/*
FILE:     pdb_extract_sf.C
*/
/*
VERSION:  1.600
*/
/*
DATE:     2/3/2005
*/
/*
  Comments and Questions to: sw-help@rcsb.rutgers.edu
*/
/*
COPYRIGHT 1999-2005 Rutgers - The State University of New Jersey

This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR
IMPLIED.  RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE
SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER
PROPRIETARY RIGHT.

The user of this software shall indemnify, hold harmless and defend
Rutgers, its governors, trustees, officers, employees, students,
agents and the authors against any and all claims, suits,
losses, liabilities, damages, costs, fees, and expenses including
reasonable attorneys' fees resulting from or arising out of the
use of this software.  This indemnification shall include, but is
not limited to, any and all claims alleging products liability.
*/
/*
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THIS "SOFTWARE, THE INDIVIDUAL OR ENTITY LICENSING THE  
SOFTWARE ("LICENSEE") IS CONSENTING TO BE BOUND BY AND IS 
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*/
/* a program to gather all the reflection data and convert it to
   cif format.   March, 2002
*/
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <ctype.h>
#include <time.h>
#include "CifFileObj.h"
#include "sf.h"
#include "util.h"

void merge_I_F(int argc, char **argv);

int main(int argc, char *argv[])
{    
    char outfile[MAXL], init_ID[40], ref_ID[40];
    int i;
    FILE *fout;
    
    
/*merge I and F in one data set from two files  */ 
    for(i=1; i<argc; i++){
        if(!strcmp_case(argv[i], "-merge") ){
            //pdb_extract_sf -merge -icif fine_name (special)
            merge_I_F(argc, argv);
            exit(0);  
        }else if(!strcmp_case(argv[i],"-o")){
            strcpy(outfile, argv[i+1]);            
        }else if(!strcmp_case(argv[i],"-dt")){
            strcpy(init_ID, argv[i+1]);
        }else if(!strcmp_case(argv[i],"-rt")){
            strcpy(ref_ID, argv[i+1]);
        }
        
    }
   
    check_input_error(argc, argv, outfile, init_ID, ref_ID);
    if(strlen(outfile)<=0) strcpy(outfile,"pdb_extract_sf.mmcif");
    
    fout = fopen(outfile, "w");

/*Extracting  reflections for refinement*/
    if(!strcmp_case(ref_ID, "-RP") ){
        fprintf(fout,"\ndata_set1_for_refinement\n");
        write_refl_refine(fout, argc, argv);
    }
    
/*Extracting reflections from initial data processing */
    if(!strcmp_case(init_ID, "-DP") ){
        fprintf(fout,"\ndata_set2_for_phasing\n");
        write_refl_initial(fout, argc, argv);
    }

   
/*Extracting imgCIF header */
//    write_refl_imgcif(fout, argc, argv);
    
    if( num_of_line(outfile)<200 ){
        printf("\nThe output file (%s) is suspicious!\n",outfile);
        printf("Please check the supported version of pdb_extract_sf or the input format.\n");
        return 0;
    }
    
    if(fout) fclose(fout);
    printf("\nChecking and rewriting the mmCIF file (%s)\n",outfile);
    cifparse(outfile);

    printf("\nThe output file name:  %s\n\n", outfile);
    
    exit(0);      
}


void check_input_error(int argc,char **argv, char *outfile,char *init_ID,
                       char *ref_ID)
/* obtaining the needed information and error messages*/
{
    int i=0, dp=0, dt=0, dlog=0,  rp=0, rt=0, r1=0, r2=0 ;
    static char *prog=(char *)"HKL, SCALEPACK, DTREK, SAINT, 3DSCALE, SCALA, CNS, OTHER";
    static char *prog_ref=(char *)"REFMAC5, SHELX, TNT, HKL, SCALEPACK, DTREK, SAINT, 3DSCALE, SCALA, CNS, XPREP,OTHER";
    static char *log=(char *)"-IDAT, -ICIF,  -ILOG";
    static char *option=(char *)"-rt, -rp, -dt, -dp, -c, -w, -IDAT, -ICIF, -ILOG, -o -merge";
   
