diff --git a/src/mol-model-props/computed/membrane.ts b/src/mol-model-props/computed/membrane-orientation.ts
similarity index 59%
rename from src/mol-model-props/computed/membrane.ts
rename to src/mol-model-props/computed/membrane-orientation.ts
index e87baefa11736cf2737693246caa48001bde4136..bcbb939d03b3b4a44f684acc7d57b328da10bbe6 100644
--- a/src/mol-model-props/computed/membrane.ts
+++ b/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
diff --git a/src/mol-model-props/computed/membrane/ANVIL.ts b/src/mol-model-props/computed/membrane-orientation/ANVIL.ts
similarity index 98%
rename from src/mol-model-props/computed/membrane/ANVIL.ts
rename to src/mol-model-props/computed/membrane-orientation/ANVIL.ts
index 80fb001ab71698da649eaf8fd0b26e16f451b717..5e0ccc1336940c8627dc91892e2de14ef1f72964 100644
--- a/src/mol-model-props/computed/membrane/ANVIL.ts
+++ b/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);
diff --git a/src/mol-model-props/computed/membrane/anvil/common.ts b/src/mol-model-props/computed/membrane-orientation/anvil/common.ts
similarity index 100%
rename from src/mol-model-props/computed/membrane/anvil/common.ts
rename to src/mol-model-props/computed/membrane-orientation/anvil/common.ts
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index 0de13541dff6ea48899fca2165607d2823d262f8..45857da4208ae2ee79e9d14d90bfee9930de94d3 100644
--- a/src/tests/browser/render-structure.ts
+++ b/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({