rino 0.1.0 → 0.2.0

data/ext/src/e_ichi_io.h

@@ -1,40 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#ifndef __ICHI_IO_H__
-#define __ICHI_IO_H__
-
-
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-extern "C" {
-#endif
-#endif
-
-
-char* fgets_up_to_lf( char* line, int line_len, FILE* inp );
-int my_fgetsUpToLfOrTab( char *szLine, int len, FILE *f );
-
-int e_my_fgetsTab( char *szLine, int len, FILE *f, int *bTooLongLine );
-int e_my_fgetsTab1( char *szLine, int len, FILE *f, int *bTooLongLine );
-
-int e_inchi_print( FILE* f, const char* lpszFormat, ... );
-int e_my_fprintf( FILE* f, const char* lpszFormat, ... );
-void e_PrintFileName( const char *fmt, FILE *output_file, const char *szFname );
-unsigned long e_ulMyGetTickCount( int bStart );
-unsigned long e_ulMyTickCountDiff( unsigned long ulTickEnd, unsigned long ulTickStart );
-
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-}
-#endif
-#endif
-
-
-#endif /* __ICHI_IO_H__ */

data/ext/src/e_ichi_parms.c

@@ -1,37 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-#include <errno.h>
-#include <limits.h>
-
-#include "e_mode.h"
-#include "inchi_api.h"
-#include "e_ctl_data.h"
-#include "e_ichi_io.h"
-#include "e_ichi_parms.h"
-#include "e_util.h"
-#include "e_ichicomp.h"
-
-#define DetectInputINChIFileType e_DetectInputINChIFileType
-#define ReadCommandLineParms     e_ReadCommandLineParms
-#define mystrncpy                e_mystrncpy
-#define my_fprintf               e_my_fprintf
-#define LtrimRtrim               e_LtrimRtrim
-#define PrintInputParms          e_PrintInputParms
-#define OpenFiles                e_OpenFiles
-#define PrintFileName            e_PrintFileName
-#define HelpCommandLineParms     e_HelpCommandLineParms
-#define inchi_print_nodisplay    fprintf
-
-#include "ichiparm.h"
-

data/ext/src/e_ichi_parms.h

@@ -1,41 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#ifndef __ICHI_PARMS_H__
-#define __ICHI_PARMS_H__
-
-
-
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-extern "C" {
-#endif
-#endif
-
-
-int e_ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *szSdfDataValue,
-                          unsigned long *ulDisplTime, int bReleaseVersion, INCHI_FILE *log_file );
-
-int e_PrintInputParms( INCHI_FILE *log_file, INPUT_PARMS *ip );
-int e_OpenFiles( FILE **inp_file, FILE **output_file, FILE **log_file, FILE **prb_file, INPUT_PARMS *ip );
-void e_HelpCommandLineParms( INCHI_FILE *f );
-
-
-
-
-
-
-
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-}
-#endif
-#endif
-
-#endif /* __ICHI_PARMS_H__ */

data/ext/src/e_ichicomp.h

@@ -1,50 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#ifndef __INCHI_COMPAT_H__
-#define __INCHI_COMPAT_H__
-
-/* compatibility */
-
-#if( defined(__GNUC__) && defined(__MINGW32__) && __GNUC__ == 3 && __GNUC_MINOR__ == 2 && __GNUC_PATCHLEVEL__ == 0 && defined(_WIN32) ) 
-/* replace with the proper definition for GNU gcc & MinGW-2.0.0-3 (mingw special 20020817-1), gcc 3.2 core */
-#define my_va_start(A,B) ((A)=(va_list)__builtin_next_arg(lpszFormat))
-#else
-#define my_va_start va_start
-#endif
-
-
-
-/*  ANSI redefinitions */
-#ifdef INCHI_ANSI_ONLY  /* { */
-#ifndef __isascii
-#define __isascii(val)  ((unsigned)(val) <= 0x7F)
-#endif
-
-/* #ifndef __GNUC__ */
-/* these non-ANSI functions are implemented in gcc */
-#include <stdio.h>
- /* this #include provides size_t definition */
- /* implementation is located in util.c */
-#if ( !defined(_MSC_VER) || defined(__STDC__) && __STDC__ == 1 )
