rino 0.1.0 → 0.2.0

data/ext/src/ichicano.c

@@ -2,8 +2,8 @@
  * International Union of Pure and Applied Chemistry (IUPAC)
  * International Chemical Identifier (InChI)
  * Version 1
- * Software version 1.00
- * April 13, 2005
+ * Software version 1.01
+ * July 21, 2006
  * Developed at NIST
  */
 
@@ -93,7 +93,7 @@ static void FillMaxMinClock(void); /* keep compiler happy */
 static void FillMaxMinClock(void)
 {
     if ( !MaxPositiveClock ) {
-        clock_t valPos, val1 = 1;
+        clock_t valPos=0, val1 = 1;
         while ( 0 < ((val1 <<= 1), (val1 |= 1)) ) {
             valPos = val1;
         }
@@ -704,23 +704,18 @@ int FillTautLinearCT2( int num_atoms, int num_at_tg, int bIsoTaut,
         int        num_t_groups      = t_group_info->num_t_groups;
         AT_NUMB   *tGroupNumber      = t_group_info->tGroupNumber;
         AT_NUMB   *tSymmRank         = tGroupNumber + TGSO_SYMM_RANK*num_t_groups;  /*  equivalence */
-        AT_NUMB   *tPrevGroupNumber  = tGroupNumber + TGSO_PREV_ORDER*num_t_groups; /*  prev. order or symm rank sort order */
-        AT_NUMB   *tSortRank         = tGroupNumber + TGSO_SORT_RANK*num_t_groups;  /*  ranks */
         AT_NUMB   *tiSymmRank        = tGroupNumber + TGSO_SYMM_IRANK*num_t_groups;
         AT_NUMB   *tiGroupNumber     = tGroupNumber + TGSO_SYMM_IORDER*num_t_groups;
-        AT_NUMB   *tiSortRank        = tGroupNumber + TGSO_SORT_IRANK*num_t_groups;
         AT_RANK    nOffset           = (AT_RANK)num_atoms;
         /*  Fill Canonical ranks and Symmetry Ranks */
-        memcpy( tPrevGroupNumber, tGroupNumber, num_t_groups*sizeof(tPrevGroupNumber[0]));
+        /* memcpy( tPrevGroupNumber, tGroupNumber, num_t_groups*sizeof(tPrevGroupNumber[0])); */
         for ( i = num_atoms, j = 0; i < num_at_tg; i ++, j ++ ) {
-            tPrevGroupNumber[j] =
+            /* tPrevGroupNumber[j] = */
             tGroupNumber[j] = nAtomNumber[i] - nOffset;
             tSymmRank[j]    = nSymmRank[i]   - nOffset;
-            tSortRank[j]    = nRank[i]       - nOffset;
-            if ( bIsoTaut /*nMaxLenLinearCTIsotopicTautomer*/ ) {
+            if ( bIsoTaut ) {
                 tiGroupNumber[j] = nAtomNumberIso[i] - nOffset;
                 tiSymmRank[j]    = nSymmRankIso[i]   - nOffset;
-                tiSortRank[j]    = nRankIso[i]       - nOffset;
             }
         }
         /*  Sort enpoints within each tautomeric group according to the canonical ranks */
@@ -766,8 +761,8 @@ int FillTautLinearCT2( int num_atoms, int num_at_tg, int bIsoTaut,
             /*  t_group header: number of endpoints */
             LinearCTTautomer[len++] = t_group->nNumEndpoints;
             /*  t_group header: */
-            /*  (a) number of mobile groups in the t_group and */
-            /*  (b) number of mobile negative charges in the t_group, currently = 0 always */
+            /*  (a) number of mobile groups in the t_group (number of H + number of (-) ) and */
+            /*  (b) number of mobile negative charges (-) in the t_group */
             for ( j = 0; j < T_NUM_NO_ISOTOPIC; j ++ ) {
                 LinearCTTautomer[len++] = t_group->num[j];
             }

data/ext/src/ichicano.h

@@ -2,8 +2,8 @@
  * International Union of Pure and Applied Chemistry (IUPAC)
  * International Chemical Identifier (InChI)
  * Version 1
- * Software version 1.00
- * April 13, 2005
+ * Software version 1.01
+ * July 21, 2006
  * Developed at NIST
  */
 

data/ext/src/ichicans.c

@@ -2,8 +2,8 @@
  * International Union of Pure and Applied Chemistry (IUPAC)
  * International Chemical Identifier (InChI)
  * Version 1
- * Software version 1.00
- * April 13, 2005
+ * Software version 1.01
+ * July 21, 2006
  * Developed at NIST
  */
 
