molstar
Version:
A comprehensive macromolecular library.
180 lines (179 loc) • 9.16 kB
JavaScript
;
/**
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Adam Midlik <midlik@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.MeshShapeTransformer = exports.ParseMeshlistTransformer = exports.MeshlistStateObject = exports.MeshlistData = exports.VolsegTransform = exports.FOREROUND_OPACITY = exports.BACKGROUND_OPACITY = void 0;
exports.createMeshFromUrl = createMeshFromUrl;
const tslib_1 = require("tslib");
/** Defines new types of State tree transformers for dealing with mesh data. */
const base_1 = require("../../mol-geo/geometry/base");
const mesh_1 = require("../../mol-geo/geometry/mesh/mesh");
const geometry_1 = require("../../mol-math/geometry");
const linear_algebra_1 = require("../../mol-math/linear-algebra");
const shape_1 = require("../../mol-model/shape");
const objects_1 = require("../../mol-plugin-state/objects");
const transforms_1 = require("../../mol-plugin-state/transforms");
const data_1 = require("../../mol-plugin-state/transforms/data");
const representation_1 = require("../../mol-plugin-state/transforms/representation");
const mol_state_1 = require("../../mol-state");
const mol_task_1 = require("../../mol-task");
const param_definition_1 = require("../../mol-util/param-definition");
const MeshUtils = tslib_1.__importStar(require("./mesh-utils"));
exports.BACKGROUND_OPACITY = 0.2;
exports.FOREROUND_OPACITY = 1;
exports.VolsegTransform = mol_state_1.StateTransformer.builderFactory('volseg');
var MeshlistData;
(function (MeshlistData) {
function empty() {
return {
segmentId: 0,
segmentName: 'Empty',
detail: 0,
meshIds: [],
mesh: mesh_1.Mesh.createEmpty(),
};
}
MeshlistData.empty = empty;
;
async function fromCIF(data, segmentId, segmentName, detail) {
const { mesh, meshIds } = await MeshUtils.meshFromCif(data);
return {
segmentId,
segmentName,
detail,
meshIds,
mesh,
};
}
MeshlistData.fromCIF = fromCIF;
function stats(meshListData) {
return `Meshlist "${meshListData.segmentName}" (detail ${meshListData.detail}): ${meshListData.meshIds.length} meshes, ${meshListData.mesh.vertexCount} vertices, ${meshListData.mesh.triangleCount} triangles`;
}
MeshlistData.stats = stats;
function getShape(data, color) {
const mesh = data.mesh;
const meshShape = shape_1.Shape.create(data.segmentName, data, mesh, () => color, () => 1,
// group => `${data.segmentName} | Segment ${data.segmentId} | Detail ${data.detail} | Mesh ${group}`,
group => data.segmentName);
return meshShape;
}
MeshlistData.getShape = getShape;
function combineBBoxes(boxes) {
let result = null;
for (const box of boxes) {
if (!box)
continue;
if (result) {
linear_algebra_1.Vec3.min(result.min, result.min, box.min);
linear_algebra_1.Vec3.max(result.max, result.max, box.max);
}
else {
result = geometry_1.Box3D.zero();
geometry_1.Box3D.copy(result, box);
}
}
return result;
}
MeshlistData.combineBBoxes = combineBBoxes;
function bbox(data) {
return MeshUtils.bbox(data.mesh);
}
MeshlistData.bbox = bbox;
function allVerticesUsed(data) {
const unusedVertices = new Set();
for (let i = 0; i < data.mesh.vertexCount; i++) {
unusedVertices.add(i);
}
for (let i = 0; i < 3 * data.mesh.triangleCount; i++) {
const v = data.mesh.vertexBuffer.ref.value[i];
unusedVertices.delete(v);
}
return unusedVertices.size === 0;
}
MeshlistData.allVerticesUsed = allVerticesUsed;
})(MeshlistData || (exports.MeshlistData = MeshlistData = {}));
// // // // // // // // // // // // // // // // // // // // // // // //
// Raw Data -> Parsed data
class MeshlistStateObject extends objects_1.PluginStateObject.Create({ name: 'Parsed Meshlist', typeClass: 'Object' }) {
}
exports.MeshlistStateObject = MeshlistStateObject;
exports.ParseMeshlistTransformer = (0, exports.VolsegTransform)({
name: 'meshlist-from-string',
from: objects_1.PluginStateObject.Format.Cif,
to: MeshlistStateObject,
params: {
label: param_definition_1.ParamDefinition.Text(MeshlistStateObject.type.name, { isHidden: true }),
segmentId: param_definition_1.ParamDefinition.Numeric(1, {}, { isHidden: true }),
