pdb_analysis.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 "pdb_analysis.h"
#include "core/histogram.h"
#include "data/pdb.h"

void ProgPdbAnalysis::defineParams()
{
    addUsageLine("Analyze a PDB file and produce different statistics");
    addParamsLine("-i <file>    : PDB to study");
    addParamsLine("--operation <op>  : Operation to perform");
    addParamsLine("    where <op>");
    addParamsLine("          distance_histogram <fileOut> <Nnearest=3> <MaxDistance=-1>: Compute the distance histogram between");
    addParamsLine("                                                                    : an atom and its N nearest neighbours");
    addParamsLine("                                                                    : The maximum distance of the neighbours may be limited (in Angstroms)");
    addExampleLine("Compute the histogram of interatomic distances",false);
    addExampleLine("xmipp_pdb_analysis -i mypdb.pdb --operation distance_histogram distance.hist");
}

void ProgPdbAnalysis::readParams()
{
    fn_pdb=getParam("-i");
    op=getParam("--operation");
    if (op=="distance_histogram")
    {
        fn_hist=getParam("--operation",1);
        Nnearest=getIntParam("--operation",2);
        maxDistance=getDoubleParam("--operation",3);
    }
}

void ProgPdbAnalysis::show()
{
    if (verbose==0)
        return;
    std::cout
    << "PDB:          " << fn_pdb << std::endl
    << "Operation:    " << op << std::endl;
    if (op=="distance_histogram")
        std::cout << "Output histogram: " << fn_hist << std::endl
                  << "Nnearest:         " << Nnearest << std::endl
                  << "MaxDistance:      " << maxDistance << std::endl;
}

void ProgPdbAnalysis::run()
{
    if (op=="distance_histogram")
    {
        PDBPhantom pdb; // It cannot be a PDBRichPhantom because it also has to work with pseudoatomic structures
        pdb.read(fn_pdb);
        Histogram1D hist;
        distanceHistogramPDB(pdb,Nnearest,maxDistance,200,hist);
        hist.write(fn_hist);
    }
}