-/* support (VC++ Language extensions) = OFF && defined(INCHI_ANSI_ONLY) */
-int   memicmp (const void*, const void*, size_t);
-int   stricmp( const char *s1, const char *s2 );
-char *_strnset( char *string, int c, size_t count );
-char *_strdup( const char *string );
-#endif
-/* #endif */
-
-#endif /* } */
-
-#define inchi_max(a,b)  (((a)>(b))?(a):(b))
-#define inchi_min(a,b)  (((a)<(b))?(a):(b))
-
-
-#endif /* __INCHI_COMPAT_H__ */

data/ext/src/e_ichierr.h

@@ -1,40 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#ifndef __INCHIERR_H__
-#define __INCHIERR_H__
-
-#define _IS_OKAY    0
-#define _IS_WARNING 1
-#define _IS_ERROR   2    /* Microsoft defined its own IS_ERROR() macro */
-#define _IS_FATAL   3
-#define _IS_UNKNOWN 4    /* unknown error: used in INChI DLL only */
-#define _IS_EOF    -1    /* end of file */
-#define _IS_SKIP   -2
-
-
-
-#define INCHI_INP_ERROR_ERR   40
-#define INCHI_INP_ERROR_RET  (-1)
-
-#define INCHI_INP_FATAL_ERR    1
-#define INCHI_INP_FATAL_RET    0
-
-#define INCHI_INP_EOF_ERR     11
-#define INCHI_INP_EOF_RET      0
-
-#define LOG_MASK_WARN  1
-#define LOG_MASK_ERR   2
-#define LOG_MASK_FATAL 4
-
-#define LOG_MASK_ALL     (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL)
-#define LOG_MASK_NO_WARN (LOG_MASK_ERR | LOG_MASK_FATAL)
-
-
-#endif /* __INCHIERR_H__ */

data/ext/src/e_ichimain.c

@@ -1,593 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-/*#define ADD_WIN_CTLC*/
-
-#if( defined( WIN32 ) && defined( _CONSOLE ) && defined(_MSC_VER) && _MSC_VER >= 800 && defined(ADD_WIN_CTLC) )
-#include <windows.h>
-#endif
-
-
-/* #define CREATE_0D_PARITIES */      /* uncomment to replace coordinates and 2D-parirties with 0D-parities */
-/* #define MAKE_INCHI_FROM_AUXINFO */ /* uncomment to create the second InChI out of AuxInfo and compare */
-#define NEIGH_ONLY_ONCE         /* comment out to include each bond in both neighboring atoms adjacency lists */
-
-#include <stdio.h>
-#include <stdlib.h>
-
-#include <string.h>
-#include <ctype.h>
-#include <stdarg.h>
-#include <errno.h>
-#include <limits.h>
-#include <float.h>
-
-#include "e_mode.h"
-#include "inchi_api.h"
-#include "e_inchi_atom.h"
-#include "e_ctl_data.h"
-#include "e_ichi_parms.h"
-#include "e_util.h"
-#include "e_ichi_io.h"
-#include "e_ichierr.h"
-#include "e_readstru.h"
-#include "e_ichicomp.h"
-#ifdef CREATE_0D_PARITIES
-#include "e_0dstereo.h"
-#endif
-
-int e_MakeOutputHeader( char *pSdfLabel, char *pSdfValue, long lSdfId, int num_inp, char *pStr1, char *pStr2 );
-char *e_GetChiralFlagString( int bChiralFlagOn );
-
-
-/*  console-specific */
-/*****************************************************************
- *
- *  Ctrl+C trap; works under Win32 + MS VC++
- *
- *****************************************************************/
-#ifndef INCHI_LIB
-
-int e_bInterrupted = 0;
-#if( defined( _WIN32 ) && defined( _CONSOLE ) )
-
-#if( defined(_MSC_VER) && _MSC_VER >= 800 && defined(ADD_WIN_CTLC) )
-BOOL WINAPI MyHandlerRoutine(
-  DWORD dwCtrlType   /*   control signal type */
-  ) {
-    if ( dwCtrlType == CTRL_C_EVENT     ||
-         dwCtrlType == CTRL_BREAK_EVENT ||
-         dwCtrlType == CTRL_CLOSE_EVENT ||
-         dwCtrlType == CTRL_LOGOFF_EVENT ) {
-        e_bInterrupted = 1;
-        return TRUE;
-    }
-    return FALSE;
-}
-#endif
-int WasInterrupted(void) {
-#ifdef _DEBUG            
-    if ( e_bInterrupted ) {
-        int stop=1;  /*  for debug only <BRKPT> */
-    }
-#endif
-    return e_bInterrupted;