    
    
    if(argc<=1 || !strcmp_case(argv[1],"-H")|| !strcmp_case(argv[1],"-HELP")){
        usage();
    }
    
    strcpy(outfile, "");
    strcpy(init_ID, "");
    strcpy(ref_ID, "");
    
    for(i=1; i<argc; i++){
        if(argv[i-1][0] =='-' && argv[i][0]=='-'){
            printf("\nInput wrong! Check arguments (%s) and (%s).\n",
                   argv[i-1],argv[i]);
            printf("Only options are allowed to start with (-)!\n\n");
            usage();
        }
        
        if(argv[i][0] =='-'){
            if(!strstr_case(option, argv[i])){
                printf("\nInput was wrong!\n");
                printf("You provided wrong option [%s]\n", argv[i]);
                printf("Option should be one of [%s]\n", option);
                usage();
            }
            if(i==argc-1){
                printf("\nInput was wrong!\n");
                printf("The option [%s] should be followed by a file name\n", argv[i]);
                usage();
            }  
        }

        if(!strcmp_case(argv[i-1], "-o")){
            strcpy(outfile, argv[i]);
        }
    }
    if(strlen(outfile)<=0) strcpy(outfile, "pdb_extract_sf.mmcif");
    
            
/* for initial data proccess */
    for(i=1; i<argc; i++){    
        if(!strcmp_case(argv[i], "-DP")){
            
            dp++;
            if(!strstr_case(prog, argv[i+1])){
                printf("\nInput is wrong after argument [-DP].\n"); 
                printf("Input (%s) is not one of (%s).\n", argv[i+1], prog);
                printf("(Note):\nIf program name is not shown above, \n");
                printf("please give 'OTHER', then provide either a CIF file\n");
                printf("or a plain text file with H,K,L,I(F),sigmaF(sigmaI) seperated by a space.\n");
                printf("The command will be 'pdb_extract_sf -dt ? -dp OTHER -c ? -w ? -idat file_name'.\n\n");
                usage();
            }
            
       }else if(!strcmp_case(argv[i],"-DT")){
            if(argc-i<2){
                printf("\nNo input after [%s  %s]!\n",argv[i-1], argv[i]);
                printf("Please provide the correct data type (I or F) after -DT.\n");
                printf("It is normally I (intensity) after data reduction.\n\n");
                usage();
            }
            
           
            dt++;
            
            if( strcmp_case(argv[i+1], "I")  && strcmp_case(argv[i+1], "F") ){
                printf("\nInput argument is wrong after [-DT].\n"); 
                printf("Please provide correct data type (I or F) after -DT.\n");
                printf("It is normally I (intensity) after data reduction.\n\n");
                usage();     
            }
            
        }else if(!strcmp_case(argv[i],"-C")){
            if(argc-i<6) {
                printf("\nNo enough arguments after [%s and %s]!\n", argv[i-1], argv[i]);
                printf("Note: '-c ? -w ? -idat (or -ilog, -icif) ?' should be together\n");
                exit(0);
            }

