refactor membrane orientation

src/mol-model-props/computed/membrane.ts → src/mol-model-props/computed/membrane-orientation.ts

@@ -10,10 +10,10 @@ import { Structure } from '../../mol-model/structure';
 import { CustomStructureProperty } from '../common/custom-structure-property';
 import { CustomProperty } from '../common/custom-property';
 import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
-import { ANVILParams, Membrane, ANVILProps } from './membrane/ANVIL';
+import { ANVILParams, MembraneOrientation, ANVILProps } from './membrane-orientation/ANVIL';
 import { AccessibleSurfaceAreaProvider } from './accessible-surface-area';
 
-function getMembraneParams(data?: Structure) {
+function getMembraneOrientationParams(data?: Structure) {
     let defaultType = 'anvil' as 'anvil' | 'opm'; // TODO flip - OPM should be default if PDB identifier is known
     return {
         type: PD.MappedStatic(defaultType, {
@@ -23,22 +23,22 @@ function getMembraneParams(data?: Structure) {
     };
 }
 
-export const MembraneParams = getMembraneParams();
-export type MembraneParams = typeof MembraneParams
-export type MembraneProps = PD.Values<MembraneParams>
+export const MembraneOrientationParams = getMembraneOrientationParams();
+export type MembraneOrientationParams = typeof MembraneOrientationParams
+export type MembraneOrientationProps = PD.Values<MembraneOrientationParams>
 
-export const MembraneProvider: CustomStructureProperty.Provider<MembraneParams, Membrane> = CustomStructureProperty.createProvider({
-    label: 'Predicted Membrane',
+export const MembraneOrientationProvider: CustomStructureProperty.Provider<MembraneOrientationParams, MembraneOrientation> = CustomStructureProperty.createProvider({
+    label: 'Membrane Orientation',
     descriptor: CustomPropertyDescriptor({
-        name: 'molstar_membrane',
+        name: 'molstar_computed_membrane_orientation',
         // TODO `cifExport`
     }),
     type: 'root',
-    defaultParams: MembraneParams,
-    getParams: (data: Structure) => MembraneParams,
+    defaultParams: MembraneOrientationParams,
+    getParams: (data: Structure) => MembraneOrientationParams,
     isApplicable: (data: Structure) => true,
-    obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<MembraneProps>) => {
-        const p = { ...PD.getDefaultValues(MembraneParams), ...props };
+    obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<MembraneOrientationProps>) => {
+        const p = { ...PD.getDefaultValues(MembraneOrientationParams), ...props };
         switch (p.type.name) {
             case 'anvil': return { value: await computeAnvil(ctx, data, p.type.params) };
             case 'opm': return { value: await computeOpm(data) };
@@ -46,12 +46,12 @@ export const MembraneProvider: CustomStructureProperty.Provider<MembraneParams,
     }
 });
 
-async function computeAnvil(ctx: CustomProperty.Context, data: Structure, props: ANVILProps): Promise<Membrane> {
+async function computeAnvil(ctx: CustomProperty.Context, data: Structure, props: ANVILProps): Promise<MembraneOrientation> {
     await AccessibleSurfaceAreaProvider.attach(ctx, data);
-    const p = { ...PD.getDefaultValues(MembraneParams), ...props };
-    return await Membrane.compute(data, p).runInContext(ctx.runtime);
+    const p = { ...PD.getDefaultValues(MembraneOrientationParams), ...props };
+    return await MembraneOrientation.compute(data, p).runInContext(ctx.runtime);
 }
 
-async function computeOpm(structure: Structure): Promise<Membrane> {
+async function computeOpm(structure: Structure): Promise<MembraneOrientation> {
     throw Error('TODO impl');
 }
\ No newline at end of file

src/mol-model-props/computed/membrane/ANVIL.ts → src/mol-model-props/computed/membrane-orientation/ANVIL.ts

@@ -27,10 +27,10 @@ export const ANVILParams = {
 export type ANVILParams = typeof ANVILParams
 export type ANVILProps = PD.Values<ANVILParams>
 
-export { Membrane };
-interface Membrane extends Array<Vec3> {}
+export { MembraneOrientation };
+interface MembraneOrientation extends Array<Vec3> {}
 
-namespace Membrane {
+namespace MembraneOrientation {
     /**
      * Implements:
      * Membrane positioning for high- and low-resolution protein structures through a binary classification approach
@@ -123,7 +123,7 @@ namespace Membrane {
         };
     }
 
-    export async function calculate(runtime: RuntimeContext, structure: Structure, params: ANVILProps): Promise<Membrane> {
+    export async function calculate(runtime: RuntimeContext, structure: Structure, params: ANVILProps): Promise<MembraneOrientation> {
         const { label_comp_id } = StructureProperties.residue;
 
         const ctx = initialize(structure, params);

src/tests/browser/render-structure.ts

@@ -26,12 +26,12 @@ import { InteractionsProvider } from '../../mol-model-props/computed/interaction
 import { SecondaryStructureProvider } from '../../mol-model-props/computed/secondary-structure';
 import { SyncRuntimeContext } from '../../mol-task/execution/synchronous';
 import { AssetManager } from '../../mol-util/assets';
-import { MembraneProvider } from '../../mol-model-props/computed/membrane';
+import { MembraneOrientationProvider } from '../../mol-model-props/computed/membrane-orientation';
 import { SpheresBuilder } from '../../mol-geo/geometry/spheres/spheres-builder';
 import { Spheres } from '../../mol-geo/geometry/spheres/spheres';
 import { Color } from '../../mol-util/color';
 import { createRenderObject } from '../../mol-gl/render-object';
-import { Membrane } from '../../mol-model-props/computed/membrane/ANVIL';
+import { MembraneOrientation } from '../../mol-model-props/computed/membrane-orientation/ANVIL';
 
 const parent = document.getElementById('app')!;
 parent.style.width = '100%';
@@ -122,7 +122,7 @@ function getGaussianSurfaceRepr() {
     return GaussianSurfaceRepresentationProvider.factory(reprCtx, GaussianSurfaceRepresentationProvider.getParams);
 }
 
-function getMembraneRepr(membrane: Membrane) {
+function getMembraneRepr(membrane: MembraneOrientation) {
     // TODO is a representation provider the right place for this?
     const spheresBuilder = SpheresBuilder.create(membrane.length, 1);
     for (let i = 0, il = membrane.length; i < il; i++) {
@@ -150,7 +150,7 @@ async function init() {
     console.timeEnd('compute SecondaryStructure');
 
     console.time('compute Membrane');
-    await MembraneProvider.attach(ctx, structure);
+    await MembraneOrientationProvider.attach(ctx, structure);
     console.timeEnd('compute Membrane');
 
     console.time('compute Interactions');
@@ -172,7 +172,7 @@ async function init() {
     const ballAndStickRepr = getBallAndStickRepr();
     const molecularSurfaceRepr = getMolecularSurfaceRepr();
     const gaussianSurfaceRepr = getGaussianSurfaceRepr();
-    const membraneRepr = getMembraneRepr(MembraneProvider.get(structure).value!);
+    const membraneRepr = getMembraneRepr(MembraneOrientationProvider.get(structure).value!);
 
     if (show.cartoon) {
         cartoonRepr.setTheme({