molstar
Version:
A comprehensive macromolecular library.
191 lines • 9.53 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.dynamicSuperpositionTest = exports.StaticSuperpositionTestData = exports.buildStaticSuperposition = void 0;
var tslib_1 = require("tslib");
var linear_algebra_1 = require("../../mol-math/linear-algebra");
var structure_1 = require("../../mol-model/structure");
var superposition_1 = require("../../mol-model/structure/structure/util/superposition");
var builder_1 = require("../../mol-script/language/builder");
var compiler_1 = require("../../mol-script/runtime/query/compiler");
var transforms_1 = require("../../mol-plugin-state/transforms");
var assets_1 = require("../../mol-util/assets");
function buildStaticSuperposition(plugin, src) {
var _this = this;
return plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var _i, src_1, s, structure, chain;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
_i = 0, src_1 = src;
_a.label = 1;
case 1:
if (!(_i < src_1.length)) return [3 /*break*/, 7];
s = src_1[_i];
return [4 /*yield*/, loadStructure(plugin, "https://www.ebi.ac.uk/pdbe/static/entry/" + s.pdbId + "_updated.cif", 'mmcif')];
case 2:
structure = (_a.sent()).structure;
return [4 /*yield*/, transform(plugin, structure, s.matrix)];
case 3:
_a.sent();
return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(structure, chainSelection(s.auth_asym_id), "Chain " + s.auth_asym_id)];
case 4:
chain = _a.sent();
if (!chain) return [3 /*break*/, 6];
return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(chain, { type: 'cartoon' })];
case 5:
_a.sent();
_a.label = 6;
case 6:
_i++;
return [3 /*break*/, 1];
case 7: return [2 /*return*/];
}
});
}); });
}
exports.buildStaticSuperposition = buildStaticSuperposition;
exports.StaticSuperpositionTestData = [
{
pdbId: '1aj5', auth_asym_id: 'A', matrix: linear_algebra_1.Mat4.identity()
},
{
pdbId: '1df0', auth_asym_id: 'B', matrix: linear_algebra_1.Mat4.ofRows([
[0.406, 0.879, 0.248, -200.633],
[0.693, -0.473, 0.544, 73.403],
[0.596, -0.049, -0.802, -14.209],
[0, 0, 0, 1]
])
},
{
pdbId: '1dvi', auth_asym_id: 'A', matrix: linear_algebra_1.Mat4.ofRows([
[-0.053, -0.077, 0.996, -45.633],
[-0.312, 0.949, 0.057, -12.255],
[-0.949, -0.307, -0.074, 53.562],
[0, 0, 0, 1]
])
}
];
function dynamicSuperpositionTest(plugin, src, comp_id) {
var _this = this;
return plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var _i, src_2, s, pivot, rest, query, xs, selections, transforms, i;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
_i = 0, src_2 = src;
_a.label = 1;
case 1:
if (!(_i < src_2.length)) return [3 /*break*/, 4];
s = src_2[_i];
return [4 /*yield*/, loadStructure(plugin, "https://www.ebi.ac.uk/pdbe/static/entry/" + s + "_updated.cif", 'mmcif')];
case 2:
_a.sent();
_a.label = 3;
case 3:
_i++;
return [3 /*break*/, 1];
case 4:
pivot = builder_1.MolScriptBuilder.struct.filter.first([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'residue-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.label_comp_id(), comp_id]),
'group-by': builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()
})
]);
rest = builder_1.MolScriptBuilder.struct.modifier.exceptBy({
0: builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
0: pivot,
radius: 5
}),
by: pivot
});
query = (0, compiler_1.compile)(pivot);
xs = plugin.managers.structure.hierarchy.current.structures;
selections = xs.map(function (s) { return structure_1.StructureSelection.toLociWithCurrentUnits(query(new structure_1.QueryContext(s.cell.obj.data))); });
transforms = (0, superposition_1.superpose)(selections);
return [4 /*yield*/, siteVisual(plugin, xs[0].cell, pivot, rest)];
case 5:
_a.sent();
i = 1;
_a.label = 6;
case 6:
if (!(i < selections.length)) return [3 /*break*/, 10];
return [4 /*yield*/, transform(plugin, xs[i].cell, transforms[i - 1].bTransform)];
case 7:
_a.sent();
return [4 /*yield*/, siteVisual(plugin, xs[i].cell, pivot, rest)];
case 8:
_a.sent();
_a.label = 9;
case 9:
i++;
return [3 /*break*/, 6];
case 10: return [2 /*return*/];
}
});
}); });
}
exports.dynamicSuperpositionTest = dynamicSuperpositionTest;
function siteVisual(plugin, s, pivot, rest) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var center, surr;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(s, pivot, 'pivot')];
case 1:
center = _a.sent();
if (!center) return [3 /*break*/, 3];
return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(center, { type: 'ball-and-stick', color: 'residue-name' })];
case 2:
_a.sent();
_a.label = 3;
case 3: return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(s, rest, 'rest')];
case 4:
surr = _a.sent();
if (!surr) return [3 /*break*/, 6];
return [4 /*yield*/, plugin.builders.structure.representation.addRepresentation(surr, { type: 'ball-and-stick', color: 'uniform', size: 'uniform', sizeParams: { value: 0.33 } })];
case 5:
_a.sent();
_a.label = 6;
case 6: return [2 /*return*/];
}
});
});
}
function loadStructure(plugin, url, format, assemblyId) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var data, trajectory, model, structure;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, plugin.builders.data.download({ url: assets_1.Asset.Url(url) })];
case 1:
data = _a.sent();
return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data, format)];
case 2:
trajectory = _a.sent();
return [4 /*yield*/, plugin.builders.structure.createModel(trajectory)];
case 3:
model = _a.sent();
return [4 /*yield*/, plugin.builders.structure.createStructure(model, assemblyId ? { name: 'assembly', params: { id: assemblyId } } : void 0)];
case 4:
structure = _a.sent();
return [2 /*return*/, { data: data, trajectory: trajectory, model: model, structure: structure }];
}
});
});
}
function chainSelection(auth_asym_id) {
return builder_1.MolScriptBuilder.struct.generator.atomGroups({
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), auth_asym_id])
});
}
function transform(plugin, s, matrix) {
var b = plugin.state.data.build().to(s)
.insert(transforms_1.StateTransforms.Model.TransformStructureConformation, { transform: { name: 'matrix', params: { data: matrix, transpose: false } } });
return plugin.runTask(plugin.state.data.updateTree(b));
}
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