pdb_sph_deform.h

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/***************************************************************************
 *
 * Authors:     David Herreros Calero (dherreros@cnb.csic.es)
 *
 * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
 *
 * 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., 59 Temple Place, Suite 330, Boston, MA
 * 02111-1307  USA
 *
 *  All comments concerning this program package may be sent to the
 *  e-mail address 'xmipp@cnb.csic.es'
 ***************************************************************************/
#ifndef _PROG_PDB_SPH_DEFORM
#define _PROG_PDB_SPH_DEFORM

#include <data/pdb.h>
#include <core/xmipp_program.h>
#include <core/xmipp_metadata_program.h>
#include <core/matrix1d.h>

class ProgPdbSphDeform: public XmippProgram
{
private:
    FileName fn_pdb;

    FileName fn_sph;

    FileName fn_out;

    bool center;

    double boxSize;    

    std::vector<double> clnm;

    std::vector<double> basisParams;

    Matrix1D<int> vL1;
    Matrix1D<int> vN;
    Matrix1D<int> vL2;
    Matrix1D<int> vM;

public:
    void defineParams() override;

    void readParams() override;

    void show() const override;

    void run() override;

    std::string readNthLine(int N) const;

    std::vector<double> string2vector(std::string const &s) const;

    void fillVectorTerms();

    void centerOfMass(PDBRichPhantom pdb, Matrix1D<double> &cm);
};
#endif