-}
-
-#endif
-
-#define EXIT_ON_ERR
-#define REPEAT_ALL  0
-/********************************************************************/
-int main( int argc, char *argv[ ] )
-{
-
-    STRUCT_DATA struct_data;
-    STRUCT_DATA *sd = &struct_data;
-    FILE *inp_file = NULL, *output_file = NULL, *log_file = NULL, *prb_file = NULL;
-
-    long num_inp, num_err, num_output;
-    char        szSdfDataValue[MAX_SDF_VALUE+1];
-    const char *p1, *p2;
-
-    unsigned long  ulDisplTime = 0;    /*  infinite, milliseconds */
-    unsigned long  ulTotalProcessingTime = 0;
-    INPUT_PARMS inp_parms;
-    INPUT_PARMS *ip = &inp_parms;
-    char        szInchiCmdLine[512];
-
-    inchi_Input  inchi_inp, *pInp = &inchi_inp;
-    inchi_Output inchi_out, *pOut = &inchi_out;
-
-
-    int             bReleaseVersion = bRELEASE_VERSION;
-#define nStrLen 256
-    char  pStrInchiId[nStrLen], pStrLogId[nStrLen];
-    int   nRet = 0, nRet1, i, k, tot_len;
-    int   inp_index, out_index;
-    long  lSdfId;
-    int   nStructNo;
-
-#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 )
-    int  num_repeat = REPEAT_ALL;
-#endif
-
-
-#if( TRACE_MEMORY_LEAKS == 1 )
-    _CrtSetDbgFlag(_CRTDBG_CHECK_ALWAYS_DF | _CRTDBG_LEAK_CHECK_DF | _CRTDBG_ALLOC_MEM_DF);
-/* for execution outside of the VC++ debugger uncomment one of the following two */
-/*#define MY_REPORT_FILE  _CRTDBG_FILE_STDERR */
-/*#define MY_REPORT_FILE  _CRTDBG_FILE_STDOUT */
-#ifdef MY_REPORT_FILE 
-   _CrtSetReportMode( _CRT_WARN, _CRTDBG_MODE_FILE );
-   _CrtSetReportFile( _CRT_WARN, MY_REPORT_FILE );
-   _CrtSetReportMode( _CRT_ERROR, _CRTDBG_MODE_FILE );
-   _CrtSetReportFile( _CRT_ERROR, MY_REPORT_FILE );
-   _CrtSetReportMode( _CRT_ASSERT, _CRTDBG_MODE_FILE );
-   _CrtSetReportFile( _CRT_ASSERT, MY_REPORT_FILE );
-#else
-    _CrtSetReportMode(_CRT_WARN | _CRT_ERROR, _CRTDBG_MODE_DEBUG);
-#endif
-   /* turn on floating point exceptions */
-    {
-        /* Get the default control word. */
-        int cw = _controlfp( 0,0 );
-
-        /* Set the exception masks OFF, turn exceptions on. */
-        /*cw &=~(EM_OVERFLOW|EM_UNDERFLOW|EM_INEXACT|EM_ZERODIVIDE|EM_DENORMAL);*/
-        cw &=~(EM_OVERFLOW|EM_UNDERFLOW|EM_ZERODIVIDE|EM_DENORMAL);
-
-        /* Set the control word. */
-        _controlfp( cw, MCW_EM );
- 
-    }
-#endif
-
-/*****************************************************************
- *
- *  Set Ctrl+C trap; works under Win32 + MS VC++
- *
- *****************************************************************/
-#if( defined( _WIN32 ) && defined( _CONSOLE ) && defined(_MSC_VER) && _MSC_VER >= 800 && defined(ADD_WIN_CTLC))
-    if ( SetConsoleCtrlHandler( MyHandlerRoutine, 1 ) ) {
-        /*ConsoleQuit = WasInterrupted*/;
-    }
-#endif
-
-
-
-#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 )
-repeat:
-    inp_file = output_file = log_file = prb_file = NULL;
-#endif
-
-    num_inp    = 0;
-    num_err    = 0;
-    num_output = 0;
-
-    if ( argc < 2 || argc==2 && ( argv[1][0]==INCHI_OPTION_PREFX ) &&
-        (!strcmp(argv[1]+1, "?") || !stricmp(argv[1]+1, "help") ) ) {
-        e_HelpCommandLineParms(stdout);
-        return 0;
-    }
-    /*  original input structure */
-    memset( pInp, 0, sizeof(*pInp) );
-    memset( pOut, 0, sizeof(*pOut) );
-
-    memset( szSdfDataValue    , 0, sizeof( szSdfDataValue    ) );
-    
-    /* explicitly cast to (const char **) to avoid a warning about "incompatible pointer type":*/