            if(strcmp_case(argv[i+2], "-W")){ 
                printf("\nInput is wrong after arguments [%s %s]!\n", argv[i], argv[i+1]);
                printf("Please provide the option [-W] after %s\n", argv[i+1]);
                printf("Note: '-c ? -w ? -idat (or -ilog, -icif) ?' should be together.\n");
                usage();                
            }else {
                if(!strstr_case(log,argv[i+4]) ){
                    printf("\nInput is wrong after arguments [%s %s]!\n", argv[i+2], argv[i+3]);
                    printf("Please provide one of the options [%s] after %s.\n", log,argv[i+3]);
                    printf("Note: '-c ? -w ? -idat (or -ilog, -icif) ?' should be together.\n");
                    usage();  
                }else{
                    if(!argv[i+5]){
                        printf("\nInput is wrong after arguments [%s %s %s ]!\n",
                               argv[i+2], argv[i+3], argv[i+4]);
                        printf("Please provide a file name after [%s].\n", argv[i+4]);
                        printf("Note: '-c ? -w ? -idat (or -ilog, -icif) ?' should be together.\n");
                        usage();
                    } else{
                        dlog++;
                    }
                }
            }
        }else if(!strcmp_case(argv[i],"-W")){
            if(argc-i<4) {
                printf("\nNo enough arguments after [%s and %s]!\n", argv[i-1], argv[i]);
                printf("Note: '-c ? -w ? -idat (or -ilog, -icif) ?' should be together\n");
                exit(0);
            }
            if(strncmp_case(argv[i+2],"-I", 2)){
                printf("Note: '-c ? -w ? -idat (or -ilog, -icif) ?' should be together.\n");
                exit(0); 
            }
            
            
        }
    }
        

//    printf("whis is data = %d %d\n", dt, dp);
    
    if(dp>1 || dt>1 ){
        printf("\nInput wrong! You entered -DT or -DP more than once.\n"); 
        printf("Command should be '-DT ? -DP ? -C ? -W ? -idat ? -ilog ?'.\n\n"); 
        usage();
    }
    if(dp==1 && dt!=1){
        printf("\nInput wrong! You used option [-DP], but no -DT option.\n"); 
        printf("Command should be '-DT ? -DP ? -C ? -W ? -idat ? -ilog ?'.\n\n"); 
        usage();
    }
    if(dt==1 && dp!=1){
        printf("\nInput wrong! You used option [-DT], but no -DP option.\n"); 
        printf("Command should be '-DT ? -DP ? -C ? -W ? -idat ? -ilog ?'.\n\n"); 
        usage();
    }
    if(dt==1 && dp==1 && dlog<=0){
        printf("\nInput wrong! There is no '-C i -W j'  option (for initial data process)\n"); 
        printf("Command should be '-DT ? -DP ? -C ? -W ? -idat ? -ilog ?'.\n\n"); 
        usage();
    }
    if(dt==1 && dp==1 && dlog>0){
        strcpy(init_ID, "-DP");      
    }
    
        

/* for final refinament */             


    for(i=1; i<argc-1; i++){
        if( !strcmp_case(argv[i],"-RT") ){
            if(!strcmp_case(argv[i+1], "I") || !strcmp_case(argv[i+1], "F") ){
                rt++;
            }else{
                printf("\nInput wrong after argument [-RT]! \n");
                printf("Please provide correct data type (F or I) after -RT.\n");
                printf("Normally, I for SHELX, F for CNS and TNT.\n");
                usage();
            }
        }
        
        if( !strcmp_case(argv[i],"-RP") ){
            if(strstr_case(prog_ref,argv[i+1])) {
                rp++;
            }else{

                printf("\nInput (%s) is wrong!\n",argv[i+1]);
                printf("Please provide correct program name for final refinement\n");
                printf("If program name is not one of (%s), give OTHER!\n", prog_ref);
                
                printf("If the structure factor is in MTZ format, convert it to mmcif format\n");
                printf("(Note: if given OTHER, you must either provide a CIF file\n");
                printf( "or a text file with H, K, L, F(I), sigmaF(sigmaI) seperated by a space.\n");
                printf("The command will be -rp OTHER -icif file_name (if CIF format)\n");
                printf("or -rp OTHER -idat file_name (if free format as mentioned above).)\n");
                usage();    
            }
            
