diff --git a/src/extensions/membrane-orientation/representation.ts b/src/extensions/membrane-orientation/representation.ts
index aaad82ebc3b25c1c762af236cd7fc09b3d04cce3..b5a571ba2c5a154815a93d4748ff52da6723150a 100644
--- a/src/extensions/membrane-orientation/representation.ts
+++ b/src/extensions/membrane-orientation/representation.ts
@@ -22,8 +22,9 @@ import { RuntimeContext } from '../../mol-task';
const MembraneOrientationParams = {
...Spheres.Params,
- color: PD.Color(ColorNames.orange),
- density: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 })
+ color: PD.Color(ColorNames.lightgrey),
+ size: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }, { description: 'Size of spheres that represent membrane planes' }),
+ density: PD.Numeric(1, { min: 0.25, max: 10, step: 0.25 }, { description: 'Distance between spheres'})
};
export type MembraneOrientationParams = typeof MembraneOrientationParams
export type MembraneOrientationProps = PD.Values<MembraneOrientationParams>
@@ -61,9 +62,7 @@ function getMembraneSpheres(ctx: RuntimeContext, data: Structure, props: Membran
const spheresBuilder = SpheresBuilder.create();
createMembraneLayer(spheresBuilder, p1, normal, density, radius);
createMembraneLayer(spheresBuilder, p2, normal, density, radius);
- const getLabel = () => '?'; // TODO
-
- return Shape.create(name, data, spheresBuilder.getSpheres(), () => props.color, () => 1, getLabel);
+ return Shape.create(name, data, spheresBuilder.getSpheres(), () => props.color, () => props.size, () => 'Membrane Boundaries');
}
function createMembraneLayer(spheresBuilder: SpheresBuilder, point: Vec3, normalVector: Vec3, density: number, radius: number) {
diff --git a/src/mol-model-props/computed/membrane-orientation.ts b/src/mol-model-props/computed/membrane-orientation.ts
index 549635f26a4b97eb281393ca5d1749ecaab1b957..8cdf29bd03f5b220a6ebd5c51277ee023ef09d7c 100644
--- a/src/mol-model-props/computed/membrane-orientation.ts
+++ b/src/mol-model-props/computed/membrane-orientation.ts
@@ -13,15 +13,14 @@ import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
import { ANVILParams, ANVILProps, computeANVIL } from './membrane-orientation/ANVIL';
import { AccessibleSurfaceAreaProvider } from './accessible-surface-area';
import { MembraneOrientation } from '../../mol-model/structure/model/properties/membrane-orientation';
-import { computeOPM } from './membrane-orientation/OPM';
function getMembraneOrientationParams(data?: Structure) {
- let defaultType = 'anvil' as 'anvil' | 'opm'; // TODO flip - OPM (or some other db-source) should be default if PDB identifier is known
+ let defaultType = 'anvil' as 'anvil' | 'db'; // TODO flip - OPM (or some other db-source) should be default if PDB identifier is known
return {
type: PD.MappedStatic(defaultType, {
- 'opm': PD.EmptyGroup({ label: 'OPM' }),
+ 'db': PD.EmptyGroup({ label: 'DB' }),
'anvil': PD.Group(ANVILParams, { label: 'ANVIL' })
- }, { options: [['opm', 'OPM'], ['anvil', 'ANVIL']] })
+ }, { options: [['db', 'DB'], ['anvil', 'ANVIL']] })
};
}
@@ -43,17 +42,13 @@ export const MembraneOrientationProvider: CustomStructureProperty.Provider<Membr
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(ctx, data) };
+ case 'db': throw Error('TODO impl');
}
}
});
-async function computeAnvil(ctx: CustomProperty.Context, data: Structure, props: ANVILProps): Promise<MembraneOrientation> {
+async function computeAnvil(ctx: CustomProperty.Context, data: Structure, props: Partial<ANVILProps>): Promise<MembraneOrientation> {
await AccessibleSurfaceAreaProvider.attach(ctx, data);
- const p = { ...PD.getDefaultValues(MembraneOrientationParams), ...props };
+ const p = { ...PD.getDefaultValues(ANVILParams), ...props };
return await computeANVIL(data, p).runInContext(ctx.runtime);
-}
-
-async function computeOpm(ctx: CustomProperty.Context, data: Structure): Promise<MembraneOrientation> {
- return await computeOPM(data).runInContext(ctx.runtime);
}
\ 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 500a345ef969e5d7cdc2734d97b9d40a7be98109..57159a4c62e62cb6205b4eac1597ff0a9e91454c 100644
--- a/src/mol-model-props/computed/membrane-orientation/ANVIL.ts
+++ b/src/mol-model-props/computed/membrane-orientation/ANVIL.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -35,23 +35,22 @@ export type ANVILProps = PD.Values<ANVILParams>
* Protein Engineering, Design & Selection, 2015, 1–5
* doi: 10.1093/protein/gzv063
*/
-export function computeANVIL(structure: Structure, props: Partial<ANVILProps> = {}) {
- const p = { ...PD.getDefaultValues(ANVILParams), ...props };
+export function computeANVIL(structure: Structure, props: ANVILProps) {
return Task.create('Compute Membrane Topology', async runtime => {
- return await calculate(runtime, structure, p);
+ return await calculate(runtime, structure, props);
});
}
const l = StructureElement.Location.create(void 0);