-    if ( 0 > e_ReadCommandLineParms( argc, (const char **)argv, ip, szSdfDataValue, &ulDisplTime, bReleaseVersion, NULL ) ) {
-        goto exit_function;
-    }
-    if ( !e_OpenFiles( &inp_file, &output_file, &log_file, &prb_file, ip ) ) {
-        goto exit_function;
-    }
-    if ( ip->bNoStructLabels ) {
-        ip->pSdfLabel = NULL;
-        ip->pSdfValue = NULL;
-    } else
-    if ( ip->nInputType == INPUT_INCHI_PLAIN  ||
-         ip->nInputType == INPUT_INCHI_XML    ||
-         ip->nInputType == INPUT_CMLFILE      ) {
-        /* the input may contain both the header and the label of the structure */
-        if ( !ip->pSdfLabel ) 
-            ip->pSdfLabel  = ip->szSdfDataHeader;
-        if ( !ip->pSdfValue )
-            ip->pSdfValue  = szSdfDataValue;
-    }
-    e_PrintInputParms( log_file, ip );
-    pStrInchiId[0] = '\0';
-    /******************************************************************/
-    /*  Main cycle */
-    /*  read input structures and create their InChI */
-    ulTotalProcessingTime = 0;
-
-    out_index = 0;
-    while ( !e_bInterrupted ) {
-        int bHasTimeout = 0;
-        if ( ip->last_struct_number && num_inp >= ip->last_struct_number ) {
-            nRet = _IS_EOF; /*  simulate end of file */
-            goto exit_function;
-        }
-        /* create command line */
-        szInchiCmdLine[0] = '\0';
-        for ( i = 1; i < argc; i ++ ) {
-            if ( argv[i] && INCHI_OPTION_PREFX == argv[i][0] && argv[i][1] ) {
-                /* omit certrain options */
-                if ( !memicmp( argv[i]+1, "start:", 6) ||
-                     !memicmp( argv[i]+1, "end:",   4) ||
-                     !stricmp( argv[i]+1, "Tabbed" )
-                     ) {
-                    continue;
-                }
-                if ( !memicmp( argv[i]+1, "w", 1 ) && isdigit( UCINT argv[i][2] ) ) {
-                    bHasTimeout = 1;
-                }
-                /* add option to szInchiCmdLine */
-                if ( strlen(szInchiCmdLine)+strlen(argv[i]) + 4 < sizeof(szInchiCmdLine) ) {
-                    if ( szInchiCmdLine[0] )
-                        strcat( szInchiCmdLine, " " );
-                    k = ( !(k=strcspn( argv[i], " \t" )) || argv[i][k] ); /* k means enclose in "" */
-                    if ( k )
-                        strcat( szInchiCmdLine, "\"" );
-                    strcat( szInchiCmdLine, argv[i] );
-                    if ( k )
-                        strcat( szInchiCmdLine, "\"" );
-                } else {
-                    e_my_fprintf( stderr, "Too many options. Option \"%s\" ignored\n", argv[i] );
-                }
-            }
-        }
-        if ( !bHasTimeout ) {
-            /* add default timeout option -W60: 60 seconds */
-            char p1[] = "  W60";
-            p1[1] = INCHI_OPTION_PREFX;
-            if ( strlen(szInchiCmdLine) + strlen( p1 ) < sizeof(szInchiCmdLine) ) {
-                strcat( szInchiCmdLine, p1 );
-            } else {
-                e_my_fprintf( stderr, "Too many options. Option \"%s\" ignored\n", p1 );
-            }
-        }
-
-        inp_index = out_index;
-        /*  read one structure from input */
-        e_FreeInchi_Input( pInp );
-        //e_my_fprintf( stderr, "\rStructure: %d.................\r", num_inp+1 );
-        nRet = e_ReadStructure( sd, ip, inp_file, log_file, output_file, prb_file, pInp, num_inp+1,
-                      /* for CML:*/ inp_index, &out_index );
-        /* simulate INChI structure header */
