/**
 * 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"
#    pragma GCC diagnostic ignored "-Wsign-compare"
#endif
#include <BALL/STRUCTURE/triangulatedSES.h>
#ifdef __GNUC__
#    pragma GCC diagnostic pop
#endif

#include "SES.h"

namespace U2 {

// SolventExcludedSurface

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

static void calcSES(BALL::Surface& surface, const QList<SharedAtom>& atoms, double TOLERANCE) {
    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;
    double density = 1000. / atoms.size();

    BALL::ReducedSurface* reduced_surface = new BALL::ReducedSurface(spheres, probeRadius);
    reduced_surface->compute();

    {
        BALL::SolventExcludedSurface* ses = new BALL::SolventExcludedSurface(reduced_surface);
        ses->compute();
        double diff = 0.01;
        uint i = 0;
        bool ok = false;
        while (!ok && (i < 10)) {
            i++;
            ok = ses->check();
            if (!ok) {
                delete ses;
                delete reduced_surface;
                probeRadius += diff;
                reduced_surface = new BALL::ReducedSurface(spheres, probeRadius);
                reduced_surface->compute();
                ses = new BALL::SolventExcludedSurface(reduced_surface);
                ses->compute();
            }
        }
        if (ok) {
            BALL::TriangulatedSES* tSurface = new BALL::TriangulatedSES(ses, density);
            tSurface->compute();
            tSurface->exportSurface(surface);
            delete tSurface;
        }
        delete ses;
    }

    delete reduced_surface;
}

void SolventExcludedSurface::calculate(const QList<SharedAtom>& atoms, int& /*progress*/) {
    //        std::vector<BALL::TSphere3<double> > spheres;
    //         foreach(const SharedAtom a, atoms)
    //         {
    //             Vector3D coord=a->coord3d;
    //             double radius=PDBFormat::getAtomCovalentRadius(a->atomicNumber)+TOLERANCE;
    //             spheres.push_back(BALL::TSphere3<double>(BALL::TVector3<double>(coord.x,coord.y,coord.z),radius));
    //         }
    //         double probeRadius=1.4;
    //         double density = 1000. / atoms.size();
    //         for(int attempt=0;attempt < 10;attempt++)
    //         {
    //             progress = 0;
    //             BALL::ReducedSurface* reducedSurface = new BALL::ReducedSurface(spheres,probeRadius);
    //             reducedSurface->compute();
    //             BALL::SolventExcludedSurface solventExcludedSurface(&reducedSurface);
    //             solventExcludedSurface.compute();
    //             if(solventExcludedSurface.check())
    //             {
    //                  BALL::TriangulatedSES triangulatedSES(&solventExcludedSurface,density);
    //                  triangulatedSES.compute(progress);
    //                  triangulatedSES.exportSurface(surface);
    //                 break;
    //             }
    //             probeRadius+=0.01;
    //         }
    //
    //
    BALL::Surface surface;
    calcSES(surface, atoms, TOLERANCE);

    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 SolventExcludedSurface::estimateMemoryUsage(int) {
    return 0;
}

// SolventExcludedSurfaceFactory

MolecularSurface* SolventExcludedSurfaceFactory::createInstance() const {
    return new SolventExcludedSurface();
}

#define MAX_ATOMS_NUMBER 10000

bool SolventExcludedSurfaceFactory::hasConstraints(const BioStruct3D& biostruc) const {
    if (biostruc.getNumberOfAtoms() > MAX_ATOMS_NUMBER) {
        return true;
    } else {
        return false;
    }
}

}  // namespace U2
