diff --git a/src/extensions/membrane-orientation/ANVIL.ts b/src/extensions/membrane-orientation/ANVIL.ts index db61ee2b8e10cc11c3ba6a5df273aa77ea549a08..3c5ed245746799f59cf8994947c4297388eec4dd 100644 --- a/src/extensions/membrane-orientation/ANVIL.ts +++ b/src/extensions/membrane-orientation/ANVIL.ts @@ -35,7 +35,7 @@ export type ANVILProps = PD.Values<ANVILParams> * doi: 10.1093/protein/gzv063 */ export function computeANVIL(structure: Structure, props: ANVILProps) { - return Task.create('Compute Membrane Topology', async runtime => { + return Task.create('Compute Membrane Orientation', async runtime => { return await calculate(runtime, structure, props); }); } @@ -124,9 +124,9 @@ export async function calculate(runtime: RuntimeContext, structure: Structure, p const membrane = initialMembrane.qmax! > alternativeMembrane.qmax! ? initialMembrane : alternativeMembrane; return { - p1: membrane.planePoint1, - p2: membrane.planePoint2, - normal: membrane.normalVector!, + planePoint1: membrane.planePoint1, + planePoint2: membrane.planePoint2, + normalVector: membrane.normalVector!, radius: ctx.extent, centroid: ctx.centroid }; diff --git a/src/extensions/membrane-orientation/behavior.ts b/src/extensions/membrane-orientation/behavior.ts index 90c1dae568e8e6e51c49a514d2e297611c1ee46c..c6ed297cdcd5abe6c634d2a24b2d547a4f5d7f97 100644 --- a/src/extensions/membrane-orientation/behavior.ts +++ b/src/extensions/membrane-orientation/behavior.ts @@ -27,7 +27,6 @@ export const MembraneOrientationData = PluginBehavior.create<{ autoAttach: boole private provider = MembraneOrientationProvider register(): void { - console.log('beh @ register'); this.ctx.state.data.actions.add(InitMembraneOrientation3D); this.ctx.customStructureProperties.register(this.provider, this.params.autoAttach); @@ -127,7 +126,6 @@ export const MembraneOrientationPreset = StructureRepresentationPresetProvider({ description: 'Shows orientation of membrane layers. Data calculated with ANVIL algorithm.' // TODO add ' or obtained via RCSB PDB' }, isApplicable(a) { - console.log(`present applicable: ${MembraneOrientationProvider.isApplicable(a.data)}`); return MembraneOrientationProvider.isApplicable(a.data); }, params: () => StructureRepresentationPresetProvider.CommonParams, @@ -138,7 +136,6 @@ export const MembraneOrientationPreset = StructureRepresentationPresetProvider({ if (!MembraneOrientationProvider.get(structure).value) { await plugin.runTask(Task.create('Membrane Orientation', async runtime => { - console.log('present: attaching'); await MembraneOrientationProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure); })); } diff --git a/src/extensions/membrane-orientation/membrane-orientation.ts b/src/extensions/membrane-orientation/membrane-orientation.ts index 3abba9d1ea98e2746905a32b804aec93e3f5500c..5e95d9d9304bf4fb1f79f5ae6d17fcc41e41754f 100644 --- a/src/extensions/membrane-orientation/membrane-orientation.ts +++ b/src/extensions/membrane-orientation/membrane-orientation.ts @@ -27,11 +27,11 @@ export type MembraneOrientationProps = PD.Values<MembraneOrientationParams> interface MembraneOrientation { // point in membrane boundary - readonly p1: Vec3, + readonly planePoint1: Vec3, // point in opposite side of membrane boundary - readonly p2: Vec3, + readonly planePoint2: Vec3, // normal vector of membrane layer - readonly normal: Vec3, + readonly normalVector: Vec3, // the radius of the membrane layer readonly radius: number, readonly centroid: Vec3 @@ -48,7 +48,7 @@ namespace MembraneOrientation { 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!; + const { normalVector: normal, planePoint1: p1, planePoint2: p2 } = membraneOrientation!; return isInMembranePlane(pos, normal, p1, p2); }) }; diff --git a/src/extensions/membrane-orientation/representation.ts b/src/extensions/membrane-orientation/representation.ts index b8d4e1922332f0c1d8e18a608eec2fd79d25bec8..fe4979b242b3b90922c0b4493f5fbb8f2cd85223 100644 --- a/src/extensions/membrane-orientation/representation.ts +++ b/src/extensions/membrane-orientation/representation.ts @@ -74,13 +74,11 @@ export type MembraneOrientationParams = typeof MembraneOrientationParams export type MembraneOrientationProps = PD.Values<MembraneOrientationParams> export function getMembraneOrientationParams(ctx: ThemeRegistryContext, structure: Structure) { - console.log('rep @ getParams'); return PD.clone(MembraneOrientationParams); } export type MembraneOrientationRepresentation = StructureRepresentation<MembraneOrientationParams> export function MembraneOrientationRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, MembraneOrientationParams>): MembraneOrientationRepresentation { - console.log('rep @ create'); return Representation.createMulti('Membrane Orientation', ctx, getParams, StructureRepresentationStateBuilder, MembraneOrientationVisuals as unknown as Representation.Def<Structure, MembraneOrientationParams>); } @@ -97,8 +95,7 @@ export const MembraneOrientationRepresentationProvider = StructureRepresentation }); function getBilayerRims(ctx: RuntimeContext, data: Structure, props: BilayerRimsProps): Shape<Lines> { - console.log('rims'); - const { p1, p2, centroid, normal, radius } = MembraneOrientationProvider.get(data).value!; + const { planePoint1: p1, planePoint2: p2, centroid, normalVector: normal, radius } = MembraneOrientationProvider.get(data).value!; const scaledRadius = props.radiusFactor * radius; const builder = LinesBuilder.create(128, 64); getLayerCircle(builder, p1, centroid, normal, scaledRadius, props); @@ -134,8 +131,7 @@ function getCircle(p: Vec3, centroid: Vec3, normal: Vec3, radius: number) { } function getBilayerPlanes(ctx: RuntimeContext, data: Structure, props: BilayerPlanesProps, shape?: Shape<Mesh>): Shape<Mesh> { - console.log('planes'); - const { p1, p2, centroid, normal, radius } = MembraneOrientationProvider.get(data).value!; + const { planePoint1: p1, planePoint2: p2, centroid, normalVector: normal, radius } = MembraneOrientationProvider.get(data).value!; const state = MeshBuilder.createState(128, 64, shape && shape.geometry); const scaledRadius = props.radiusFactor * radius; getLayerPlane(state, p1, centroid, normal, scaledRadius); @@ -152,12 +148,12 @@ function getLayerPlane(state: MeshBuilder.State, p: Vec3, centroid: Vec3, normal function getBilayerSpheres(ctx: RuntimeContext, data: Structure, props: BilayerSpheresProps): Shape<Spheres> { const { density } = props; - const { radius, p1, p2, normal } = MembraneOrientationProvider.get(data).value!; + const { radius, planePoint1, planePoint2, normalVector } = MembraneOrientationProvider.get(data).value!; const scaledRadius = (props.radiusFactor * radius) * (props.radiusFactor * radius); const spheresBuilder = SpheresBuilder.create(); - getLayerSpheres(spheresBuilder, p1, normal, density, scaledRadius); - getLayerSpheres(spheresBuilder, p2, normal, density, scaledRadius); + getLayerSpheres(spheresBuilder, planePoint1, normalVector, density, scaledRadius); + getLayerSpheres(spheresBuilder, planePoint2, normalVector, density, scaledRadius); return Shape.create(name, data, spheresBuilder.getSpheres(), () => props.color, () => props.sphereSize, () => ''); }