-        lSdfId    = ( ip->bGetSdfileId )? ip->lSdfId : 0; /* if requested then CAS r.n. otherwise struct. number*/
-        nStructNo = ( ip->lMolfileNumber > 0 )? ip->lMolfileNumber : num_inp+1;
-        e_MakeOutputHeader( ip->pSdfLabel, ip->pSdfValue, lSdfId, nStructNo, pStrInchiId, pStrLogId );
-        if ( sd->pStrErrStruct && sd->pStrErrStruct[0] ) {
-            p1 = "; ";
-            p2 = sd->pStrErrStruct;
-        } else {
-            p1 = p2 = "";
-        }
-        /* e_ReadStructure() outputs the error/warning messages, so we do not need to re-output them here */
-        switch ( nRet ) {
-        case _IS_FATAL:
-            num_inp ++;
-            num_err ++;
-            goto exit_function;
-        case _IS_EOF:
-            //e_my_fprintf( stderr, "\rStructure %d could not be read: Detected end of file. \r", num_inp+1 );
-            goto exit_function;
-        case _IS_ERROR:
-            num_inp ++;
-            num_err ++;
-            continue;
-        case _IS_SKIP:
-            num_inp ++;
-            continue;
-        }
-        if ( nRet != _IS_WARNING ) {
-            //e_my_fprintf( stderr, "\r%s   \r", pStrLogId );
-        }
-        /* chiral flag */
-        /* *****************************************************************************
-         * Chiral flags are set in: 
-         * - RunICHI.c #1610 -- ReadTheStructure()     -- cInChI, wInChI
-         * - e_IchiMain.c #273 -- main()               -- C example of calling InChI dll (here)
-         * - inchi_dll.c  #1662 -- ExtractOneStructure -- InChI dll code 
-         *******************************************************************************/   
-
-        p1 = NULL;
-        if ( (ip->nMode & REQ_MODE_CHIR_FLG_STEREO) && (ip->nMode & REQ_MODE_STEREO) &&
-             ( ip->bChiralFlag & (FLAG_SET_INP_AT_CHIRAL | FLAG_SET_INP_AT_NONCHIRAL) ) ) {
-                ; /* cmd line has priority over the chiral flag in Molfile */
-        } else
-        if ( sd->bChiralFlag & FLAG_INP_AT_CHIRAL ) {
-            p1 =  e_GetChiralFlagString( 1 );  /* input file has chiral flag */
-        } else
-        if ( (ip->nMode & REQ_MODE_CHIR_FLG_STEREO) && (ip->nMode & REQ_MODE_STEREO) ||
-             (sd->bChiralFlag & FLAG_INP_AT_NONCHIRAL) ) { /* fix 04/05/2005 D.T.*/
-            /* chiral flag requested (/SUCF) or input has non-chiral flag */
-            p1 =  e_GetChiralFlagString( 0 );
-        }
-        if ( p1 ) {
-            if ( strlen(szInchiCmdLine) + strlen( p1 ) < sizeof(szInchiCmdLine) ) {
-                strcat( szInchiCmdLine, p1 );
-            } else {
-                e_my_fprintf( stderr, "Too many options. Option \"%s\" ignored\n", p1 );
-            }
-        }
-
-        /* create INChI for each connected component of the structure and optionally display them */
-        /* output INChI for the whole structure */
-        FreeINCHI ( pOut );
-        pInp->szOptions = szInchiCmdLine;
-#ifdef CREATE_0D_PARITIES
-        if ( !pInp->stereo0D && !pInp->num_stereo0D ) {
-            int bPointedEdgeStereo = (0 != (TG_FLAG_POINTED_EDGE_STEREO & ip->bTautFlags));
-            set_0D_stereo_parities( pInp, bPointedEdgeStereo );
-            Clear3D2Dstereo(pInp);
-        }
-#endif
-#ifdef NEIGH_ONLY_ONCE
-        e_RemoveRedundantNeighbors( pInp );
-#endif
-        /********************************************
-         *
-         *  CREATE  INCHI
-         *
-         ********************************************/
