molstar
Version:
A comprehensive macromolecular library.
73 lines (72 loc) • 2.98 kB
JavaScript
;
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Fred Ludlow <Fred.Ludlow@astx.com>
*
* based in part on NGL (https://github.com/arose/ngl)
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.HydrophobicProvider = exports.HydrophobicAtomProvider = void 0;
const param_definition_1 = require("../../../mol-util/param-definition");
const features_1 = require("./features");
const util_1 = require("../chemistry/util");
const common_1 = require("./common");
const HydrophobicParams = {
distanceMax: param_definition_1.ParamDefinition.Numeric(4.0, { min: 1, max: 5, step: 0.1 }),
};
/**
* Hydropbobic atoms
* - Carbon only bonded to carbon or hydrogen
* - Fluorine
*/
function addHydrophobicAtom(structure, unit, builder) {
const { elements } = unit;
const { x, y, z } = unit.model.atomicConformation;
for (let i = 0, il = elements.length; i < il; ++i) {
const element = (0, util_1.typeSymbol)(unit, i);
let flag = false;
if (element === "C" /* Elements.C */) {
flag = true;
(0, util_1.eachBondedAtom)(structure, unit, i, (unitB, indexB) => {
const elementB = (0, util_1.typeSymbol)(unitB, indexB);
if (elementB !== "C" /* Elements.C */ && elementB !== "H" /* Elements.H */)
flag = false;
});
}
else if (element === "F" /* Elements.F */) {
flag = true;
}
if (flag) {
builder.add(8 /* FeatureType.HydrophobicAtom */, common_1.FeatureGroup.None, x[elements[i]], y[elements[i]], z[elements[i]], i);
}
}
}
function isHydrophobicContact(ti, tj) {
return ti === 8 /* FeatureType.HydrophobicAtom */ && tj === 8 /* FeatureType.HydrophobicAtom */;
}
function testHydrophobic(structure, infoA, infoB, distanceSq) {
const typeA = infoA.types[infoA.feature];
const typeB = infoB.types[infoB.feature];
if (!isHydrophobicContact(typeA, typeB))
return;
const indexA = infoA.members[infoA.offsets[infoA.feature]];
const indexB = infoB.members[infoB.offsets[infoB.feature]];
if ((0, util_1.typeSymbol)(infoA.unit, indexA) === "F" /* Elements.F */ && (0, util_1.typeSymbol)(infoB.unit, indexB) === "F" /* Elements.F */)
return;
return common_1.InteractionType.Hydrophobic;
}
//
exports.HydrophobicAtomProvider = features_1.Features.Provider([8 /* FeatureType.HydrophobicAtom */], addHydrophobicAtom);
exports.HydrophobicProvider = {
name: 'hydrophobic',
params: HydrophobicParams,
createTester: (props) => {
return {
maxDistance: props.distanceMax,
requiredFeatures: new Set([8 /* FeatureType.HydrophobicAtom */]),
getType: (structure, infoA, infoB, distanceSq) => testHydrophobic(structure, infoA, infoB, distanceSq)
};
}
};