molstar
Version:
A comprehensive macromolecular library.
237 lines • 13.1 kB
JavaScript
;
/**
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.VolumeFromDensityServerCif = exports.AssignColorVolume = exports.VolumeFromDx = exports.VolumeFromCube = exports.VolumeFromDsn6 = exports.VolumeFromCcp4 = void 0;
var tslib_1 = require("tslib");
var cif_1 = require("../../mol-io/reader/cif");
var linear_algebra_1 = require("../../mol-math/linear-algebra");
var ccp4_1 = require("../../mol-model-formats/volume/ccp4");
var density_server_1 = require("../../mol-model-formats/volume/density-server");
var dsn6_1 = require("../../mol-model-formats/volume/dsn6");
var mol_task_1 = require("../../mol-task");
var param_definition_1 = require("../../mol-util/param-definition");
var objects_1 = require("../objects");
var cube_1 = require("../../mol-model-formats/volume/cube");
var dx_1 = require("../../mol-model-formats/volume/dx");
var mol_state_1 = require("../../mol-state");
var VolumeFromCcp4 = objects_1.PluginStateTransform.BuiltIn({
name: 'volume-from-ccp4',
display: { name: 'Volume from CCP4/MRC/MAP', description: 'Create Volume from CCP4/MRC/MAP data' },
from: objects_1.PluginStateObject.Format.Ccp4,
to: objects_1.PluginStateObject.Volume.Data,
params: function (a) {
return {
voxelSize: param_definition_1.ParamDefinition.Vec3(linear_algebra_1.Vec3.create(1, 1, 1)),
offset: param_definition_1.ParamDefinition.Vec3(linear_algebra_1.Vec3.create(0, 0, 0)),
entryId: param_definition_1.ParamDefinition.Text(''),
};
}
})({
apply: function (_a) {
var _this = this;
var a = _a.a, params = _a.params;
return mol_task_1.Task.create('Create volume from CCP4/MRC/MAP', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var volume, props;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, (0, ccp4_1.volumeFromCcp4)(a.data, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { label: a.data.name || a.label })).runInContext(ctx)];
case 1:
volume = _a.sent();
props = { label: volume.label || 'Volume', description: "Volume " + a.data.header.NX + "\u00D7" + a.data.header.NX + "\u00D7" + a.data.header.NX };
return [2 /*return*/, new objects_1.PluginStateObject.Volume.Data(volume, props)];
}
});
}); });
},
dispose: function (_a) {
var b = _a.b;
b === null || b === void 0 ? void 0 : b.data.customProperties.dispose();
}
});
exports.VolumeFromCcp4 = VolumeFromCcp4;
var VolumeFromDsn6 = objects_1.PluginStateTransform.BuiltIn({
name: 'volume-from-dsn6',
display: { name: 'Volume from DSN6/BRIX', description: 'Create Volume from DSN6/BRIX data' },
from: objects_1.PluginStateObject.Format.Dsn6,
to: objects_1.PluginStateObject.Volume.Data,
params: function (a) {
return {
voxelSize: param_definition_1.ParamDefinition.Vec3(linear_algebra_1.Vec3.create(1, 1, 1)),
entryId: param_definition_1.ParamDefinition.Text(''),
};
}
})({
apply: function (_a) {
var _this = this;
var a = _a.a, params = _a.params;
return mol_task_1.Task.create('Create volume from DSN6/BRIX', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var volume, props;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, (0, dsn6_1.volumeFromDsn6)(a.data, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { label: a.data.name || a.label })).runInContext(ctx)];
case 1:
volume = _a.sent();
props = { label: volume.label || 'Volume', description: "Volume " + a.data.header.xExtent + "\u00D7" + a.data.header.yExtent + "\u00D7" + a.data.header.zExtent };
return [2 /*return*/, new objects_1.PluginStateObject.Volume.Data(volume, props)];
}
});
}); });
},
dispose: function (_a) {
var b = _a.b;
b === null || b === void 0 ? void 0 : b.data.customProperties.dispose();
}
});
exports.VolumeFromDsn6 = VolumeFromDsn6;
var VolumeFromCube = objects_1.PluginStateTransform.BuiltIn({
name: 'volume-from-cube',
display: { name: 'Volume from Cube', description: 'Create Volume from Cube data' },
from: objects_1.PluginStateObject.Format.Cube,
to: objects_1.PluginStateObject.Volume.Data,
params: function (a) {
var dataIndex = a ? param_definition_1.ParamDefinition.Select(0, a.data.header.dataSetIds.map(function (id, i) { return [i, "" + id]; })) : param_definition_1.ParamDefinition.Numeric(0);
return {
dataIndex: dataIndex,
entryId: param_definition_1.ParamDefinition.Text(''),
};
}
})({
apply: function (_a) {
var _this = this;
var a = _a.a, params = _a.params;
return mol_task_1.Task.create('Create volume from Cube', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var volume, props;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, (0, cube_1.volumeFromCube)(a.data, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { label: a.data.name || a.label })).runInContext(ctx)];
case 1:
volume = _a.sent();
props = { label: volume.label || 'Volume', description: "Volume " + a.data.header.dim[0] + "\u00D7" + a.data.header.dim[1] + "\u00D7" + a.data.header.dim[2] };
return [2 /*return*/, new objects_1.PluginStateObject.Volume.Data(volume, props)];
}
});
}); });
},
dispose: function (_a) {
var b = _a.b;
b === null || b === void 0 ? void 0 : b.data.customProperties.dispose();
}
});
exports.VolumeFromCube = VolumeFromCube;