-        nRet1 = GetINCHI( pInp, pOut );
-
-        ulTotalProcessingTime += sd->ulStructTime;
-        nRet = nRet1;
-#ifdef MAKE_INCHI_FROM_AUXINFO
-        /**************************************************
-         *
-         *  CREATE one more INCHI FROM AuxInfo and compare
-         *
-         *  it to to the first INCHI
-         *
-         *  Note: This should double the elapsed CPU time
-         *
-         **************************************************/
-        if ( nRet1 == inchi_Ret_OKAY || nRet1 == inchi_Ret_WARNING ) {
-            char *szInchiAuxInfo = pOut->szAuxInfo, *p1 /* shadowing previous definition */;
-            int   bDoNotAddH = ip->bDoNotAddH;
-            int   nRet2;
-            inchi_Input  inchi_inp2, *pInp2 = &inchi_inp2;
-            inchi_Output inchi_out2, *pOut2 = &inchi_out2;
-            InchiInpData idat;
-            /* setup input for Get_inchi_Input_FromAuxInfo */
-            idat.pInp = pInp2;
-            pInp2->szOptions = NULL; /* not needed */
-            
-            /* Make InChI input out of AuxInfo */
-            nRet2 = Get_inchi_Input_FromAuxInfo( szInchiAuxInfo, bDoNotAddH, &idat );
-            
-            if ( inchi_Ret_OKAY == nRet2 || inchi_Ret_WARNING == nRet2 ) {
-                /* set chiral flag */
-                p1 = NULL;
-                if ( (ip->nMode & REQ_MODE_CHIR_FLG_STEREO) && (ip->nMode & REQ_MODE_STEREO) &&
-                     ( ip->bChiralFlag & (FLAG_SET_INP_AT_CHIRAL | FLAG_SET_INP_AT_NONCHIRAL) ) ) {
-                        ; /* cmd line has priority over the chiral flag in Molfile */
-                } else
-                if ( idat.bChiral & FLAG_INP_AT_CHIRAL ) { /* fix 04/05/2005 D.T.*/
-                    p1 = e_GetChiralFlagString( 1 );  /* input file has chiral flag */
-                } else
-                if ( (ip->nMode & REQ_MODE_CHIR_FLG_STEREO) && (ip->nMode & REQ_MODE_STEREO) ||
-                     (idat.bChiral & FLAG_INP_AT_NONCHIRAL) ) { /* fix 04/05/2005 D.T.*/
-                    /* chiral flag requested (/SUCF) or input has non-chiral flag */
-                    p1 = e_GetChiralFlagString( 0 );
-                }
-                if ( p1 ) {
-                    if ( strlen(szInchiCmdLine) + strlen( p1 ) < sizeof(szInchiCmdLine) ) {
-                        strcat( szInchiCmdLine, p1 );
-                    } else {
-                        e_my_fprintf( stderr, "Too many options. Option \"%s\" ignored\n", p1 );
-                    }
-                }
-
-                /* Make InChI out of InChI input out of AuxInfo */
-                pInp2->szOptions = pInp->szOptions;
-                memset( pOut2, 0, sizeof(*pOut2) );
-                nRet2 = GetINCHI( pInp2, pOut2 );
-                /* Compare the two InChI */
-                if ( nRet2 == inchi_Ret_OKAY || nRet2 == inchi_Ret_WARNING ) {
-                    if ( !pOut2->szInChI || strcmp( pOut->szInChI, pOut2->szInChI ) ) {
-                        e_my_fprintf( stderr, "InChI from AuxInfo Is Different!\n" );
-                    }
-                } else {
-                    e_my_fprintf( stderr, "InChI from AuxInfo could not be produced: \"%s\"\n", pOut2->szMessage );
-                }
-                FreeINCHI( pOut2 );
-            }
-            Free_inchi_Input( pInp2 );
-        }
-#endif
-
-        /*****************************/
-        /*     output err/warn       */
-        /*****************************/