@@ -1577,11 +1577,16 @@ int GetPermutationParity( sp_ATOM *at, AT_RANK nAvoidNeighbor, AT_RANK *nCanonRa
                 nNeighRank[k++] = nCanonRank[(int)at->neighbor[j]];
             }
         }
-        parity = insertions_sort( nNeighRank, k, sizeof(nNeighRank[0]), comp_AT_RANK);
-        if ( nNeighRank[0] ) {
-            parity = 2 - parity % 2;
+        if ( k ) {
+            parity = insertions_sort( nNeighRank, k, sizeof(nNeighRank[0]), comp_AT_RANK);
+            if ( nNeighRank[0] ) {
+                parity = 2 - parity % 2;
+            } else {
+                parity = 0; /*  not all ranks are known */
+            }
         } else {
-            parity = 0; /*  not all ranks are known */
+            /* special case: HX= with implicit H */
+            parity = 2;
         }
     }
     return parity;

data/ext/src/ichicant.h

@@ -2,8 +2,8 @@
  * International Union of Pure and Applied Chemistry (IUPAC)
  * International Chemical Identifier (InChI)
  * Version 1
- * Software version 1.00
- * April 13, 2005
+ * Software version 1.01
+ * July 21, 2006
  * Developed at NIST
  */
 

data/ext/src/ichicomn.h

@@ -2,8 +2,8 @@
  * International Union of Pure and Applied Chemistry (IUPAC)
  * International Chemical Identifier (InChI)
  * Version 1
- * Software version 1.00
- * April 13, 2005
+ * Software version 1.01
+ * July 21, 2006
  * Developed at NIST
  */
 

data/ext/src/ichicomp.h

@@ -2,15 +2,21 @@
  * International Union of Pure and Applied Chemistry (IUPAC)
  * International Chemical Identifier (InChI)
  * Version 1
- * Software version 1.00
- * April 13, 2005
+ * Software version 1.01
+ * July 21, 2006
  * Developed at NIST
  */
 
 #ifndef __INCHI_COMPAT_H__
 #define __INCHI_COMPAT_H__
 
-/* compatibility */
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+extern "C" {
+#endif
+#endif
+
+    /* 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 */
@@ -32,7 +38,10 @@
 #include <stdio.h>
  /* this #include provides size_t definition */
  /* implementation is located in util.c */
-#if ( !defined(_MSC_VER) || defined(__STDC__) && __STDC__ == 1 )
+/*#if ( !defined(_MSC_VER) || defined(__STDC__) && __STDC__ == 1 )*/
+
+#if ( defined(ADD_NON_ANSI_FUNCTIONS) || 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 );
@@ -46,5 +55,11 @@ char *_strdup( const char *string );
 #define inchi_max(a,b)  (((a)>(b))?(a):(b))
 #define inchi_min(a,b)  (((a)<(b))?(a):(b))
 
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+}
+#endif
+#endif
+
 
 #endif /* __INCHI_COMPAT_H__ */

data/ext/src/ichidrp.h

@@ -2,8 +2,8 @@
  * International Union of Pure and Applied Chemistry (IUPAC)
  * International Chemical Identifier (InChI)
  * Version 1
- * Software version 1.00
- * April 13, 2005
+ * Software version 1.01
+ * July 21, 2006
  * Developed at NIST
  */
 
@@ -62,7 +62,7 @@ typedef struct tagDrawParms {
 #define MAX_NUM_PATHS 4
 #endif
 
-typedef enum tagInputType { INPUT_NONE=0, INPUT_MOLFILE=1, INPUT_SDFILE=2, INPUT_INCHI_XML=3, INPUT_INCHI_PLAIN=4, INPUT_CMLFILE=5, INPUT_MAX } INPUT_TYPE;
+typedef enum tagInputType { INPUT_NONE=0, INPUT_MOLFILE=1, INPUT_SDFILE=2, INPUT_INCHI_XML=3, INPUT_INCHI_PLAIN=4, INPUT_CMLFILE=5, INPUT_INCHI=6, INPUT_MAX } INPUT_TYPE;
 typedef struct tagInputParms {
     char            szSdfDataHeader[MAX_SDF_HEADER+1];
     char           *pSdfLabel;
@@ -85,8 +85,8 @@ typedef struct tagInputParms {
 */
     const char     *path[MAX_NUM_PATHS];
     int             num_paths;
-    int             first_struct_number;
-    int             last_struct_number;
+    long            first_struct_number;
+    long            last_struct_number;
     INPUT_TYPE      nInputType;
     INCHI_MODE      nMode;
     int             bAbcNumbers;
@@ -101,6 +101,7 @@ typedef struct tagInputParms {
 