        }
        if(i<argc-2 && (!strcmp_case(argv[i],"-RT") && !strcmp_case(argv[i+2],"-RP")) ||
           (!strcmp_case(argv[i],"-RP") && !strcmp_case(argv[i+2],"-RT"))){
            r1++;
        }
        
        if(i<argc-2 && (!strcmp_case(argv[i],"-RT") || !strcmp_case(argv[i],"-RP")) &&
           (!strcmp_case(argv[i+2],"-idat") || !strcmp_case(argv[i+2],"-icif"))){
            r2++;
        }
        
    }
        
        
    if(rp>1 || rt>1 ){
        printf("\nInput wrong! You entered -RT or -RP more than once.\n\n"); 
        printf("Command should be '-RT ? -RP ? -idat ? -ilog ?'.\n\n"); 
        usage();
    }
    if(rp==1 && rt!=1){
        printf("\nInput wrong! There is no -RT option\n\n"); 
        printf("Command should be '-RT ? -RP ? -idat ? -ilog ?'.\n\n"); 
        usage();
    }
    if(rt==1 && rp!=1){
        printf("\nInput wrong! There is no -RP option\n\n"); 
        printf("Command should be '-RT ? -RP ? -idat ? -ilog ?'.\n\n"); 
        usage();
    }
    
    if(rt==1 && rp==1){
        strcpy(ref_ID, "-RP");
        
        if(r2<=0){
            printf("\nInput wrong! \n"); 
            printf("The right input should be ( -rt ? -rp ?  -idat ?)\n"); 
            usage();
        }
    }
}



/*****************  extracting headers of image CIF file   ****************/
void write_refl_imgcif(FILE *fout, int argc, char **argv)
{
    int i=0;
    char infile[MAXL];
    
    for(i=1; i<argc-1; i++){  
        if(argv[i][0] =='-' && toupper(argv[i][1]) =='I' && 
           toupper(argv[i][2]) =='M' && toupper(argv[i][3])=='G' ){
            
            if(argv[i+1][0] !='-'){
                strcpy(infile, argv[i+1]);
                read_imgCIF_header(fout, infile);
                break;
            } else{ 
                printf("\nInput wrong!!\n");
                printf("The option (-imgCIF) should be followed by filename!\n");
                printf("The filename! (%s) should not be started with (-)!\n", argv[i+1]);
                usage();           
            }      
        }
    }
    
}

void read_imgCIF_header(FILE *fout, char *inpfile)
{
    char str[512];
    FILE *fp;
    
    printf("\nimgCIF file_name: %s\n", inpfile);
    
    if((fp = fopen(inpfile, "r"))==NULL) {        
        printf("Can not open the file %s\n",inpfile);
        return;
    }
    while (fgets(str, sizeof str, fp) != NULL) {
        if(strstr(str, "###_END_OF_HEADER")
           ||strstr(str, "CIF-BINARY-FORMAT-SECTION") )break;   
            
        fprintf(fout,"%s", str);
    }
    fclose(fp);
}

        

void cifparse(char *iFile)
{
  char *diags=NULL, oFile[256];
  CifFileObj * fobjR = NULL;
//  int len=0; 

  strcpy(oFile, iFile);
  
  fobjR = new CifFileObj("", WRITE_MODE, 80, "?", 0);
  fobjR->Read(iFile,diags);
  
//  len =  strlen(diags);
// if (diags) printf(" Diagnostics [ %d  %s] \n", len, diags );
 if (diags) printf(" Diagnostics [ %s] \n", diags );
  
  fobjR->Write(oFile,1);
  fobjR->CloseFile(1);
  if (fobjR) delete fobjR;
  