const centroidHelper = new CentroidHelper();
-function initialize(structure: Structure, params: ANVILProps): ANVILContext {
+function initialize(structure: Structure, props: ANVILProps): ANVILContext {
const { label_atom_id, x, y, z } = StructureProperties.atom;
const elementCount = structure.polymerResidueCount;
centroidHelper.reset();
l.structure = structure;
let offsets = new Int32Array(elementCount);
- let exposed: boolean[] = new Array<boolean>(elementCount);
+ let exposed = new Array<boolean>(elementCount);
const accessibleSurfaceArea = structure && AccessibleSurfaceAreaProvider.get(structure);
const asa = accessibleSurfaceArea.value!;
@@ -83,7 +82,7 @@ function initialize(structure: Structure, params: ANVILProps): ANVILContext {
// keep track of offsets and exposed state to reuse
offsets[m] = l.element;
- exposed[m] = AccessibleSurfaceArea.getValue(l, asa) > params.afilter;
+ exposed[m] = AccessibleSurfaceArea.getValue(l, asa) > props.afilter;
m++;
}
@@ -104,13 +103,8 @@ function initialize(structure: Structure, params: ANVILProps): ANVILContext {
const extent = 1.2 * Math.sqrt(centroidHelper.radiusSq);
return {
+ ...props,
structure: structure,
- numberOfSpherePoints: params.numberOfSpherePoints,
- stepSize: params.stepSize,
- minThickness: params.maxThickness,
- maxThickness: params.minThickness,
- afilter: params.afilter,
- membranePointDensity: params.membranePointDensity,
offsets: offsets,
exposed: exposed,
@@ -139,8 +133,7 @@ interface MembraneCandidate {
stats: HphobHphil,
normalVector?: Vec3,
spherePoint?: Vec3,
- qmax?: number,
- membraneAtoms?: Vec3[]
+ qmax?: number
}
namespace MembraneCandidate {
@@ -161,14 +154,13 @@ namespace MembraneCandidate {
stats: stats,
normalVector: diam_vect,
spherePoint: spherePoint,
- qmax: qmax,
- membraneAtoms: []
+ qmax: qmax
};
}
}
function findMembrane(ctx: ANVILContext, spherePoints: Vec3[], initialStats: HphobHphil, label_comp_id: StructureElement.Property<string>): MembraneCandidate {
- const { centroid, stepSize, minThickness, maxThickness } = ctx;
+ const { centroid, stepSize, maxThickness } = ctx;
// best performing membrane
let membrane: MembraneCandidate;
// score of the best performing membrane
@@ -194,7 +186,7 @@ function findMembrane(ctx: ANVILContext, spherePoints: Vec3[], initialStats: Hph
qvartemp.push(MembraneCandidate.initial(c1, c2, stats));
}
- let jmax = (minThickness / stepSize) - 1;
+ let jmax = (maxThickness / stepSize) - 1; // TODO should be minThickness but causes weird results if actually in place
for (let width = 0, widthl = maxThickness; width < widthl;) {
const imax = qvartemp.length - 1 - jmax;
diff --git a/src/mol-model-props/computed/membrane-orientation/OPM.ts b/src/mol-model-props/computed/membrane-orientation/OPM.ts
deleted file mode 100644
index 17e2adbb8d32b911f7d1a6ed7aab1cc025fc794a..0000000000000000000000000000000000000000
--- a/src/mol-model-props/computed/membrane-orientation/OPM.ts
+++ /dev/null
@@ -1,18 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- */
-import { Structure } from '../../../mol-model/structure/structure';
-import { Task, RuntimeContext } from '../../../mol-task';
-import { MembraneOrientation } from '../../../mol-model/structure/model/properties/membrane-orientation';
-
-export function computeOPM(structure: Structure) {
- return Task.create('Parse Membrane Topology', async runtime => {
- return await calculate(runtime, structure);
- });
-}
-
-export async function calculate(runtime: RuntimeContext, structure: Structure): Promise<MembraneOrientation> {
- throw Error('impl me');
-}
\ No newline at end of file
diff --git a/src/mol-model-props/computed/membrane-orientation/anvil/common.ts b/src/mol-model-props/computed/membrane-orientation/anvil/common.ts
index 18a25a7fc5f8c5da3bb2267a88c2bc18181d81f1..743c46a4680d2ad58f71246cf0e00cb1422115d3 100644
--- a/src/mol-model-props/computed/membrane-orientation/anvil/common.ts
+++ b/src/mol-model-props/computed/membrane-orientation/anvil/common.ts
@@ -9,6 +9,7 @@ import { Vec3 } from '../../../../mol-math/linear-algebra';
export interface ANVILContext {
structure: Structure,
+
numberOfSpherePoints: number,
stepSize: number,
minThickness: number,
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index 875813461d836f4c57837f4a4f05111df5ff46e5..42dfaf9c731cd8e577d0f4fcedd061980a098d02 100644
--- a/src/tests/browser/render-structure.ts
+++ b/src/tests/browser/render-structure.ts
@@ -208,7 +208,7 @@ async function init() {
size: reprCtx.sizeThemeRegistry.create('physical', { structure })
});
console.time('membrane orientation');
- await membraneOrientationRepr.createOrUpdate({}, structure).run();
+ await membraneOrientationRepr.createOrUpdate({ ...MembraneOrientationRepresentationProvider.defaultValues, quality: 'auto' }, structure).run();
console.timeEnd('membrane orientation');
}