     long            ulDisplTime; /* not used: max structure or question display time */
     int             bDisplay;
+    int             bDisplayIfRestoreWarnings; /* InChI->Struct debug */
     int             bMergeAllInputStructures;
     int             bSaveWarningStructsAsProblem;
     int             bSaveAllGoodStructsAsProblem;
@@ -114,6 +115,9 @@ typedef struct tagInputParms {
     int             bAllowEmptyStructure;
     INCHI_MODE      bTautFlags;
     INCHI_MODE      bTautFlagsDone;
+#if( READ_INCHI_STRING == 1 )
+    int             bReadInChIOptions;
+#endif
 } INPUT_PARMS;
 
 #endif /* __INCHIDRP_H__ */

data/ext/src/ichierr.h

@@ -2,8 +2,8 @@
  * International Union of Pure and Applied Chemistry (IUPAC)
  * International Chemical Identifier (InChI)
  * Version 1
- * Software version 1.00
- * April 13, 2005
+ * Software version 1.01
+ * July 21, 2006
  * Developed at NIST
  */
 
@@ -37,7 +37,8 @@
 #define CT_CALC_STEREO_ERR   (CT_ERR_FIRST-15)  /*(-30015) */
 #define CT_CANON_ERR         (CT_ERR_FIRST-16)  /*(-30016) */
 #define CT_STEREO_CANON_ERR  (CT_ERR_FIRST-17)  /*(-30017) */
-#define CT_UNKNOWN_ERR       (CT_ERR_FIRST-18)  /*(-30018) */
+#define CT_WRONG_FORMULA     (CT_ERR_FIRST-18)  /*(-30017) */
+#define CT_UNKNOWN_ERR       (CT_ERR_FIRST-19)  /*(-30019) */
 
 #define CT_ERR_MIN CT_UNKNOWN_ERR
 #define CT_ERR_MAX CT_ERR_FIRST
@@ -60,6 +61,7 @@
 #define BNS_CAP_FLOW_ERR   (BNS_ERR + 10) /*(-9989)*/
 #define BNS_RADICAL_ERR    (BNS_ERR + 11) /*(-9988)*/
 #define BNS_REINIT_ERR     (BNS_ERR + 12) /*(-9987)*/
+#define BNS_ALTBOND_ERR    (BNS_ERR + 13) /*(-9986)*/
 
 #define BNS_MAX_ERR_VALUE  (BNS_ERR + 19) /*(-9980)*/
 

data/ext/src/ichiisot.c

@@ -2,8 +2,8 @@
  * International Union of Pure and Applied Chemistry (IUPAC)
  * International Chemical Identifier (InChI)
  * Version 1
- * Software version 1.00
- * April 13, 2005
+ * Software version 1.01
+ * July 21, 2006
  * Developed at NIST
  */
 