//  if (iFile) free(iFile);
//  if (oFile) free(oFile);
}

void usage()
{
    printf("------------------------------------------------------\n");
    printf("usage:    pdb_extract_sf [OPTION]... [FILE]...\n\n");
    printf(" -o  followed by the given output file name\n");
    printf("-dt  followed by data type (I or F) after data reduction.\n");
    printf("-dp  followed by program for processing data(HKL|SCALEPACK|DTREK|SAINT|SCALA|3DSCALE|OTHER ).\n");
    printf(" -c  followed by crystal number (like -c 1 ).\n");
    printf(" -w  followed by wavelength number (like -w 1).\n");
    
    printf("-rt  followed by data type used for final refinement (I or F).\n");
    printf("-rp  followed by reflection data format used for final refinement(CNS|TNT|SHELX).\n");
    printf("     (CNS|TNT|SHELX|HKL|SCALEPACK|DTREK|SAINT|SCALA|3DSCALE|OTHER)\n");
    printf("-iDAT  followed by a file name containing reflection data.\n");    
    printf("       (Format corresponds to each program used).\n");    
    printf("-iCIF  followed by a file name containing reflection data or statistics.\n");    
    printf("       The format is in mmcif (see http://pdb.rutgers.edu/mmcif/).\n");
    printf("-iLOG  followed by a LOG file name containing statistics only.\n");    
    printf("       (Format corresponds to each program used).\n\n");    
    printf("Examples:\n");
    printf("To convert reflection data (2 data sets after data reduction) to cif format:\n");
    printf("pdb_extract_sf -o output -dt I -dp HKL -c 1 -w 1 -iDAT name1.sca  -iLOG \n");
    printf("               name1.log -c 1 -w 2 -iDAT name2.sca  -iLOG name2.log\n\n");
    
    printf("To convert reflection data (used for final refinement) to cif format:\n");
    printf("pdb_extract_sf -o output -rt F -rp CNS -iDAT name1.hkl \n\n");
    
    exit(0);
}

    
void write_data_type_head(FILE *fout, char *I_F_type)
/* write the data head */
{
    
    if(!strcmp_case(I_F_type,"F")){

        fprintf(fout, "\n#reflection data type is amplitude.\n\n");
        fprintf(fout, "loop_\n");
        fprintf(fout, " _refln.crystal_id \n");
        fprintf(fout, " _refln.wavelength_id \n");
        fprintf(fout, " _refln.scale_group_code\n");
        fprintf(fout, " _refln.index_h\n");
        fprintf(fout, " _refln.index_k\n");
        fprintf(fout, " _refln.index_l\n");
        fprintf(fout, " _refln.F_meas_au\n" );
        fprintf(fout, " _refln.F_meas_sigma_au \n" );
        fprintf(fout, " _refln.status\n" );
        
    }else if(!strcmp_case(I_F_type,"I")){  
        fprintf(fout, "\n\n# reflection data type is intensity\n\n" );
        fprintf(fout, "loop_\n");
        fprintf(fout, " _refln.crystal_id \n");
        fprintf(fout, " _refln.wavelength_id \n");
        fprintf(fout, " _refln.scale_group_code\n");
        fprintf(fout, " _refln.index_h\n");
        fprintf(fout, " _refln.index_k\n");
        fprintf(fout, " _refln.index_l\n");
        fprintf(fout, " _refln.intensity_meas\n" );
        fprintf(fout, " _refln.intensity_sigma\n" );
        fprintf(fout, " _refln.status\n" );

    }
    else{
        printf("Data-type (%s) is wrong! (It should be either (F) or (I))\n",
               I_F_type );
        exit(0);
    }
}


void merge_I_F(int argc, char **argv)
//merge two data sets in one file (I and F) into one mmCIF category
//pdb_extract_sf -merge -icif fine_name
{
    char  iFile[512], outfile[512];
    char *diags=NULL, *blockId=NULL, *fnx=(char *)"cif2cif_from_cifparse";
    char **H1, **K1, **L1, **H2, **K2, **L2 , **status1, **status2;
    char **Fo_au1, **sFo_au1, **Io1, **sIo1, **Fo_au2, **sFo_au2, **Io2, **sIo2;
    long n1, n2,n, i, j;
    FILE *fout, *fp;
    
    strcpy(outfile, "");
    for(i=1; i<argc-1; i++){
        if(!strcmp_case(argv[i], "-o") ){
            strcpy(outfile,argv[i+1]);
        }else if (!strcmp_case(argv[i], "-icif") ){
            strcpy(iFile,argv[i+1]);
        }
    }
    
    if(strlen(outfile)<=0) strcpy(outfile, "pdb_extract_sf.mmcif");
    
    fout = fopen(outfile, "w");
    if(strlen(iFile)<=0) {
        printf("\nError! Input file does not exist! \n");
        exit(0);
    }

