molstar
Version:
A comprehensive macromolecular library.
163 lines (162 loc) • 6.93 kB
JavaScript
;
/**
* Copyright (c) 2017-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Fred Ludlow <Fred.Ludlow@astx.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Paul Pillot <paul.pillot@tandemai.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.AtomGeometryAngles = exports.AtomGeometry = void 0;
exports.geometryLabel = geometryLabel;
exports.assignGeometry = assignGeometry;
exports.calcAngles = calcAngles;
exports.calcPlaneAngle = calcPlaneAngle;
exports.closestHydrogenIndex = closestHydrogenIndex;
const misc_1 = require("../../../mol-math/misc");
const linear_algebra_1 = require("../../../mol-math/linear-algebra");
const util_1 = require("./util");
/**
* Numbering mostly inline with coordination number from VSEPR,
* breaks with `SquarePlanar = 7`
*/
var AtomGeometry;
(function (AtomGeometry) {
AtomGeometry[AtomGeometry["Spherical"] = 0] = "Spherical";
AtomGeometry[AtomGeometry["Terminal"] = 1] = "Terminal";
AtomGeometry[AtomGeometry["Linear"] = 2] = "Linear";
AtomGeometry[AtomGeometry["Trigonal"] = 3] = "Trigonal";
AtomGeometry[AtomGeometry["Tetrahedral"] = 4] = "Tetrahedral";
AtomGeometry[AtomGeometry["TrigonalBiPyramidal"] = 5] = "TrigonalBiPyramidal";
AtomGeometry[AtomGeometry["Octahedral"] = 6] = "Octahedral";
AtomGeometry[AtomGeometry["SquarePlanar"] = 7] = "SquarePlanar";
AtomGeometry[AtomGeometry["Unknown"] = 8] = "Unknown";
})(AtomGeometry || (exports.AtomGeometry = AtomGeometry = {}));
function geometryLabel(geometry) {
switch (geometry) {
case AtomGeometry.Spherical:
return 'Spherical';
case AtomGeometry.Terminal:
return 'Terminal';
case AtomGeometry.Linear:
return 'Linear';
case AtomGeometry.Trigonal:
return 'Trigonal';
case AtomGeometry.Tetrahedral:
return 'Tetrahedral';
case AtomGeometry.TrigonalBiPyramidal:
return 'Trigonal Bi-Pyramidal';
case AtomGeometry.Octahedral:
return 'Octahedral';
case AtomGeometry.SquarePlanar:
return 'Square Planar';
case AtomGeometry.Unknown:
return 'Unknown';
}
}
function assignGeometry(totalCoordination) {
switch (totalCoordination) {
case 0: return AtomGeometry.Spherical;
case 1: return AtomGeometry.Terminal;
case 2: return AtomGeometry.Linear;
case 3: return AtomGeometry.Trigonal;
case 4: return AtomGeometry.Tetrahedral;
default: return AtomGeometry.Unknown;
}
}
exports.AtomGeometryAngles = new Map([
[AtomGeometry.Linear, (0, misc_1.degToRad)(180)],
[AtomGeometry.Trigonal, (0, misc_1.degToRad)(120)],
[AtomGeometry.Tetrahedral, (0, misc_1.degToRad)(109.4721)],
[AtomGeometry.Octahedral, (0, misc_1.degToRad)(90)]
]);
// tmp objects for `calcAngles` and `calcPlaneAngle`
const tmpDir1 = (0, linear_algebra_1.Vec3)();
const tmpDir2 = (0, linear_algebra_1.Vec3)();
const tmpPosA = (0, linear_algebra_1.Vec3)();
const tmpPosB = (0, linear_algebra_1.Vec3)();
const tmpPosX = (0, linear_algebra_1.Vec3)();
/**
* Calculate the angles x-a1-a2 for all x where x is a heavy atom (not H) bonded to ap1.
