molstar
Version:
A comprehensive macromolecular library.
124 lines (123 loc) • 4.9 kB
JavaScript
;
/**
* Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.Coordinates = void 0;
exports.Time = Time;
const mol_util_1 = require("../../../mol-util");
const db_1 = require("../../../mol-data/db");
function Time(value, unit) {
return { value, unit };
}
var Coordinates;
(function (Coordinates) {
function create(frames, deltaTime, timeOffset) {
const hasCell = !!frames[0].cell;
const hasVelocities = !!frames[0].velocities;
const hasForces = !!frames[0].forces;
return {
id: mol_util_1.UUID.create22(),
frames,
hasCell,
hasVelocities,
hasForces,
deltaTime,
timeOffset,
};
}
Coordinates.create = create;
/**
* Only use ordering if it's not identity.
*/
function getAtomicConformation(frame, fields, ordering) {
var _a, _b;
let { x, y, z } = frame;
if (frame.xyzOrdering.frozen) {
if (ordering) {
if (frame.xyzOrdering.isIdentity) {
// simple list reordering
x = getOrderedCoords(x, ordering);
y = getOrderedCoords(y, ordering);
z = getOrderedCoords(z, ordering);
}
else if (!(0, mol_util_1.arrayEqual)(frame.xyzOrdering.index, ordering)) {
x = getSourceOrderedCoords(x, frame.xyzOrdering.index, ordering);
y = getSourceOrderedCoords(y, frame.xyzOrdering.index, ordering);
z = getSourceOrderedCoords(z, frame.xyzOrdering.index, ordering);
}
}
else if (!frame.xyzOrdering.isIdentity) {
x = getInvertedCoords(x, frame.xyzOrdering.index);
y = getInvertedCoords(y, frame.xyzOrdering.index);
z = getInvertedCoords(z, frame.xyzOrdering.index);
}
}
else if (ordering) {
if (frame.xyzOrdering.isIdentity) {
frame.xyzOrdering.isIdentity = false;
frame.xyzOrdering.index = ordering;
reorderCoordsInPlace(x, ordering);
reorderCoordsInPlace(y, ordering);
reorderCoordsInPlace(z, ordering);
}
else {
// is current ordering is not the same as requested?
// => copy the conformations into a new array
if (!(0, mol_util_1.arrayEqual)(frame.xyzOrdering.index, ordering)) {
x = getSourceOrderedCoords(x, frame.xyzOrdering.index, ordering);
y = getSourceOrderedCoords(y, frame.xyzOrdering.index, ordering);
z = getSourceOrderedCoords(z, frame.xyzOrdering.index, ordering);
}
}
}
// once the conformation has been accessed at least once, freeze it.
// => any other request to the frame with different ordering will result in a copy.
frame.xyzOrdering.frozen = true;
return {
id: mol_util_1.UUID.create22(),
atomId: fields.atomId,
occupancy: (_a = fields.occupancy) !== null && _a !== void 0 ? _a : db_1.Column.ofConst(1, frame.elementCount, db_1.Column.Schema.int),
B_iso_or_equiv: (_b = fields.B_iso_or_equiv) !== null && _b !== void 0 ? _b : db_1.Column.ofConst(0, frame.elementCount, db_1.Column.Schema.float),
xyzDefined: true,
x,
y,
z,
};
}
Coordinates.getAtomicConformation = getAtomicConformation;
const _reorderBuffer = [0.123];
function reorderCoordsInPlace(xs, index) {
const buffer = _reorderBuffer;
for (let i = 0, _i = xs.length; i < _i; i++) {
buffer[i] = xs[index[i]];
}
for (let i = 0, _i = xs.length; i < _i; i++) {
xs[i] = buffer[i];
}
}
function getSourceOrderedCoords(xs, srcIndex, index) {
const ret = new Float32Array(xs.length);
for (let i = 0, _i = xs.length; i < _i; i++) {
ret[i] = xs[srcIndex[index[i]]];
}
return ret;
}
function getOrderedCoords(xs, index) {
const ret = new Float32Array(xs.length);
for (let i = 0, _i = xs.length; i < _i; i++) {
ret[i] = xs[index[i]];
}
return ret;
}
function getInvertedCoords(xs, index) {
const ret = new Float32Array(xs.length);
for (let i = 0, _i = xs.length; i < _i; i++) {
ret[index[i]] = xs[i];
}
return ret;
}
})(Coordinates || (exports.Coordinates = Coordinates = {}));