pdb_nma_deform.cpp

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/***************************************************************************
 *
 * Authors:
 *
 * Carlos Oscar S. Sorzano (coss@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'
 ***************************************************************************/

#include <fstream>
#include "pdb_nma_deform.h"
#include "core/metadata_vec.h"
#include "data/pdb.h"

void ProgPdbNmaDeform::defineParams()
{
    addUsageLine("Deform a PDB according to a list of NMA modes");
    addUsageLine("+It is assumed that there is a deformation value per mode, and that the number of vectors in the mode is the same as the number of atoms in the PDB");
    addParamsLine("--pdb <file>    : PDB to deform");
    addParamsLine("--nma <metadata_file>  : List of modes, the metadata must use the label NMAModefile");
    addParamsLine("--deformations <...> : Deformation amplitudes in each direction");
    addParamsLine("-o <file>       : Deformed PDB");
    addExampleLine("xmipp_pdb_nma_deform --pdb 2tbv.pdb -o 2tbv_deformed.pdb --nma modelist.xmd --deformations 15");
}

void ProgPdbNmaDeform::readParams()
{
    fn_pdb=getParam("--pdb");
    fn_nma=getParam("--nma");
    fn_out=getParam("-o");
    StringVector listDeformations;
    getListParam("--deformations",listDeformations);
    deformations.resizeNoCopy(listDeformations.size());
    FOR_ALL_ELEMENTS_IN_ARRAY1D(deformations)
    deformations(i)=textToFloat(listDeformations[i]);
}

void ProgPdbNmaDeform::show()
{
    if (verbose==0)
        return;
    std::cout
    << "PDB:          " << fn_pdb << std::endl
    << "NMA list:     " << fn_nma << std::endl
    << "Output:       " << fn_out << std::endl
    << "Deformations: "
    ;
    FOR_ALL_ELEMENTS_IN_ARRAY1D(deformations)
        std::cout << deformations(i) << " ";
    std::cout << std::endl;
}

void ProgPdbNmaDeform::run()
{
    PDBRichPhantom pdb;
    MetaDataVec modes;
    pdb.read(fn_pdb);
    modes.read(fn_nma);
    modes.removeDisabled();
    int j=0;
    FileName fnMode;
    MultidimArray<double> mode;
    mode.resizeNoCopy(pdb.getNumberOfAtoms(),3);

    for (size_t objId : modes.ids())
    {
        // Read mode
        modes.getValue(MDL_NMA_MODEFILE,fnMode,objId);
        std::ifstream fhMode;
        fhMode.open(fnMode.c_str());
        if (!fhMode)
            REPORT_ERROR(ERR_IO_NOREAD,fnMode);
        fhMode >> mode;
        fhMode.close();

        // Apply mode
        double lambda=A1D_ELEM(deformations,j);
        for (size_t i=0; i<YSIZE(mode); ++i)
        {
            RichAtom& atom_i=pdb.atomList[i];
            atom_i.x+=lambda*DIRECT_A2D_ELEM(mode,i,0);
            atom_i.y+=lambda*DIRECT_A2D_ELEM(mode,i,1);
            atom_i.z+=lambda*DIRECT_A2D_ELEM(mode,i,2);
        }
        j++;
    }
    pdb.write(fn_out);
}