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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 -o ss_distr ss_distr.c
*/

#include "Include/ens.h"


enum toolsPrograms TP = __SS_DISTR__;


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

    // Initialization of the main data variable (Must always be initialized that way)
    PDBListData ENSData = {0, 0, NULL, NULL};

    // IO files
    char *PDBListFileName = NULL, *outFileName = NULL;

    // PDB files
    FILE *outFile;
    residueList residueNbs = {0, NULL};

    // Secondary structure statistics
    secondaryStructure statSecStr = {NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0};


    /***********************************************************\
    |*                                                         *|
    |*                                                         *|
    |*                Arguments and Environment                *|
    |*                                                         *|
    |*                                                         *|
    \***********************************************************/
    // Checking the number of arguments
    if (argc < 2)
    {
        _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
        __USAGE__
    }

    for (count=1; count<argc; count++)
    {
        if (!strcmp(argv[count], "-f"))
        {
            ++count;
            if (argc>count)
            {
                if (argv[count][0] == '-')
                {
                    _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
                    fatal_error("INVALID_ARGUMENT", argv[count]);
                }

                if ((PDBListFileName = malloc((strlen(argv[count]) + 1) * CHAR_SIZE)) == NULL)
                {
                    _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
                    fatal_error("MEMORY", "create PDBListFileName variable");
                }
                strcpy(PDBListFileName, argv[count]);
            }
            else
            {
                _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
                fatal_error("NO_ARGUMENT_FLAG", "-f");
            }
        }
        else if (!strcmp(argv[count], "-o"))
        {
            ++count;
            if (argc>count)
            {
                if (argv[count][0] == '-')
                {
                    _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
                    fatal_error("INVALID_ARGUMENT", argv[count]);
                }

                if ((outFileName = malloc(strlen(argv[count]) * CHAR_SIZE + 1)) == NULL)
                {
                    _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
                    fatal_error("MEMORY", "create outFileName variable");
                }
                strcpy(outFileName, argv[count]);
            }
            else
            {
                _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
                fatal_error("NO_ARGUMENT_FLAG", "-o");
            }
        }
    }

    if (PDBListFileName == NULL)
    {
        _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
        __USAGE__;
    }

    /***********************************************************\
    |*                                                         *|
    |*                                                         *|
    |*                  Reading PDB file list                  *|
    |*                  Creating distribution                  *|
    |*                                                         *|
    |*                                                         *|
    \***********************************************************/
    // Recording structure coordinates
    if (getCoords(&ENSData, PDBListFileName, NULL))
    {
        _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
        fatal_error("A problem occured while recording coordinates from the %s list file.", PDBListFileName);
    }

    // Get the number of residues
    if (getResidueNumbers(&residueNbs, &ENSData))
    {
        _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
        fatal_error("A problem occured while recording residue numbers from the %s list file.", PDBListFileName);
    }
    if (!residueNbs.nb)
    {
        _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
        fatal_error("A problem occured while recording residue numbers from atom headers.", NULL);
    }

    // Get the secondary structure
    statSecStr = getSecondaryStructure(&ENSData);
    if (!statSecStr.nbResidues)
    {
        _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);
        fatal_error("The program encountered a critical problem while attempting to get the secondary structure distribution of the ensemble!", NULL);
    }


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


    /* LATER, THIS PART WILL BECOME GRAPHICAL */
    fprintf(outFile, "Residue    Helix     Pi_Helix  Helix3_10 Strand    Coil      Turn      Bridge\n");
    for (resiNb=0; resiNb<residueNbs.nb; resiNb++)
    {
        fprintf(outFile, "%-7d    %-6.2f    %-6.2f    %-6.2f    %-6.2f    %-6.2f    %-6.2f    %-6.2f\n", residueNbs.nbs[resiNb],\
                                                                               (float)statSecStr.Helix[resiNb]/ENSData.nbConfs,\
                                                                               (float)statSecStr.Pihelix[resiNb]/ENSData.nbConfs,\
                                                                               (float)statSecStr.Helix310[resiNb]/ENSData.nbConfs,\
                                                                               (float)statSecStr.Strand[resiNb]/ENSData.nbConfs,\
                                                                               (float)statSecStr.Coil[resiNb]/ENSData.nbConfs,\
                                                                               (float)statSecStr.Turn[resiNb]/ENSData.nbConfs,\
                                                                               (float)statSecStr.Bridge[resiNb]/ENSData.nbConfs);
    }

    fprintf(outFile, "\n\n\nResidue        Helix          Strand         Coil&Turn      Bridge\n");
    for (resiNb=0; resiNb<statSecStr.nbResidues; resiNb++)
    {
        fprintf(outFile, "%-7d        %-6.2f         %-6.2f         %-6.2f         %-6.2f\n", residueNbs.nbs[resiNb],\
                                                    (float)(statSecStr.Helix[resiNb]+statSecStr.Pihelix[resiNb]+statSecStr.Helix310[resiNb])/ENSData.nbConfs,\
                                                    (float)statSecStr.Strand[resiNb]/ENSData.nbConfs,\
                                                    (float)(statSecStr.Coil[resiNb]+statSecStr.Turn[resiNb])/ENSData.nbConfs,\
                                                    (float)statSecStr.Bridge[resiNb]/ENSData.nbConfs);
    }

    // Releasing memory
    _clean_ss_distr(&ENSData, &statSecStr, &residueNbs, PDBListFileName, outFileName);


    return 0;
}