segmentName: param_definition_1.ParamDefinition.Text('Segment'),
detail: param_definition_1.ParamDefinition.Numeric(1, {}, { isHidden: true }),
/** Reference to the object which manages this meshlist (e.g. `MeshStreaming.Behavior`) */
ownerId: param_definition_1.ParamDefinition.Text('', { isHidden: true }),
}
})({
apply({ a, params }, globalCtx) {
return mol_task_1.Task.create('Create Parsed Meshlist', async (ctx) => {
const meshlistData = await MeshlistData.fromCIF(a.data, params.segmentId, params.segmentName, params.detail);
meshlistData.ownerId = params.ownerId;
const es = meshlistData.meshIds.length === 1 ? '' : 'es';
return new MeshlistStateObject(meshlistData, { label: params.label, description: `${meshlistData.segmentName} (${meshlistData.meshIds.length} mesh${es})` });
});
}
});
var MeshShapeProvider;
(function (MeshShapeProvider) {
function fromMeshlistData(meshlist, color) {
const theColor = color !== null && color !== void 0 ? color : MeshUtils.ColorGenerator.next().value;
return {
label: 'Mesh',
data: meshlist,
params: meshShapeProviderParams,
geometryUtils: mesh_1.Mesh.Utils,
getShape: (ctx, data) => MeshlistData.getShape(data, theColor),
};
}
MeshShapeProvider.fromMeshlistData = fromMeshlistData;
})(MeshShapeProvider || (MeshShapeProvider = {}));
const meshShapeProviderParams = {
...mesh_1.Mesh.Params,
quality: param_definition_1.ParamDefinition.Select('custom', base_1.VisualQualityOptions, { isEssential: true, description: 'Visual/rendering quality of the representation.' }), // use 'custom' when wanting to apply doubleSided
doubleSided: param_definition_1.ParamDefinition.Boolean(true, base_1.BaseGeometry.CustomQualityParamInfo),
// set `flatShaded`: true to see the real mesh vertices and triangles
transparentBackfaces: param_definition_1.ParamDefinition.Select('on', param_definition_1.ParamDefinition.arrayToOptions(['off', 'on', 'opaque']), base_1.BaseGeometry.ShadingCategory), // 'on' means: show backfaces with correct opacity, even when opacity < 1 (requires doubleSided) ¯\_(ツ)_/¯
};
exports.MeshShapeTransformer = (0, exports.VolsegTransform)({
name: 'shape-from-meshlist',
display: { name: 'Shape from Meshlist', description: 'Create Shape from Meshlist data' },
from: MeshlistStateObject,
to: objects_1.PluginStateObject.Shape.Provider,
params: {
color: param_definition_1.ParamDefinition.Value(undefined), // undefined means random color
},
})({
apply({ a, params }) {
const shapeProvider = MeshShapeProvider.fromMeshlistData(a.data, params.color);
return new objects_1.PluginStateObject.Shape.Provider(shapeProvider, { label: objects_1.PluginStateObject.Shape.Provider.type.name, description: a.description });
}
});
// // // // // // // // // // // // // // // // // // // // // // // //
/** Download data and create state tree hierarchy down to visual representation. */
async function createMeshFromUrl(plugin, meshDataUrl, segmentId, detail, collapseTree, color, parent, transparentIfBboxAbove, name, ownerId) {
const update = parent ? plugin.build().to(parent) : plugin.build().toRoot();
const rawDataNodeRef = update.apply(data_1.Download, { url: meshDataUrl, isBinary: true, label: `Downloaded Data ${segmentId}` }, { state: { isCollapsed: collapseTree } }).ref;
const parsedDataNode = await update.to(rawDataNodeRef)
.apply(transforms_1.StateTransforms.Data.ParseCif)
.apply(exports.ParseMeshlistTransformer, { label: undefined, segmentId: segmentId, segmentName: name !== null && name !== void 0 ? name : `Segment ${segmentId}`, detail: detail, ownerId: ownerId }, {})
.commit();
let transparent = false;
if (transparentIfBboxAbove !== undefined && parsedDataNode.data) {
const bbox = MeshlistData.bbox(parsedDataNode.data) || geometry_1.Box3D.zero();
transparent = geometry_1.Box3D.volume(bbox) > transparentIfBboxAbove;
}
await plugin.build().to(parsedDataNode)
.apply(exports.MeshShapeTransformer, { color: color })
.apply(representation_1.ShapeRepresentation3D, { alpha: transparent ? exports.BACKGROUND_OPACITY : exports.FOREROUND_OPACITY }, { tags: ['mesh-segment-visual', `segment-${segmentId}`] })
.commit();
return rawDataNodeRef;
}