molstar
Version:
A comprehensive macromolecular library.
113 lines • 6.95 kB
JavaScript
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
*/
import { __assign } from "tslib";
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
import { Representation } from '../../mol-repr/representation';
import { Structure } from '../../mol-model/structure';
import { StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../../mol-repr/structure/representation';
import { ShapeRepresentation } from '../../mol-repr/shape/representation';
import { Shape } from '../../mol-model/shape';
import { Lines } from '../../mol-geo/geometry/lines/lines';
import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
import { LinesBuilder } from '../../mol-geo/geometry/lines/lines-builder';
import { Circle } from '../../mol-geo/primitive/circle';
import { transformPrimitive } from '../../mol-geo/primitive/primitive';
import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
import { MembraneOrientationProvider } from './prop';
import { MarkerActions } from '../../mol-util/marker-action';
import { lociLabel } from '../../mol-theme/label';
import { ColorNames } from '../../mol-util/color/names';
var SharedParams = {
color: PD.Color(ColorNames.lightgrey),
radiusFactor: PD.Numeric(1.2, { min: 0.1, max: 3.0, step: 0.01 }, { description: 'Scale the radius of the membrane layer' })
};
var BilayerPlanesParams = __assign(__assign(__assign({}, Mesh.Params), SharedParams), { sectorOpacity: PD.Numeric(0.5, { min: 0, max: 1, step: 0.01 }) });
var BilayerRimsParams = __assign(__assign(__assign({}, Lines.Params), SharedParams), { lineSizeAttenuation: PD.Boolean(true), linesSize: PD.Numeric(0.3, { min: 0.01, max: 50, step: 0.01 }), dashedLines: PD.Boolean(true) });
var MembraneOrientationVisuals = {
'bilayer-planes': function (ctx, getParams) { return ShapeRepresentation(getBilayerPlanes, Mesh.Utils, { modifyState: function (s) { return (__assign(__assign({}, s), { markerActions: MarkerActions.Highlighting })); }, modifyProps: function (p) { return (__assign(__assign({}, p), { alpha: p.sectorOpacity, ignoreLight: true, doubleSided: false })); } }); },
'bilayer-rims': function (ctx, getParams) { return ShapeRepresentation(getBilayerRims, Lines.Utils, { modifyState: function (s) { return (__assign(__assign({}, s), { markerActions: MarkerActions.Highlighting })); } }); }
};
export var MembraneOrientationParams = __assign(__assign(__assign({}, BilayerPlanesParams), BilayerRimsParams), { visuals: PD.MultiSelect(['bilayer-planes', 'bilayer-rims'], PD.objectToOptions(MembraneOrientationVisuals)) });
export function getMembraneOrientationParams(ctx, structure) {
return PD.clone(MembraneOrientationParams);
}
export function MembraneOrientationRepresentation(ctx, getParams) {
return Representation.createMulti('Membrane Orientation', ctx, getParams, StructureRepresentationStateBuilder, MembraneOrientationVisuals);
}
export var MembraneOrientationRepresentationProvider = StructureRepresentationProvider({
name: 'membrane-orientation',
label: 'Membrane Orientation',
description: 'Displays a grid of points representing membrane layers.',
factory: MembraneOrientationRepresentation,
getParams: getMembraneOrientationParams,
defaultValues: PD.getDefaultValues(MembraneOrientationParams),
defaultColorTheme: { name: 'shape-group' },
defaultSizeTheme: { name: 'shape-group' },
isApplicable: function (structure) { return structure.elementCount > 0; },
ensureCustomProperties: {
attach: function (ctx, structure) { return MembraneOrientationProvider.attach(ctx, structure, void 0, true); },
detach: function (data) { return MembraneOrientationProvider.ref(data, false); }
}
});
function membraneLabel(data) {
return lociLabel(Structure.Loci(data)) + " | Membrane Orientation";
}
function getBilayerRims(ctx, data, props, shape) {
var _a = MembraneOrientationProvider.get(data).value, p1 = _a.planePoint1, p2 = _a.planePoint2, centroid = _a.centroid, radius = _a.radius;
var scaledRadius = props.radiusFactor * radius;
var builder = LinesBuilder.create(128, 64, shape === null || shape === void 0 ? void 0 : shape.geometry);
getLayerCircle(builder, p1, centroid, scaledRadius, props);
getLayerCircle(builder, p2, centroid, scaledRadius, props);
return Shape.create('Bilayer rims', data, builder.getLines(), function () { return props.color; }, function () { return props.linesSize; }, function () { return membraneLabel(data); });
}
function getLayerCircle(builder, p, centroid, radius, props, shape) {
var circle = getCircle(p, centroid, radius);
var indices = circle.indices, vertices = circle.vertices;
for (var j = 0, jl = indices.length; j < jl; j += 3) {
if (props.dashedLines && j % 2 === 1)
continue; // draw every other segment to get dashes
var start = indices[j] * 3;
var end = indices[j + 1] * 3;
var startX = vertices[start];
var startY = vertices[start + 1];
var startZ = vertices[start + 2];
var endX = vertices[end];
var endY = vertices[end + 1];
var endZ = vertices[end + 2];
builder.add(startX, startY, startZ, endX, endY, endZ, 0);
}
}
var tmpMat = Mat4();
var tmpV = Vec3();
function getCircle(p, centroid, radius) {
if (Vec3.dot(Vec3.unitY, Vec3.sub(tmpV, p, centroid)) === 0) {
Mat4.targetTo(tmpMat, p, centroid, Vec3.unitY);
}
else {
Mat4.targetTo(tmpMat, p, centroid, Vec3.unitX);
}
Mat4.setTranslation(tmpMat, p);
Mat4.mul(tmpMat, tmpMat, Mat4.rotX90);
var circle = Circle({ radius: radius, segments: 64 });
return transformPrimitive(circle, tmpMat);
}
function getBilayerPlanes(ctx, data, props, shape) {
var _a = MembraneOrientationProvider.get(data).value, p1 = _a.planePoint1, p2 = _a.planePoint2, centroid = _a.centroid, radius = _a.radius;
var state = MeshBuilder.createState(128, 64, shape && shape.geometry);
var scaledRadius = props.radiusFactor * radius;
getLayerPlane(state, p1, centroid, scaledRadius);
getLayerPlane(state, p2, centroid, scaledRadius);
return Shape.create('Bilayer planes', data, MeshBuilder.getMesh(state), function () { return props.color; }, function () { return 1; }, function () { return membraneLabel(data); });
}
function getLayerPlane(state, p, centroid, radius) {
var circle = getCircle(p, centroid, radius);
state.currentGroup = 0;
MeshBuilder.addPrimitive(state, Mat4.id, circle);
MeshBuilder.addPrimitiveFlipped(state, Mat4.id, circle);
}
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