TARIS-BuildTree.cpp

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/***************************************************************************
 *   Copyright (C) 2007 by Universidad Nacional de Colombia                *
 *   http://www.unal.edu.co                                                *
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#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <iostream>
#include <cstdlib>
using namespace std;

#include <HyperSurface.h>
#include <Surface.h>
#include <TarisApplication.h>
#include <Tree.h>
#include <vector>

namespace Programs{

class TARIS_BuildTree{
        public:
                static string usage()
                {
                        system("clear") ;
                        return
                        "=============================\n"
                        "TARIS-BuildTree (" __DATE__ ")\n"
                        "=============================\n"
                        "\n"
                        "Produces files in GML format containing the information that allows \n"
                        "to visualize the corresponding molecule's tree, taking as parameters \n"
                        "the .cube file, the initial cutoff, the final cutoff and the step-size\n"
                        "for the scan \n"
                        "\n"
                        "Syntax:\n"
                        "   $ TARIS-BuildTree -c file [PARAMETERS]\n"
                        "\n"
                        "Required parameters:\n"
                        "   -c   file\n"
                        "           This is the name of the cube file containing the electrostatic\n"
                        "           potential data\n"
                        "\n"
                        "Optional parameters:\n"
                        "   -b   cutoffBegin\n"
                        "           Initial cutoff for the scan\n"
                        "           (default=-0.1)\n"
                        "   -e   cutoffEnd\n"
                        "           Final cutoff for the scan\n"
                        "           (default=-0.07)\n"
                        "   -s   stepSize\n"
                        "           Step-size for the scan\n"
                        "           (default=-0.005)\n"
                        "   -o   output\n"
                        "           Name of the gml output file\n"
                        "           (default=screen)\n"
                        "\n"
                        "For example:\n"
                        "   $ TARIS-BuildTree -c file.cube -o file.gml\n"
                        "\n"
                        "Authors:\n"
                        "   Nestor F. Aguirre, Ray M. Marin and Edgar E. Daza\n"
                        "   Universidad Nacional de Colombia\n"
                        ;
                }
                
                static int main( int argc, char **argv )
                {
                        
                        if( argc > 1 ){
                                
                                string cubeFileName = TarisApplication::extractParameter( argc, argv, "-c" ) ;
                                double cutoffBegin = atof( TarisApplication::extractParameter( argc, argv, "-b", "-0.1" ) ) ;
                                double cutoffEnd = atof( TarisApplication::extractParameter( argc, argv, "-e", "-0.07" ) ) ;
                                double stepSize = atof( TarisApplication::extractParameter( argc, argv, "-s", "0.005" ) ) ;
                                string outputFileName = TarisApplication::extractParameter( argc, argv, "-o", "screen" ) ;
                                
                                HyperSurface hs ;
                                hs.load( cubeFileName ) ;
                                
                                Tree output = hs.buildAreaTree( cutoffBegin, cutoffEnd, stepSize ) ;
                                
                                Tree::print( output, cout ) ;
                                
                                if( outputFileName != "screen" ){
                                        output.save( outputFileName.c_str() ) ;
                                }else{
                                        cout << "---------------" << endl ;
                                        cout << "GML FILE" << endl ;
                                        cout << "---------------" << endl ;
                                        cout << endl ;
                                        output.save( &cout ) ;
                                }
                                
                        }else{
                                cout << usage() << endl ;
                        }

                        return EXIT_SUCCESS;
                }
};

}

int main( int argc, char **argv )
{
        return Programs::TARIS_BuildTree::main( argc, argv ) ;
}

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