    CifFileObj * fobjR = NULL;
    fp = fopen(iFile, "r");
    if(fp==NULL){
        open_file_error(iFile, "merge_I_F");
    }
    
    fobjR = new CifFileObj(fnx, WRITE_MODE, 80, "?", 1);
    fobjR->Read(iFile,diags);
    if (diags != NULL) fprintf(stderr, "Diags for file %s: %s\n",iFile,diags);
    fobjR->CloseFile();
    if (fobjR) delete fobjR;

    fobjR = new CifFileObj(fnx, READ_MODE);
    blockId = fobjR->GetBlockName(0);
    
    printf("blockid1= %s\n", blockId);
   
    H1 = get_attribute_values(fobjR, blockId, "refln", "index_h", &n1);
    K1 = get_attribute_values(fobjR, blockId, "refln", "index_k", &n1);
    L1 = get_attribute_values(fobjR, blockId, "refln", "index_l", &n1);
    
    Fo_au1 = get_attribute_values(fobjR, blockId, "refln", "F_meas_au", &n1);
    sFo_au1 = get_attribute_values(fobjR, blockId, "refln", "F_meas_sigma_au", &n1);

    Io1 = get_attribute_values(fobjR, blockId, "refln", "intensity_meas", &n1);
    sIo1 = get_attribute_values(fobjR, blockId, "refln", "intensity_sigma", &n1);
    
    status1 = get_attribute_values(fobjR, blockId, "refln", "status", &n1);
    
    printf("Number of reflections   n1 = %ld\n\n", n1);

    if(! fobjR->GetBlockName(1)){
        printf("\nError! The file does not have the second block!\n");
        exit(0);
    }
       
    blockId = fobjR->GetBlockName(1); //second block
    printf("blockid2= %s\n", blockId);

    H2 = get_attribute_values(fobjR, blockId, "refln", "index_h", &n2);
    K2 = get_attribute_values(fobjR, blockId, "refln", "index_k", &n2);
    L2 = get_attribute_values(fobjR, blockId, "refln", "index_l", &n2);
    
    Fo_au2 = get_attribute_values(fobjR, blockId, "refln", "F_meas_au", &n2);
    sFo_au2 = get_attribute_values(fobjR, blockId, "refln", "F_meas_sigma_au", &n2);

    Io2 = get_attribute_values(fobjR, blockId, "refln", "intensity_meas", &n2);
    sIo2 = get_attribute_values(fobjR, blockId, "refln", "intensity_sigma", &n2);

    status2 = get_attribute_values(fobjR, blockId, "refln", "status", &n2);
    printf("Number of reflections  n2 = %ld\n\n", n2);


    
    if(n1>0 && n2>0 &&( Io1 && Fo_au2  || Io2 && Fo_au1)){
        fprintf(fout, "loop_\n");
        fprintf(fout, " _refln.crystal_id\n");
        fprintf(fout, " _refln.wavelength_id\n");
        fprintf(fout, " _refln.scale_group_code\n" );
        fprintf(fout, " _refln.status\n" );
        
        fprintf(fout, " _refln.index_h\n");
        fprintf(fout, " _refln.index_k\n");
        fprintf(fout, " _refln.index_l\n");
        