-        if ( pOut->szMessage && pOut->szMessage[0] ) {
-            p1 = "; ";
-            p2 = pOut->szMessage;
-        } else {
-            p1 = p2 = "";
-        }
-        switch ( nRet ) {
-        case inchi_Ret_UNKNOWN:
-        case inchi_Ret_FATAL: /* fatal processing error -- typically, memory allocation error */
-            num_inp ++;
-            num_err ++;
-#if( defined(EXIT_ON_ERR) && defined(REPEAT_ALL) && REPEAT_ALL > 0 )
-            num_repeat = 0;
-#endif
-            e_my_fprintf( log_file, "Fatal Error (No INChI%s%s) %s\n", p1, p2, pStrLogId );
-            goto exit_function;
-        case inchi_Ret_EOF: /* typically, no input structure provided or help requested */
-            /* output previous structure number and message */
-            e_my_fprintf( log_file, "End of file detected after structure %d\n", num_inp );
-            goto exit_function;
-        case inchi_Ret_ERROR:
-            num_inp ++;
-            num_err ++;
-            e_my_fprintf( log_file, "Error (No INChI%s%s) %s\n", p1, p2, pStrLogId );
-#if( defined(EXIT_ON_ERR) && defined(REPEAT_ALL) && REPEAT_ALL > 0 )
-            num_repeat = 0;
-            goto exit_function;
-#endif
-            continue;
-        case inchi_Ret_SKIP:
-            num_inp ++;
-            e_my_fprintf( log_file, "Skipped %s\n", pStrLogId );
-            goto exit_function;
-        case inchi_Ret_OKAY:
-            break;
-        case inchi_Ret_WARNING:
-            e_my_fprintf( log_file, "Warning (%s) %s\n", p2, pStrLogId );
-            break; /* ok */
-        }
-
-        num_inp ++;
-        tot_len = 0;
-        if ( pOut->szInChI && pOut->szInChI[0] ) {
-            if (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY ) {
-                /*****************************/
-                /*       output SDfile       */
-                /*****************************/
-                char *start;
-                unsigned len;
-                int bAddLabel = 0;
-                /*******************************************************************************/
-                /* output a SDfile. pOut->szInChI contains Molfile ending with "$$$$\n" line.  */
-                /* Replace the 1st line with the structure number                              */
-                /* Replace the last line with the SDfile header, label, and new "$$$$\n" line  */
-                /*******************************************************************************/
-                /* 1. remove the 1st line (later replace it with the actual structure number) */
-                if ( start = strchr( pOut->szInChI, '\n' ) ) {
-                    e_inchi_print( output_file, "Structure #%ld", nStructNo );
-                } else {
-                    start = pOut->szInChI;
-                }
-                /* 2. SDfile header and data: write zero to the 1st byte of
-                 *    the last line "$$$$\n" to remove this line with purpose to relpace it */
-                if ( ip->pSdfLabel && ip->pSdfLabel[0] && ip->pSdfValue && ip->pSdfValue[0] &&
-                     (len = strlen(start)) && len > 5 && '$' == start[len-5] && '\n' == start[len-6] ) {
-                    start[len-5] = '\0';
-                    bAddLabel = 1;
-                }
-                /* 3. Output the whole Molfile */
-                e_inchi_print( output_file, "%s", start );
-                if ( bAddLabel ) {
-                    e_inchi_print( output_file, ">  <%s>\n%s\n\n$$$$\n", ip->pSdfLabel, ip->pSdfValue );
