//

// Molekel - Molecular Visualization Program

// Copyright (C) 2006, 2007 Swiss National Supercomputing Centre (CSCS)

//

// 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.

//

// $Author$

// $Date$

// $Revision$

//

#include <openbabel/mol.h>

#include <openbabel/obconversion.h>

#include <openbabel/obmolecformat.h>

#include <openbabel/mol.h>

#include <openbabel/atom.h>

#include <openbabel/elements.h>

#include <openbabel/obiter.h>

#include <openbabel/data.h>

#include <iostream>

using namespace std;

namespace OpenBabel

{

//==============================================================================

/// Class to output a molecule in XYZR MSMS input format for further computation

/// of Connolly surface.

/// Michel Sanner page with info on MSMS:

/// http://www.scripps.edu/~sanner/

class OBMSMSFormat : public OpenBabel::OBMoleculeFormat

{

public:

    /// Constructor: register 'msms' and "MSMS" format.

    OBMSMSFormat()

    {

        OpenBabel::OBConversion::RegisterFormat( "msms", this );

    }

    /// Return description.

    const char* Description() override  // required

    {

        return

        "M.F. Sanner's MSMS input format\n"

        "Generates input to the MSMS (Michael Sanner Molecular Surface) program to compute solvent surfaces.\n\n"

        "Write Options, e.g. -xa\n"

        "  a output atom names\n";

    }

    /// Return a specification url, not really a specification since

    /// I couldn't find it but close enough.

    const char* SpecificationURL() override

    {

        return "http://www.scripps.edu/~sanner";

    }

    /// Return MIME type, NULL in this case.

    const char* GetMIMEType() override { return nullptr; }

      /// Return read/write flag: read only.

    unsigned int Flags() override

    {

        return WRITEONEONLY | NOTREADABLE;

    }

    /// Skip to object: used for multi-object file formats.

    int SkipObjects(int n, OpenBabel::OBConversion* pConv) override { return 0; }

    /// Read: always return false.

    bool ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*) override

    {

        return false;

    }

    /// Write.

    bool WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*) override;

};

//------------------------------------------------------------------------------

// Global variable used to register MSMS format.

OBMSMSFormat msmsFormat__;

//------------------------------------------------------------------------------

//==============================================================================

//------------------------------------------------------------------------------

bool OBMSMSFormat::WriteMolecule( OBBase* pOb, OBConversion* pConv )

{

    OBMol* pmol = dynamic_cast< OBMol* >(pOb);

    if (pmol == nullptr) return false;

    ostream& os = *pConv->GetOutStream();

    const bool atomNames = pConv->IsOption("a", OBConversion::OUTOPTIONS) != nullptr;

    // write header ?

    // iterate through atoms and write <atom x> <atom y> <atom z> <atom radius>

    // and optionally <atomic number> in case atomNames == true

    FOR_ATOMS_OF_MOL( a, *pmol )

    {

        const double* c = a->GetCoordinate();

        os << c[ 0 ] << '\t' << c[ 1 ] << '\t' << c[ 2 ] << '\t' <<

        OBElements::GetVdwRad( a->GetAtomicNum() );

        if( atomNames ) os << '\t' << a->GetAtomicNum();

        os << '\n';

    }

    os.flush();

    return true;

}

}