- })
- ])
- ])
-]), {
- description: 'Select residues that are embedded between the membrane layers.',
- category: StructureSelectionCategory.Residue,
- ensureCustomProperties: (ctx, structure) => {
- return MembraneOrientationProvider.attach(ctx, structure);
- }
-});
-
export const MembraneOrientationPreset = StructureRepresentationPresetProvider({
id: 'preset-membrane-orientation',
display: {
diff --git a/src/extensions/membrane-orientation/membrane-orientation.ts b/src/extensions/membrane-orientation/membrane-orientation.ts
index 759ebab796ed942fbc1d3bda1fc55d167e50e3c6..3abba9d1ea98e2746905a32b804aec93e3f5500c 100644
--- a/src/extensions/membrane-orientation/membrane-orientation.ts
+++ b/src/extensions/membrane-orientation/membrane-orientation.ts
@@ -6,13 +6,18 @@
*/
import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { Structure } from '../../mol-model/structure';
+import { Structure, StructureProperties } from '../../mol-model/structure';
import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
-import { ANVILParams, ANVILProps, computeANVIL } from './ANVIL';
-import { MembraneOrientation } from '../../mol-model/structure/model/properties/membrane-orientation';
+import { ANVILParams, ANVILProps, computeANVIL, isInMembranePlane } from './ANVIL';
import { CustomStructureProperty } from '../../mol-model-props/common/custom-structure-property';
import { CustomProperty } from '../../mol-model-props/common/custom-property';
import { AccessibleSurfaceAreaProvider } from '../../mol-model-props/computed/accessible-surface-area';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
+import { CustomPropSymbol } from '../../mol-script/language/symbol';
+import Type from '../../mol-script/language/type';
+import { StructureSelectionQuery, StructureSelectionCategory } from '../../mol-plugin-state/helpers/structure-selection-query';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
export const MembraneOrientationParams = {
...ANVILParams
@@ -20,10 +25,59 @@ export const MembraneOrientationParams = {
export type MembraneOrientationParams = typeof MembraneOrientationParams
export type MembraneOrientationProps = PD.Values<MembraneOrientationParams>
+interface MembraneOrientation {
+ // point in membrane boundary
+ readonly p1: Vec3,
+ // point in opposite side of membrane boundary
+ readonly p2: Vec3,
+ // normal vector of membrane layer
+ readonly normal: Vec3,
+ // the radius of the membrane layer
+ readonly radius: number,
+ readonly centroid: Vec3
+}
+
+namespace MembraneOrientation {
+ const pos = Vec3();
+ export const symbols = {
+ isTransmembrane: QuerySymbolRuntime.Dynamic(CustomPropSymbol('membrane-orientation', 'is-transmembrane', Type.Bool),
+ ctx => {
+ const structure = ctx.currentStructure;
+ const { x, y, z } = StructureProperties.atom;
+ if (!structure.isAtomic) return false;
+ const membraneOrientation = MembraneOrientationProvider.get(structure).value;
+ if (!membraneOrientation) return false;
+ Vec3.set(pos, x(ctx.element), y(ctx.element), z(ctx.element));
+ const { normal, p1, p2 } = membraneOrientation!;
+ return isInMembranePlane(pos, normal, p1, p2);
+ })
+ };
+
+ export const isTransmembrane = StructureSelectionQuery('Residues embedded in membrane', MS.struct.modifier.union([
+ MS.struct.modifier.wholeResidues([
+ MS.struct.modifier.union([
+ MS.struct.generator.atomGroups({
+ 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+ 'atom-test': symbols.isTransmembrane.symbol(),
+ })
+ ])
+ ])
+ ]), {
+ description: 'Select residues that are embedded between the membrane layers.',
+ category: StructureSelectionCategory.Residue,
+ ensureCustomProperties: (ctx, structure) => {
+ return MembraneOrientationProvider.attach(ctx, structure);
+ }
+ });
+}
+
+export { MembraneOrientation };
+
export const MembraneOrientationProvider: CustomStructureProperty.Provider<MembraneOrientationParams, MembraneOrientation> = CustomStructureProperty.createProvider({
label: 'Membrane Orientation',
descriptor: CustomPropertyDescriptor({
name: 'molstar_computed_membrane_orientation',
+ symbols: MembraneOrientation.symbols
// TODO `cifExport`
}),
type: 'root',
diff --git a/src/extensions/membrane-orientation/representation.ts b/src/extensions/membrane-orientation/representation.ts
index 741af39cda27ede2630662c481d8da126e57d76a..76b4cba0cf56ec0546ed92a1d25727f2651a753b 100644
--- a/src/extensions/membrane-orientation/representation.ts
+++ b/src/extensions/membrane-orientation/representation.ts
@@ -12,7 +12,7 @@ import { Structure } from '../../mol-model/structure';
import { Spheres } from '../../mol-geo/geometry/spheres/spheres';
import { SpheresBuilder } from '../../mol-geo/geometry/spheres/spheres-builder';
import { StructureRepresentationProvider, StructureRepresentation, StructureRepresentationStateBuilder } from '../../mol-repr/structure/representation';
-import { MembraneOrientation } from '../../mol-model/structure/model/properties/membrane-orientation';
+import { MembraneOrientation } from './membrane-orientation';
import { ThemeRegistryContext } from '../../mol-theme/theme';
import { ShapeRepresentation } from '../../mol-repr/shape/representation';
import { Shape } from '../../mol-model/shape';
diff --git a/src/mol-model/structure/model/properties/membrane-orientation.ts b/src/mol-model/structure/model/properties/membrane-orientation.ts
deleted file mode 100644
index 72a8d0313820b9978600eef50b6842def2aad510..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/model/properties/membrane-orientation.ts
+++ /dev/null
@@ -1,25 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- */
-
-import { Vec3 } from '../../../../mol-math/linear-algebra';
-
-interface MembraneOrientation {
- // point in membrane boundary
- readonly p1: Vec3,
- // point in opposite side of membrane boundary
- readonly p2: Vec3,
- // normal vector of membrane layer
- readonly normal: Vec3,
- // the radius of the membrane layer
- readonly radius: number,
- readonly centroid: Vec3
-}
-
-function MembraneOrientation(p1: Vec3, p2: Vec3, normal: Vec3, radius: number, centroid: Vec3): MembraneOrientation {
- return { p1, p2, normal, radius, centroid };
-}
-
-export { MembraneOrientation };
\ No newline at end of file