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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**                                                                                 **
**                                                                                 **
**                                 E N S E M B L E                                 **
**                                                                                 **
**                                   Version 2.1                                   **
**                                                                                 **
**                                                                                 **
**                   Principal Investigator: Julie D. Forman-Kay                   **
**                                                                                 **
**                           Author:  Mickaël Krzeminski                           **
**                                                                                 **
**                               Date: November 2012                               **
**                                                                                 **
**                                                                                 **
*************************************************************************************
**                                                                                 **
**                                                                                 **
**   Copyright (C) The Hospital for Sick Children, 2001                            **
**                                                                                 **
**   Distribution of substantively modified versions of this module is prohibited  **
**  without the explicit permission of the copyright holder.                       **
**                                                                                 **
**   Any use of this work or derivative works in whole or in part for any          **
**  commercial purpose or for monetary gain is prohibited.                         **
**                                                                                 **
**                                                                                 **
**                                   NO WARRANTY                                   **
**   This software package is provided 'as is' without warranty of any kind,       **
**  expressed or implied.                                                          **
**                                                                                 **
**                                                                                 **
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
\* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

/*
   COMPILATION
                gcc -O3 -Wall -lm -o rg rg.c
*/

#include "Include/ens.h"


enum toolsPrograms TP = __RG__;

int main(int argc, char *argv[])
{
    /***********************************************************\
    |*                                                         *|
    |*                                                         *|
    |*                  Variables declaration                  *|
    |*                                                         *|
    |*                                                         *|
    \***********************************************************/
    // Counters
    counter count, confNb;

    // Verbose mode
    short verboseMode = FALSE;

    // Radius of gyration
    radiaOfGyration rog = {0, NULL, {0., 0.}};
    float *atomMasses = NULL;

    // PDB files
    char *ensFileName = NULL;
    char *outFileName = NULL;
    PDBListData ENSData = {0, 0, NULL, NULL};

    FILE *outFile;

    /***********************************************************\
    |*                                                         *|
    |*                                                         *|
    |*                  Retrieving  arguments                  *|
    |*                                                         *|
    |*                                                         *|
    \***********************************************************/
    for (count=1; count<argc; count++)
    {
        if (!strcmp(argv[count], "-f"))
        {
            ++count;
            if (argc>count)
            {
                if (argv[count][0] == '-') fatal_error("INVALID_ARGUMENT", argv[count]);
                if ((ensFileName = malloc((strlen(argv[count]) + 1) * CHAR_SIZE)) == NULL)
                {
                    _cleanRG(&ENSData, &rog, atomMasses, ensFileName, outFileName);
                    fatal_error("MEMORY", "create ensFileName variable");
                }
                strcpy(ensFileName, argv[count]);
            }
            else
            {
                    _cleanRG(&ENSData, &rog, atomMasses, ensFileName, outFileName);
                fatal_error("NO_ARGUMENT_FLAG", "-f");
            }
        }
        else if (!strcmp(argv[count], "-v"))        // Verbose mode (Display the radius of gyration of each conformer)
        {
            verboseMode = 1;
            }
        else
        {
            if (ensFileName != NULL)        // If more than one ENSEMBLE file is given as argument
            {
                   _cleanRG(&ENSData, &rog, atomMasses, ensFileName, outFileName);
                __USAGE__
            }
            else
            {
                if ((ensFileName = malloc((strlen(argv[count]) + 1) * CHAR_SIZE)) == NULL)
                {
                    _cleanRG(&ENSData, &rog, atomMasses, ensFileName, outFileName);
                    fatal_error("MEMORY", "create ensFileName variable");
                }
                strcpy(ensFileName, argv[count]);
            }
        }
    }


    // Verification of arguments coherence
    if (ensFileName == NULL)
    {
        _cleanRG(&ENSData, &rog, atomMasses, ensFileName, outFileName);
        __USAGE__
    }

    /***********************************************************\
    |*                                                         *|
    |*                                                         *|
    |*          Getting coordinates of all PDB files           *|
    |*                                                         *|
    |*                                                         *|
    \***********************************************************/
    // Recording the specified pdb files and calculating the Rg
    if (getCoords(&ENSData, ensFileName, NULL))
    {
        _cleanRG(&ENSData, &rog, atomMasses, ensFileName, outFileName);
        fatal_error("A problem occured while recording coordinates from the %s ENSEMBLE file.", ensFileName);
    }

    if (getMasses(&atomMasses, &ENSData))
    {
        _cleanRG(&ENSData, &rog, atomMasses, ensFileName, outFileName);
        fatal_error("A problem occured while recording masses from %s list.", ensFileName);
    }

    rog = getRoG(&ENSData, &atomMasses);
    if (rog.rg == NULL)
    {
        _cleanRG(&ENSData, &rog, atomMasses, ensFileName, outFileName);
            fatal_error("A problem occured while calculating radia of gyration from %s.", ensFileName);
    }

    // Displaying the results in an elegant way
    if (outFileName == NULL)
    {
        outFile = stdout;
    }
    else
    {
        if ((outFile = fopen(outFileName, "a")) == NULL)
        {
            error("Impossible to open the %s file.\nThe results will be displayed on screen.\n\n", outFileName);
            outFile = stdout;
        }
    }

    if (verboseMode)
    {
        for (confNb=0; confNb<rog.nb; confNb++)
        {
            fprintf(outFile, "Radius of gyration of conformer %u: %.2f\n", confNb+1, rog.rg[confNb]);
        }
    }

    fprintf(outFile, "Average radius of gyration: %.2f +/- %.2f A\n", rog.mean.average, rog.mean.stdv);


    // Releasing memory
    _cleanRG(&ENSData, &rog, atomMasses, ensFileName, outFileName);

        return 0;
}