pdb_reduce_pseudoatoms.cpp

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/***************************************************************************
 *
 * Authors: Javier Mota Garcia (jmota@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 <iostream>
#include <algorithm>
#include "pdb_reduce_pseudoatoms.h"
#include "data/pdb.h"

ProgPdbReduce::ProgPdbReduce()
{
    thresh = 0.0;
    num = -1.0;
}

void ProgPdbReduce::defineParams()
{
    addUsageLine("Reduce the number of pseudoatoms in a volume.");
    addExampleLine("   xmipp_pdb_reduce_pseudoatoms -i 1o7d.vol -o 1o7dreduced.vol --threshold 0.15");

    addParamsLine("   -i <pdb_file>                          : File to process");
    addParamsLine("  [-o <fn_root>]                          : Root name for output");
    addParamsLine("  [--number <num=-1.0>]                   : Number of pseudoatoms to keep based on intensity");
    addParamsLine("  [--threshold <thresh=0.0>]              : Intensity threshold for removing pseudoatoms");
}

void ProgPdbReduce::readParams()
{
    fn_volume = getParam("-i");
    fn_out = checkParam("-o") ? getParam("-o") : fn_volume.withoutExtension();
    num = getDoubleParam("--number");
    thresh = getDoubleParam("--threshold");

}

/* Show -------------------------------------------------------------------- */
void ProgPdbReduce::show()
{
    std::cout << "PDB file:           " << fn_volume           << std::endl
              << "Number:             " << num                 << std::endl
              << "Threshold:          " << thresh              << std::endl;
}

void ProgPdbReduce::reduceNumberPseudoatoms()
{
    PDBRichPhantom pdb;
    if(thresh != 0.0)
        pdb.read(fn_volume, false, thresh);
    else
    {
        pdb.read(fn_volume, true);
        std::sort(pdb.intensities.rbegin(), pdb.intensities.rend());
        thresh = pdb.intensities.at(num);
        pdb.atomList.clear();
        pdb.remarks.clear();
        pdb.read(fn_volume, false, thresh);
    }
    pdb.write(fn_out, true); // keep renumbering
}

void ProgPdbReduce::run()
{
    reduceNumberPseudoatoms();
}