TmMolStar/src/extensions/tmdet/algorithm.ts

/**
 * 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>
 */
/**
 * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
 *
 * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
 *
 * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
 * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
 */

import { Vec3 } from '../../mol-math/linear-algebra';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import '../../mol-util/polyfill';

export const TMDETParams = {
    numberOfSpherePoints: PD.Numeric(140, { min: 35, max: 700, step: 1 }, { description: 'Number of spheres/directions to test for membrane placement. Original value is 350.' }),
    stepSize: PD.Numeric(1, { min: 0.25, max: 4, step: 0.25 }, { description: 'Thickness of membrane slices that will be tested' }),
    minThickness: PD.Numeric(20, { min: 10, max: 30, step: 1}, { description: 'Minimum membrane thickness used during refinement' }),
    maxThickness: PD.Numeric(40, { min: 30, max: 50, step: 1}, { description: 'Maximum membrane thickness used during refinement' }),
    adjust: PD.Numeric(14, { min: 0, max: 30, step: 1 }, { description: 'Minimum length of membrane-spanning regions (original values: 14 for alpha-helices and 5 for beta sheets). Set to 0 to not optimize membrane thickness.' }),
};
export type TMDETParams = typeof TMDETParams
export type TMDETProps = PD.Values<TMDETParams>

const v3dot = Vec3.dot;

export function isInMembranePlane(testPoint: Vec3, normalVector: Vec3, planePoint1: Vec3, planePoint2: Vec3): boolean {
    const d1 = -v3dot(normalVector, planePoint1);
    const d2 = -v3dot(normalVector, planePoint2);
    return _isInMembranePlane(testPoint, normalVector, Math.min(d1, d2), Math.max(d1, d2));
}

function _isInMembranePlane(testPoint: Vec3, normalVector: Vec3, min: number, max: number): boolean {
    const d = -v3dot(normalVector, testPoint);
    return d > min && d < max;
}