*/
function calcAngles(structure, unitA, indexA, unitB, indexB, ignoreHydrogens = true) {
const angles = [];
const anglesH = [];
unitA.conformation.position(unitA.elements[indexA], tmpPosA);
unitB.conformation.position(unitB.elements[indexB], tmpPosB);
linear_algebra_1.Vec3.sub(tmpDir1, tmpPosB, tmpPosA);
(0, util_1.eachBondedAtom)(structure, unitA, indexA, (unitX, indexX) => {
if ((0, util_1.typeSymbol)(unitX, indexX) !== "H" /* Elements.H */) {
unitX.conformation.position(unitX.elements[indexX], tmpPosX);
linear_algebra_1.Vec3.sub(tmpDir2, tmpPosX, tmpPosA);
angles.push(linear_algebra_1.Vec3.angle(tmpDir1, tmpDir2));
}
else if (!ignoreHydrogens) {
unitX.conformation.position(unitX.elements[indexX], tmpPosX);
linear_algebra_1.Vec3.sub(tmpDir2, tmpPosX, tmpPosA);
anglesH.push(linear_algebra_1.Vec3.angle(tmpDir1, tmpDir2));
}
});
return [angles, anglesH];
}
/**
* Find two neighbours of ap1 to define a plane (if possible) and
* measure angle out of plane to ap2
* @param {AtomProxy} ap1 First atom (angle centre)
* @param {AtomProxy} ap2 Second atom (out-of-plane)
* @return {number} Angle from plane to second atom
*/
function calcPlaneAngle(structure, unitA, indexA, unitB, indexB) {
unitA.conformation.position(unitA.elements[indexA], tmpPosA);
unitB.conformation.position(unitB.elements[indexB], tmpPosB);
linear_algebra_1.Vec3.sub(tmpDir1, tmpPosB, tmpPosA);
const neighbours = [(0, linear_algebra_1.Vec3)(), (0, linear_algebra_1.Vec3)()];
let ni = 0;
let unitX1;
let indexX1;
(0, util_1.eachBondedAtom)(structure, unitA, indexA, (unitX, indexX) => {
if (ni > 1)
return;
if ((0, util_1.typeSymbol)(unitX, indexX) !== "H" /* Elements.H */) {
unitX1 = unitX;
indexX1 = indexX;
unitX.conformation.position(unitX.elements[indexX], tmpPosX);
linear_algebra_1.Vec3.sub(neighbours[ni++], tmpPosX, tmpPosA);
}
});
if (ni === 1 && unitX1 && indexX1) {
(0, util_1.eachBondedAtom)(structure, unitX1, indexX1, (unitX, indexX) => {
if (ni > 1)
return;
if (unitX === unitA && indexX === indexA)
return;
if ((0, util_1.typeSymbol)(unitX, indexX) !== "H" /* Elements.H */) {
unitX.conformation.position(unitX.elements[indexX], tmpPosX);
linear_algebra_1.Vec3.sub(neighbours[ni++], tmpPosX, tmpPosA);
}
});
}
if (ni !== 2) {
return;
}
linear_algebra_1.Vec3.cross(tmpDir2, neighbours[0], neighbours[1]);
return Math.abs((Math.PI / 2) - linear_algebra_1.Vec3.angle(tmpDir2, tmpDir1));
}
function closestHydrogenIndex(structure, unitA, indexA, unitB, indexB) {
let hIndex = indexA;
unitA.conformation.position(unitA.elements[indexA], tmpPosA);
unitB.conformation.position(unitB.elements[indexB], tmpPosB);
linear_algebra_1.Vec3.sub(tmpDir1, tmpPosB, tmpPosA);
let minDistSq = linear_algebra_1.Vec3.squaredDistance(tmpPosA, tmpPosB);
(0, util_1.eachBondedAtom)(structure, unitA, indexA, (unitX, indexX) => {
if ((0, util_1.typeSymbol)(unitX, indexX) === "H" /* Elements.H */) {
unitX.conformation.position(unitX.elements[indexX], tmpPosX);
const dist = linear_algebra_1.Vec3.squaredDistance(tmpPosX, tmpPosB);
if (dist < minDistSq) {
minDistSq = dist;
hIndex = indexX;
}
}
});
return hIndex;
}