data/ext/src/ichimain.c

@@ -0,0 +1,461 @@
+/*
+ * International Union of Pure and Applied Chemistry (IUPAC)
+ * International Chemical Identifier (InChI)
+ * Version 1
+ * Software version 1.01
+ * July 21, 2006
+ * Developed at NIST
+ */
+
+#include "mode.h"
+
+#ifndef INCHI_ANSI_ONLY
+#ifndef INCHI_LIB
+#include <windows.h>
+#endif
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+
+#ifndef INCHI_ANSI_ONLY
+#include <conio.h>
+#endif
+
+#include <string.h>
+#include <ctype.h>
+#include <stdarg.h>
+#include <errno.h>
+#include <limits.h>
+#include <float.h>
+
+#include "ichitime.h"
+#include "inpdef.h"
+#include "ichi.h"
+#include "strutil.h"
+#include "util.h"
+#include "ichidrp.h"
+#include "ichierr.h"
+#include "ichimain.h"
+
+#include "ichicomp.h"
+
+#if( ADD_CMLPP == 1 )
+#include "readcml.hpp"
+#endif
+
+/*  console-specific */
+#ifndef INCHI_ANSI_ONLY
+/********************************************************************/
+int user_quit( const char *msg, unsigned long ulMaxTime )
+{
+#ifdef INCHI_LIB
+    return 0;
+#endif
+#if( defined(_WIN32) && !defined(INCHI_LIB) )
+    int quit, enter, ret;
+    printf(msg);
+    if ( ulMaxTime ) {
+        inchiTime  ulEndTime;
+        InchiTimeGet( &ulEndTime );
+        InchiTimeAddMsec( &ulEndTime, ulMaxTime );
+        while ( !_kbhit() ) {
+            if ( bInchiTimeIsOver( &ulEndTime ) ) {
+                printf("\n");
+                return 0;
+            }
+            MySleep( 100 );
+        }
+    }
+    while( 1 ) {
+        quit  = ( 'q' == (ret = _getch()) || 'Q'==ret || /*Esc*/ 27==ret );
+        enter = ( '\r' == ret );
+        if ( ret == 0xE0 )
+            ret = _getch();
+        else {
+            _putch(ret); /* echo */
+        }
+        if ( quit || enter )
+            break;
+        printf( "\r" );
+        printf( msg );
+    }
+
+    _putch('\n');
+    return quit;
+#else
+    return 0;
+#endif
+}
+/*****************************************************************/
+void eat_keyboard_input( void )
+{
+#ifndef INCHI_LIB
+    while ( _kbhit() ) {
+        if ( 0xE0 == _getch() )
+            _getch();
+    }
+#endif
+}
+#endif /* ifndef INCHI_ANSI_ONLY */
+
+#ifdef INCHI_ANSI_ONLY
+/*****************************************************************/
+int user_quit( const char *msg, unsigned long ulMaxTime )
+{
+    return 0;
+}
+/*****************************************************************/
+void eat_keyboard_input( void )
+{
+}
+#endif
+
+
+/*****************************************************************/
+#ifndef INCHI_LIB
+
+int bInterrupted = 0;
+#if( defined( _WIN32 ) && defined( _CONSOLE ) )
+
+#ifndef INCHI_ANSI_ONLY
+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 ) {
+        bInterrupted = 1;
+        return TRUE;
+    }
+    return FALSE;
+}
+int WasInterrupted(void) {
+#ifdef _DEBUG            
+    if ( bInterrupted ) {
+        int stop=1;  /*  for debug only <BRKPT> */
+    }
+#endif
+    return bInterrupted;
+}
+#endif
+
+#endif
+
+#define REPEAT_ALL  0
+/*#define TEST_FPTRS*/ /* uncomment for INCHI_LIB testing only */
+/********************************************************************/
+int run( int argc, char **argv);
+
+int run( 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;
+    char szTitle[MAX_SDF_HEADER+MAX_SDF_VALUE+256];
+    /* long rcPict[4] = {0,0,0,0}; */
+
+    int   i;
+    long  num_err, num_output;
+    long num_inp;
+    char      szSdfDataValue[MAX_SDF_VALUE+1];
+
+    PINChI2     *pINChI[INCHI_NUM];
+    PINChI_Aux2 *pINChI_Aux[INCHI_NUM];
+
+    unsigned long  ulDisplTime = 0;    /*  infinite, milliseconds */
+    unsigned long  ulTotalProcessingTime = 0;
+    /*long     fPtrStart=0L, fPtrEnd=0L;*/
+    INPUT_PARMS inp_parms;
+    INPUT_PARMS *ip = &inp_parms;
+
+    ORIG_ATOM_DATA OrigAtData; /* 0=> disconnected, 1=> original */
+    ORIG_ATOM_DATA *orig_inp_data = &OrigAtData;
+    ORIG_ATOM_DATA PrepAtData[2]; /* 0=> disconnected, 1=> original */
