/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2024 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#include <U2Algorithm/MolecularSurface.h>

#include <U2Core/Counter.h>
#ifdef __GNUC__
#    pragma GCC diagnostic push
#    pragma GCC diagnostic ignored "-Wdeprecated"
#endif
#include <BALL/STRUCTURE/triangulatedSAS.h>
#ifdef __GNUC__
#    pragma GCC diagnostic pop
#endif

#include "SAS.h"

namespace U2 {

// SolventAccessibleSurface

SolventAccessibleSurface::SolventAccessibleSurface() {
    GCOUNTER(cvar, "SolventAccessibleSurface");
}

void SolventAccessibleSurface::calculate(const QList<SharedAtom>& atoms, int& /*progress*/) {
    BALL::Surface surface;
    {
        std::vector<BALL::TSphere3<double>> spheres;
        foreach (const SharedAtom a, atoms) {
            Vector3D coord = a->coord3d;
            double radius = AtomConstants::getAtomCovalentRadius(a->atomicNumber) + TOLERANCE;
            spheres.push_back(BALL::TSphere3<double>(BALL::TVector3<double>(coord.x, coord.y, coord.z), radius));
        }
        double probeRadius = 1.4;
        BALL::ReducedSurface reducedSurface(spheres, probeRadius);
        reducedSurface.compute();
        BALL::SolventAccessibleSurface solventAccessibleSurface(&reducedSurface);
        solventAccessibleSurface.compute();
        double density = 1000.0 / atoms.size();
        BALL::TriangulatedSAS triangulatedSAS(&solventAccessibleSurface, density);
        triangulatedSAS.compute();
        triangulatedSAS.exportSurface(surface);
    }
    for (unsigned int faceIndex = 0; faceIndex < surface.getNumberOfTriangles(); faceIndex++) {
        const BALL::Surface::Triangle& triangle = surface.getTriangle(faceIndex);
        Face face;
        for (int coordIndex = 0; coordIndex < 3; coordIndex++) {
            face.v[0][coordIndex] = surface.getVertex(triangle.v1)[coordIndex];
            face.v[1][coordIndex] = surface.getVertex(triangle.v2)[coordIndex];
            face.v[2][coordIndex] = surface.getVertex(triangle.v3)[coordIndex];
            face.n[0][coordIndex] = surface.getNormal(triangle.v1)[coordIndex];
            face.n[1][coordIndex] = surface.getNormal(triangle.v2)[coordIndex];
            face.n[2][coordIndex] = surface.getNormal(triangle.v3)[coordIndex];
        }
        faces.append(face);
    }
}

qint64 SolventAccessibleSurface::estimateMemoryUsage(int) {
    return 0;
}

// SolventAccessibleSurfaceFactory

MolecularSurface* SolventAccessibleSurfaceFactory::createInstance() const {
    return new SolventAccessibleSurface();
}

}  // namespace U2
