molstar
Version:
A comprehensive macromolecular library.
84 lines • 4.35 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.getCoarse = exports.EmptyCoarse = void 0;
var tslib_1 = require("tslib");
var coarse_1 = require("../../../mol-model/structure/model/properties/coarse");
var coarse_keys_1 = require("../../../mol-model/structure/model/properties/utils/coarse-keys");
var mol_util_1 = require("../../../mol-util");
var int_1 = require("../../../mol-data/int");
var linear_algebra_1 = require("../../../mol-math/linear-algebra");
var coarse_ranges_1 = require("../../../mol-model/structure/model/properties/utils/coarse-ranges");
var schema_1 = require("./schema");
exports.EmptyCoarse = { hierarchy: coarse_1.CoarseHierarchy.Empty, conformation: void 0 };
function getCoarse(data, properties) {
var ihm_sphere_obj_site = data.ihm_sphere_obj_site, ihm_gaussian_obj_site = data.ihm_gaussian_obj_site;
if (ihm_sphere_obj_site._rowCount === 0 && ihm_gaussian_obj_site._rowCount === 0)
return exports.EmptyCoarse;
var sphereData = getData(ihm_sphere_obj_site);
var sphereConformation = getSphereConformation(ihm_sphere_obj_site);
var sphereKeys = (0, coarse_keys_1.getCoarseKeys)(sphereData, data.entities);
var sphereRanges = (0, coarse_ranges_1.getCoarseRanges)(sphereData, properties.chemicalComponentMap);
var gaussianData = getData(ihm_gaussian_obj_site);
var gaussianConformation = getGaussianConformation(ihm_gaussian_obj_site);
var gaussianKeys = (0, coarse_keys_1.getCoarseKeys)(gaussianData, data.entities);
var gaussianRanges = (0, coarse_ranges_1.getCoarseRanges)(gaussianData, properties.chemicalComponentMap);
return {
hierarchy: {
isDefined: true,
spheres: (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, sphereData), sphereKeys), sphereRanges),
gaussians: (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, gaussianData), gaussianKeys), gaussianRanges),
},
conformation: {
id: mol_util_1.UUID.create22(),
spheres: sphereConformation,
gaussians: gaussianConformation
}
};
}
exports.getCoarse = getCoarse;
function getSphereConformation(data) {
return {
x: data.Cartn_x.toArray({ array: Float32Array }),
y: data.Cartn_y.toArray({ array: Float32Array }),
z: data.Cartn_z.toArray({ array: Float32Array }),
radius: data.object_radius.toArray({ array: Float32Array }),
rmsf: data.rmsf.toArray({ array: Float32Array })
};
}
function getGaussianConformation(data) {
var matrix_space = schema_1.BasicSchema.ihm_gaussian_obj_site.covariance_matrix.space;
var covariance_matrix = [];
var cm = data.covariance_matrix;
for (var i = 0, _i = cm.rowCount; i < _i; i++) {
covariance_matrix[i] = linear_algebra_1.Tensor.toMat3((0, linear_algebra_1.Mat3)(), matrix_space, cm.value(i));
}
return {
x: data.mean_Cartn_x.toArray({ array: Float32Array }),
y: data.mean_Cartn_y.toArray({ array: Float32Array }),
z: data.mean_Cartn_z.toArray({ array: Float32Array }),
weight: data.weight.toArray({ array: Float32Array }),
covariance_matrix: covariance_matrix
};
}
function getSegments(asym_id, seq_id_begin, seq_id_end) {
var chainOffsets = [0];
for (var i = 1, _i = asym_id.rowCount; i < _i; i++) {
var newChain = !asym_id.areValuesEqual(i - 1, i);
if (newChain)
chainOffsets[chainOffsets.length] = i;
}
return {
chainElementSegments: int_1.Segmentation.ofOffsets(chainOffsets, int_1.Interval.ofBounds(0, asym_id.rowCount))
};
}
function getData(data) {
var entity_id = data.entity_id, seq_id_begin = data.seq_id_begin, seq_id_end = data.seq_id_end, asym_id = data.asym_id;
return (0, tslib_1.__assign)({ count: entity_id.rowCount, entity_id: entity_id, asym_id: asym_id, seq_id_begin: seq_id_begin, seq_id_end: seq_id_end }, getSegments(asym_id, seq_id_begin, seq_id_end));
}
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