+    ORIG_ATOM_DATA *prep_inp_data = PrepAtData;
+    int             bReleaseVersion = bRELEASE_VERSION;
+    const int nStrLen = INCHI_SEGM_BUFLEN;
+    char *pStr = NULL;
+    int   nRet = 0, nRet1;
+
+#ifndef TEST_FPTRS
+    STRUCT_FPTRS *pStructPtrs = NULL;
+#else
+    STRUCT_FPTRS struct_fptrs, *pStructPtrs =&struct_fptrs; /* INCHI_LIB debug only */
+#endif
+
+#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 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
+    /*
+    inp_norm_data[0] = &InpNormAtData;
+    inp_norm_data[1] = &InpNormTautData;
+    inp_norm_data[2] = &InpNormAtDataR;
+    inp_norm_data[3] = &InpNormTautDataR;
+    */
+#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 )
+repeat:
+    inp_file = output_file = log_file = prb_file = NULL;
+    pStr = NULL;
+#endif
+
+    num_inp    = 0;
+    num_err    = 0;
+    num_output = 0;
+    sd->bUserQuit  = 0;
+
+#if( defined( _WIN32 ) && defined( _CONSOLE ) && !defined( INCHI_ANSI_ONLY ) )
+    if ( SetConsoleCtrlHandler( MyHandlerRoutine, 1 ) ) {
+        ConsoleQuit = WasInterrupted;
+    }
+#endif
+
+
+    if ( argc == 1 || argc==2 && ( argv[1][0]==INCHI_OPTION_PREFX ) &&
+        (!strcmp(argv[1]+1, "?") || !stricmp(argv[1]+1, "help") ) ) {
+        //HelpCommandLineParms(stdout);
+        return 0;
+    }
+    /*  original input structure */
+    memset( orig_inp_data     , 0,   sizeof( *orig_inp_data  ) );
+    memset( prep_inp_data     , 0, 2*sizeof( *prep_inp_data  ) );
+    memset( pINChI,     0, sizeof(pINChI    ) );
+    memset( pINChI_Aux, 0, sizeof(pINChI_Aux) );
+
+    /*
+    memset( inp_cur_data      , 0, sizeof( *inp_cur_data     ) );
+    memset( inp_norm_data[0]  , 0, sizeof( *inp_norm_data[0] ) );
+    memset( inp_norm_data[1]  , 0, sizeof( *inp_norm_data[0] ) );
+    */
+    memset( szSdfDataValue    , 0, sizeof( szSdfDataValue    ) );
+
+    /* explicitly cast to (const char **) to avoid a warning about "incompatible pointer type":*/
+    if ( 0 > ReadCommandLineParms( argc, (const char **)argv, ip, szSdfDataValue, &ulDisplTime, bReleaseVersion, stderr ) ) {
+        goto exit_function;
+    }
+    if ( !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_XML || ip->nInputType == INPUT_INCHI_PLAIN  ||
+         ip->nInputType == INPUT_CMLFILE   || ip->nInputType == INPUT_INCHI  ) {
+        /* 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;
+    }
+    //PrintInputParms( log_file, ip );
+    if ( !(pStr = (char*)inchi_malloc(nStrLen))) {
+        my_fprintf( log_file, "Cannot allocate output buffer. Terminating\n");
+        goto exit_function;
+    }
+    pStr[0] = '\0';
+
+#if( READ_INCHI_STRING == 1 )
+    if ( ip->nInputType == INPUT_INCHI ) {
+        memset( sd, 0, sizeof(*sd) );
+        ReadWriteInChI( inp_file, output_file, log_file, ip,  sd, NULL, NULL, NULL, 0, NULL);
+        ulTotalProcessingTime = sd->ulStructTime;
+        num_inp               = sd->fPtrStart;
+        num_err               = sd->fPtrEnd;
+        goto exit_function;
+    }
+#endif
+    /**********************************************************************************************/
+    /*  Main cycle */
+    /*  read input structures and create their INChI */
+    ulTotalProcessingTime = 0;
+
+    if ( pStructPtrs ) {
+        memset ( pStructPtrs, 0, sizeof(pStructPtrs[0]) );
+        /* debug: set CML reading sequence
+        pStructPtrs->fptr = (INCHI_FPTR *)inchi_calloc(16, sizeof(INCHI_FPTR));
+        for ( i = 0; i < 15; i ++ )
+            pStructPtrs->fptr[i] = 15-i;
+        pStructPtrs->cur_fptr = 7;
+        pStructPtrs->len_fptr = 16;
+        pStructPtrs->max_fptr = 14;
+        */
+    }
+
+    while ( !sd->bUserQuit && !bInterrupted ) {
+        if ( ip->last_struct_number && num_inp >= ip->last_struct_number ) {
+            nRet = _IS_EOF; /*  simulate end of file */
+            goto exit_function;
+        }
+
+        /*  read one structure from input and display optionally it */