        fprintf(fout, " _refln.F_meas_au\n");
        fprintf(fout, " _refln.F_meas_sigma_au\n");
        fprintf(fout, " _refln.intensity_meas\n");
        fprintf(fout, " _refln.intensity_sigma\n");
        
        if(Io1 && Fo_au2){ //file2 has F
            printf("Number of reflections for F =  %ld\n", n2);
            
            for(i=0; i<n2; i++){
                fprintf(fout, " 1 1 1  ");
                (status2)? fprintf(fout,"%s ", status2[i]) :  fprintf(fout," ? ");
                fprintf(fout,"%s ", H2[i]) ;
                fprintf(fout,"%s ", K2[i]) ;
                fprintf(fout,"%s ", L2[i]) ;
                fprintf(fout,"%s ", Fo_au2[i]);
                (sFo_au2) ? fprintf(fout,"%s ", sFo_au2[i]) : fprintf(fout," 0 ");
                
                n=0;
                for(j=0; j<n1; j++){
                    if(!strcmp(H2[i], H1[j]) && !strcmp(K2[i], K1[j]) &&
                       !strcmp(L2[i], L1[j])){
                        fprintf(fout," %s ", Io1[j]);
                        (sIo1)? fprintf(fout," %s \n", sIo1[j]) : fprintf(fout," 0 \n");
                        n++;
                        break;
                    }
                }
                if (n==0) fprintf(fout," 0  0 \n");
            }
        }else if (Io2 && Fo_au1){ //file1 has F
            printf("Number of reflections for F =  %ld\n", n1);
            
            for(i=0; i<n1; i++){
                fprintf(fout, " 1 1 1 ");
                (status1[i])? fprintf(fout,"%s ", status1[i]) :  fprintf(fout," ? ");
                fprintf(fout,"%s ", H1[i]) ;
                fprintf(fout,"%s ", K1[i]) ;
                fprintf(fout,"%s ", L1[i]) ;
                fprintf(fout,"%s ", Fo_au1[i]);
                (sFo_au1)? fprintf(fout,"%s ", sFo_au1[i]) : fprintf(fout," 0 ");
                
                n=0;
                for(j=0; j<n2; j++){
                    if(!strcmp(H2[j], H1[i]) && !strcmp(K2[j], K1[i]) && !strcmp(L2[j], L1[i])){
                        fprintf(fout,"%s ",Io2[j]);
                        (sIo2)? fprintf(fout,"%s \n", sIo2[j]) : fprintf(fout," 0 \n");
                        n++;
                        break;
                    }
                }
                if (n==0) fprintf(fout," 0 0 \n");
            }
        }
    }else{
        printf("\nThe two files are not merged! \n");
        printf("One file should have intensity and the other file should have amplitude\n");
        delete_file("cif2cif_from_cifparse");
        exit(0);
    }
        
    delete_file("cif2cif_from_cifparse");
    fclose(fout);
    printf("\nChecking and rewriting the mmCIF file (%s)\n",outfile);
    if(H1) free_memory_2d(H1, n1);
    if(K1) free_memory_2d(K1, n1);
    if(L1) free_memory_2d(L1, n1);
    if(Fo_au1) free_memory_2d(Fo_au1, n1);
    if(sFo_au1) free_memory_2d(sFo_au1, n1);
    if(Io1) free_memory_2d(Io1, n1);
    if(sIo1) free_memory_2d(sIo1, n1);
    if(status1) free_memory_2d(status1, n1);
    
    if(H2) free_memory_2d(H2, n2);
    if(K2) free_memory_2d(K2, n2);
    if(L2) free_memory_2d(L2, n2);
    if(Fo_au2) free_memory_2d(Fo_au2, n2);
    if(sFo_au2) free_memory_2d(sFo_au2, n2);
    if(Io2) free_memory_2d(Io2, n2);
    if(sIo2) free_memory_2d(sIo2, n2);
    if(status2) free_memory_2d(status2, n2);

    
    cifparse(outfile);
}