-                }
-
-            } else {
-                /*****************************/
-                /*       output InChI        */
-                /*****************************/
-                int bTabbed  = 0 != ( ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT );
-                int bAuxInfo = !( ip->bINChIOutputOptions & INCHI_OUT_ONLY_AUX_INFO ) &&
-                               pOut->szAuxInfo && pOut->szAuxInfo[0];
-                const char *pLF  = "\n";
-                const char *pTAB = bTabbed? "\t" : pLF;
-                if ( !ip->bNoStructLabels ) {
-                    /* or print a previously created label string */
-                    e_inchi_print( output_file, "%s%s", pStrInchiId, pTAB );
-                }
-                /* output INChI Identifier */
-                e_inchi_print( output_file, "%s%s", pOut->szInChI, bAuxInfo? pTAB : pLF );
-                /* output INChI Aux Info */
-                if ( bAuxInfo ) {
-                    e_inchi_print( output_file, "%s\n",pOut->szAuxInfo );
-                }
-            }
-        }
-    }
-
-exit_function:
-    e_my_fprintf( log_file, "\nProcessed %d structure%s, %d error%s.\n",
-                 num_inp, (num_inp==1)?"":"s", num_err, (num_err==1)?"":"s" );
-
-
-    e_FreeInchi_Input( pInp );
-    FreeINCHI ( pOut );
-
-#if( ADD_CMLPP == 1 )
-        /* BILLY 8/6/04 */
-        /* free CML memory */
-        FreeCml ();
-        FreeCmlDoc( 1 );
-#endif
-
-    if ( inp_file && inp_file != stdin) {
-        fclose ( inp_file );
-    }
-    if ( prb_file ) {
-        fclose ( prb_file );
-    }
-    if ( output_file && output_file != stdout ) {
-        fclose( output_file );
-    }
-
-    if ( log_file && log_file != stderr ) {
-        fclose( log_file );
-    }
-    for ( i = 0; i < MAX_NUM_PATHS; i ++ ) {
-        if ( ip->path[i] ) {
-            e_inchi_free( (void*) ip->path[i] ); /*  cast deliberately discards 'const' qualifier */
-            ip->path[i] = NULL;
-        }
-    }
-
-#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 )
-    if ( --num_repeat > 0 ) {
-        goto repeat;
-    }
-#endif
-
-
-    return 0;
-}
-
-
-#endif
-
-/**********************************************************/
-int e_MakeOutputHeader( char *pSdfLabel, char *pSdfValue, long lSdfId, int num_inp, char *pStr1, char *pStr2  )
-{
-    int tot_len1 = 0, tot_len2 = 0;
-    pStr1[0] = '\0';
-    if ( !(pSdfLabel && pSdfLabel[0]) && !(pSdfValue && pSdfValue[0]) ) {
-        tot_len1 = sprintf( pStr1, "Structure: %d", num_inp );
-        tot_len2 = sprintf( pStr2, "structure #%d", num_inp );
-    } else {
-        tot_len1 = sprintf( pStr1, "Structure: %d.%s%s%s%s",
-            num_inp,
-            SDF_LBL_VAL(pSdfLabel, pSdfValue) );
-
-        tot_len2 = sprintf( pStr2, "structure #%d.%s%s%s%s",
-            num_inp,
-            SDF_LBL_VAL(pSdfLabel, pSdfValue) );
-        if ( lSdfId ) {
-            tot_len1 += sprintf( pStr1 + tot_len1, ":%ld", lSdfId );
-            tot_len2 += sprintf( pStr2 + tot_len2, ":%ld", lSdfId );
-        }
-    }
-    return tot_len1;
-}
-/************************************************************/
-char *e_GetChiralFlagString( int bChiralFlagOn )
-{
-    static char szChiralFlag[64];
-    szChiralFlag[0] = ' ';
-    szChiralFlag[1] = INCHI_OPTION_PREFX;
-    sprintf( szChiralFlag+2, "ChiralFlag%s", bChiralFlagOn? "On":"Off" );
-    return szChiralFlag;
-}
-
-