+        nRet = GetOneStructure( sd, ip, szTitle, inp_file, log_file, output_file, prb_file,
+                                orig_inp_data, &num_inp, pStr, nStrLen, pStructPtrs );
+
+        if ( pStructPtrs ) {
+            pStructPtrs->cur_fptr ++;
+        }
+
+        if ( sd->bUserQuit ) {
+            break;
+        }
+        switch ( nRet ) {
+        case _IS_FATAL:
+            num_err ++;
+        case _IS_EOF:
+            goto exit_function;
+        case _IS_ERROR:
+            num_err ++;
+        case _IS_SKIP:
+            continue;
+        }
+
+        /* create INChI for each connected component of the structure and optionally display them */
+        /* output INChI for the whole structure */
+        nRet1 = ProcessOneStructure( sd, ip, szTitle, pINChI, pINChI_Aux,
+                                     inp_file, log_file, output_file, prb_file,
+                                     orig_inp_data, prep_inp_data,
+                                     num_inp, pStr, nStrLen );
+        
+        /*  free INChI memory */
+        FreeAllINChIArrays( pINChI, pINChI_Aux, sd->num_components );
+        /* free structure data */
+        FreeOrigAtData( orig_inp_data );
+        FreeOrigAtData( prep_inp_data );
+        FreeOrigAtData( prep_inp_data+1 );
+
+        ulTotalProcessingTime += sd->ulStructTime;
+        nRet = inchi_max(nRet, nRet1);
+        switch ( nRet ) {
+        case _IS_FATAL:
+            num_err ++;
+            goto exit_function;
+        case _IS_ERROR:
+            num_err ++;
+            continue;
+        }
+   /*   --- debug only ---
+        if ( pStructPtrs->cur_fptr > 5 ) {
+            pStructPtrs->cur_fptr = 5;
+        }
+   */
+
+    }
+
+exit_function:
+    if ( (ip->bINChIOutputOptions & INCHI_OUT_XML) && sd->bXmlStructStarted > 0 ) {
+        if ( !OutputINChIXmlStructEndTag( output_file, pStr, nStrLen, 1 ) ) {
+            my_fprintf( log_file, "Cannot create end xml tag for structure #%ld.%s%s%s%s Terminating.\n", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+            sd->bXmlStructStarted = -1; /*  do not repeat same message */
+        }
+    }
+
+
+    if ( (ip->bINChIOutputOptions & INCHI_OUT_XML) && ip->bXmlStarted ) {
+        OutputINChIXmlRootEndTag( output_file );
+        ip->bXmlStarted = 0;
+    }
+
+    
+    /* avoid memory leaks in case of fatal error */
+    if ( pStructPtrs && pStructPtrs->fptr ) {
+        inchi_free( pStructPtrs->fptr );
+    }
+
+    /*  free INChI memory */
+    FreeAllINChIArrays( pINChI, pINChI_Aux, sd->num_components );
+    /* free structure data */
+    FreeOrigAtData( orig_inp_data );
+    FreeOrigAtData( prep_inp_data );
+    FreeOrigAtData( prep_inp_data+1 );
+
+#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 )
+    {
+        int hours, minutes, seconds, mseconds;
+        SplitTime( ulTotalProcessingTime, &hours, &minutes, &seconds, &mseconds );
+        //my_fprintf( log_file, "Finished processing %ld structure%s: %ld error%s, processing time %d:%02d:%02d.%02d\n",
+        //                        num_inp, num_inp==1?"":"s",
+        //                        num_err, num_err==1?"":"s",
+        //                       hours, minutes, seconds,mseconds/10);
+    }
+    if ( log_file && log_file != stderr ) {
+        fclose( log_file );
+    }
+    if ( pStr ) {
+        inchi_free( pStr );
+    }
+    for ( i = 0; i < MAX_NUM_PATHS; i ++ ) {
+        if ( ip->path[i] ) {
+            inchi_free( (void*) ip->path[i] ); /*  cast deliberately discards 'const' qualifier */
+            ip->path[i] = NULL;
+        }
+    }
+    SetBitFree( );
+
+#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 )
+    if ( num_repeat-- > 0 ) {
+        goto repeat;
+    }
+#endif
+
+#if( bRELEASE_VERSION != 1 && defined(_DEBUG) )
+    if ( inp_file && inp_file != stdin ) {
+        user_quit("Press Enter to exit ?", ulDisplTime);
+    }
+#endif
+
+
+    return 0;
+}
+
+#endif  /* ifndef INCHI_LIB */