var VolumeFromDx = objects_1.PluginStateTransform.BuiltIn({
name: 'volume-from-dx',
display: { name: 'Parse DX', description: 'Create volume from DX data.' },
from: objects_1.PluginStateObject.Format.Dx,
to: objects_1.PluginStateObject.Volume.Data
})({
apply: function (_a) {
var _this = this;
var a = _a.a;
return mol_task_1.Task.create('Parse DX', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var volume, props;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, (0, dx_1.volumeFromDx)(a.data, { label: a.data.name || a.label }).runInContext(ctx)];
case 1:
volume = _a.sent();
props = { label: volume.label || 'Volume', description: "Volume " + a.data.header.dim[0] + "\u00D7" + a.data.header.dim[1] + "\u00D7" + a.data.header.dim[2] };
return [2 /*return*/, new objects_1.PluginStateObject.Volume.Data(volume, props)];
}
});
}); });
},
dispose: function (_a) {
var b = _a.b;
b === null || b === void 0 ? void 0 : b.data.customProperties.dispose();
}
});
exports.VolumeFromDx = VolumeFromDx;
var VolumeFromDensityServerCif = objects_1.PluginStateTransform.BuiltIn({
name: 'volume-from-density-server-cif',
display: { name: 'Volume from density-server CIF', description: 'Identify and create all separate models in the specified CIF data block' },
from: objects_1.PluginStateObject.Format.Cif,
to: objects_1.PluginStateObject.Volume.Data,
params: function (a) {
if (!a) {
return {
blockHeader: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Text(void 0, { description: 'Header of the block to parse. If none is specifed, the 1st data block in the file is used.' })),
entryId: param_definition_1.ParamDefinition.Text(''),
};
}
var blocks = a.data.blocks.slice(1); // zero block contains query meta-data
return {
blockHeader: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Select(blocks[0] && blocks[0].header, blocks.map(function (b) { return [b.header, b.header]; }), { description: 'Header of the block to parse' })),
entryId: param_definition_1.ParamDefinition.Text(''),
};
}
})({
isApplicable: function (a) { return a.data.blocks.length > 0; },
apply: function (_a) {
var _this = this;
var a = _a.a, params = _a.params;
return mol_task_1.Task.create('Parse density-server CIF', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var header, block, densityServerCif, volume, _a, x, y, z, props;
var _b;
return (0, tslib_1.__generator)(this, function (_c) {
switch (_c.label) {
case 0:
header = params.blockHeader || a.data.blocks[1].header;
block = a.data.blocks.find(function (b) { return b.header === header; });
if (!block)
throw new Error("Data block '" + [header] + "' not found.");
densityServerCif = cif_1.CIF.schema.densityServer(block);
return [4 /*yield*/, (0, density_server_1.volumeFromDensityServerData)(densityServerCif, { entryId: params.entryId }).runInContext(ctx)];
case 1:
volume = _c.sent();
_a = volume.grid.cells.space.dimensions, x = _a[0], y = _a[1], z = _a[2];
props = { label: (_b = params.entryId) !== null && _b !== void 0 ? _b : densityServerCif.volume_data_3d_info.name.value(0), description: "Volume " + x + "\u00D7" + y + "\u00D7" + z };
return [2 /*return*/, new objects_1.PluginStateObject.Volume.Data(volume, props)];
}
});
}); });
},
dispose: function (_a) {
var b = _a.b;
b === null || b === void 0 ? void 0 : b.data.customProperties.dispose();
}
});
exports.VolumeFromDensityServerCif = VolumeFromDensityServerCif;
var AssignColorVolume = objects_1.PluginStateTransform.BuiltIn({
name: 'assign-color-volume',
display: { name: 'Assign Color Volume', description: 'Assigns another volume to be available for coloring.' },
from: objects_1.PluginStateObject.Volume.Data,
to: objects_1.PluginStateObject.Volume.Data,
isDecorator: true,
params: function (a, plugin) {
if (!a)
return { ref: param_definition_1.ParamDefinition.Text() };
var cells = plugin.state.data.select(mol_state_1.StateSelection.Generators.root.subtree().ofType(objects_1.PluginStateObject.Volume.Data).filter(function (cell) { var _a; return !!cell.obj && !((_a = cell.obj) === null || _a === void 0 ? void 0 : _a.data.colorVolume) && cell.obj !== a; }));
if (cells.length === 0)
return { ref: param_definition_1.ParamDefinition.Text('', { isHidden: true }) };
return { ref: param_definition_1.ParamDefinition.Select(cells[0].transform.ref, cells.map(function (c) { return [c.transform.ref, c.obj.label]; })) };
}
})({
apply: function (_a) {
var _this = this;
var a = _a.a, params = _a.params, dependencies = _a.dependencies;
return mol_task_1.Task.create('Assign Color Volume', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var colorVolume, volume, props;
return (0, tslib_1.__generator)(this, function (_a) {
if (!dependencies || !dependencies[params.ref]) {
throw new Error('Dependency not available.');
}
colorVolume = dependencies[params.ref].data;
volume = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, a.data), { colorVolume: colorVolume });
props = { label: a.label, description: 'Volume + Colors' };
return [2 /*return*/, new objects_1.PluginStateObject.Volume.Data(volume, props)];
});
}); });
}
});
exports.AssignColorVolume = AssignColorVolume;
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