molstar
Version:
A comprehensive macromolecular library.
86 lines (85 loc) • 4.11 kB
JavaScript
;
/**
* Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.MembraneOrientationProvider = exports.MembraneOrientation = exports.MembraneOrientationParams = void 0;
const param_definition_1 = require("../../mol-util/param-definition");
const structure_1 = require("../../mol-model/structure");
const custom_property_1 = require("../../mol-model/custom-property");
const algorithm_1 = require("./algorithm");
const custom_structure_property_1 = require("../../mol-model-props/common/custom-structure-property");
const linear_algebra_1 = require("../../mol-math/linear-algebra");
const base_1 = require("../../mol-script/runtime/query/base");
const symbol_1 = require("../../mol-script/language/symbol");
const type_1 = require("../../mol-script/language/type");
exports.MembraneOrientationParams = {
...algorithm_1.ANVILParams
};
var MembraneOrientation;
(function (MembraneOrientation) {
let Tag;
(function (Tag) {
Tag["Representation"] = "membrane-orientation-3d";
})(Tag = MembraneOrientation.Tag || (MembraneOrientation.Tag = {}));
const pos = (0, linear_algebra_1.Vec3)();
MembraneOrientation.symbols = {
isTransmembrane: base_1.QuerySymbolRuntime.Dynamic((0, symbol_1.CustomPropSymbol)('computed', 'membrane-orientation.is-transmembrane', type_1.Type.Bool), ctx => {
const { unit, structure } = ctx.element;
const { x, y, z } = structure_1.StructureProperties.atom;
if (!structure_1.Unit.isAtomic(unit))
return 0;
const membraneOrientation = exports.MembraneOrientationProvider.get(structure).value;
if (!membraneOrientation)
return 0;
linear_algebra_1.Vec3.set(pos, x(ctx.element), y(ctx.element), z(ctx.element));
const { normalVector, planePoint1, planePoint2 } = membraneOrientation;
return (0, algorithm_1.isInMembranePlane)(pos, normalVector, planePoint1, planePoint2);
})
};
})(MembraneOrientation || (exports.MembraneOrientation = MembraneOrientation = {}));
exports.MembraneOrientationProvider = custom_structure_property_1.CustomStructureProperty.createProvider({
label: 'Membrane Orientation',
descriptor: (0, custom_property_1.CustomPropertyDescriptor)({
name: 'anvil_computed_membrane_orientation',
symbols: MembraneOrientation.symbols,
// TODO `cifExport`
}),
type: 'root',
defaultParams: exports.MembraneOrientationParams,
getParams: (data) => exports.MembraneOrientationParams,
isApplicable,
obtain: async (ctx, data, props) => {
const p = { ...param_definition_1.ParamDefinition.getDefaultValues(exports.MembraneOrientationParams), ...props };
try {
return { value: await computeAnvil(ctx, data, p) };
}
catch (e) {
// the "Residues Embedded in Membrane" symbol may bypass isApplicable() checks
console.warn('Failed to predict membrane orientation. This happens for short peptides and entries without amino acids.');
return { value: undefined };
}
}
});
function isApplicable(structure) {
if (!structure.isAtomic)
return false;
for (const model of structure.models) {
const { byEntityKey } = model.sequence;
for (const key of Object.keys(byEntityKey)) {
const { kind, length } = byEntityKey[+key].sequence;
if (kind !== 'protein')
continue; // can only process protein chains
if (length >= 15)
return true; // short peptides might fail
}
}
return false;
}
async function computeAnvil(ctx, data, props) {
const p = { ...param_definition_1.ParamDefinition.getDefaultValues(algorithm_1.ANVILParams), ...props };
return await (0, algorithm_1.computeANVIL)(data, p).runInContext(ctx.runtime);
}