Example #1
0
int e_TreatReadTheStructureErrors(  STRUCT_DATA *sd, INPUT_PARMS *ip,
                                  INCHI_IOSTREAM *inp_file,
                                  INCHI_IOSTREAM* log_file, INCHI_IOSTREAM* output_file, INCHI_IOSTREAM *prb_file,
                                  inchi_Input *pInp, long *num_inp )
{
    int nRet = _IS_OKAY;
    /*  End of file */
    if ( 10 < sd->nStructReadError && sd->nStructReadError < 20 ) {
        nRet = _IS_EOF;
        goto exit_function; /*  end of file */
    }
    /*  Skipping the structures */
    if ( *num_inp < ip->first_struct_number ) {
        if ( log_file->f != stderr ) {
            inchi_fprintf( stderr, "\rSkipping structure #%ld.%s%s%s%s...\r", *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue));
        }
        nRet = sd->nErrorType = _IS_SKIP;
        goto exit_function;
    }

    sd->nErrorType = e_GetInpStructErrorType( ip, sd->nStructReadError, sd->pStrErrStruct, pInp->num_atoms );

    /*  Fatal error */
    if ( sd->nErrorType == _IS_FATAL ) {
        inchi_ios_eprint( log_file, "Fatal Error %d (aborted; %s) inp structure #%ld.%s%s%s%s\n",
                    sd->nStructReadError, sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
#if( bRELEASE_VERSION == 1 || EXTR_FLAGS == 0 )
        if ( prb_file->f && 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd && !ip->bSaveAllGoodStructsAsProblem ) {
            e_CopyMOLfile(inp_file->f, sd->fPtrStart, sd->fPtrEnd, prb_file->f, *num_inp);
        }
#endif
        /* goto exit_function; */
    }
    /*  Non-fatal errors: do not produce INChI */
    if ( sd->nErrorType == _IS_ERROR ) {  /*  70 => too many atoms */
        inchi_ios_eprint( log_file, "Error %d (no INChI; %s) inp structure #%ld.%s%s%s%s\n",
                    sd->nStructReadError, sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
#if( bRELEASE_VERSION == 1 || EXTR_FLAGS == 0 )
        if ( prb_file->f && 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd && !ip->bSaveAllGoodStructsAsProblem) {
            e_CopyMOLfile(inp_file->f, sd->fPtrStart, sd->fPtrEnd, prb_file->f, *num_inp);
        }
#endif
    }
    /*  Warnings: try to produce INChI */
    if ( sd->nErrorType == _IS_WARNING ) {
        inchi_ios_eprint( log_file, "Warning: (%s) inp structure #%ld.%s%s%s%s\n",
                    sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
    }
exit_function:
    if ( nRet <= _IS_OKAY && sd->nErrorType > 0 ) {
        nRet = sd->nErrorType;
    }
    return nRet;
}
Example #2
0
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Local helper.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
int e_MakeOutputHeader( char *pSdfLabel, char *pSdfValue, long lSdfId, long 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: %ld", num_inp );
        tot_len2 = sprintf( pStr2, "structure #%ld", num_inp );
    }
    else
    {
        tot_len1 = sprintf( pStr1, "Structure: %ld.%s%s%s%s",
            num_inp, SDF_LBL_VAL(pSdfLabel, pSdfValue) );

        tot_len2 = sprintf( pStr2, "structure #%ld.%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;
}
Example #3
0
int process_single_input( int argc, char *argv[ ] )
/**************************************************/
{

/**************************************/
#endif /* #if ( BUILD_WITH_AMI == 1 ) */
/**************************************/
                                /* if not in AMI mode, main() starts here */
                                
    
    int bReleaseVersion = bRELEASE_VERSION;
    const int nStrLen = INCHI_SEGM_BUFLEN;
    int   nRet = 0, nRet1;
    int	i, k;
    long num_err, num_output, num_inp;
    /* long rcPict[4] = {0,0,0,0}; */
    unsigned long  ulDisplTime = 0;    /*  infinite, milliseconds */
    unsigned long  ulTotalProcessingTime = 0;

    char szTitle[MAX_SDF_HEADER+MAX_SDF_VALUE+256];
    char szSdfDataValue[MAX_SDF_VALUE+1];
    char *pStr = NULL;

    INPUT_PARMS inp_parms;
    INPUT_PARMS *ip = &inp_parms;

    STRUCT_DATA struct_data;
    STRUCT_DATA *sd = &struct_data;

    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;

    PINChI2     *pINChI[INCHI_NUM];
    PINChI_Aux2 *pINChI_Aux[INCHI_NUM];

    INCHI_IOSTREAM outputstr, logstr, prbstr, instr;
    INCHI_IOSTREAM *pout=&outputstr, *plog = &logstr, *pprb = &prbstr, *inp_file = &instr;
#ifdef TARGET_EXE_STANDALONE
    char ik_string[256];    /*^^^ Resulting InChIKey string */
    int ik_ret=0;           /*^^^ InChIKey-calc result code */
    int xhash1, xhash2;
    char szXtra1[65], szXtra2[65];
    int inchi_ios_type = INCHI_IOSTREAM_STRING;
#else
    int inchi_ios_type = INCHI_IOSTREAM_FILE;
#endif



/* internal tests --- */
#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 

#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 )
repeat:
    inchi_ios_close(inp_file);
    inchi_ios_close(pout);
    inchi_ios_close(plog);
    inchi_ios_close(pprb);
    pStr = NULL;
#endif
/* --- internal tests */



    sd->bUserQuit  = 0;
#if ( defined( _WIN32 ) && defined( _CONSOLE ) && !defined( COMPILE_ANSI_ONLY ) )
    if ( SetConsoleCtrlHandler( MyHandlerRoutine, 1 ) ) 
        ConsoleQuit = WasInterrupted;
#endif
    
    num_inp    = 0;
    num_err    = 0;
    num_output = 0;
    
    inchi_ios_init(inp_file, INCHI_IOSTREAM_FILE, NULL);
    inchi_ios_init(pout, inchi_ios_type, NULL);
    inchi_ios_init(plog, inchi_ios_type, stdout);
    inchi_ios_init(pprb, inchi_ios_type, NULL);

    
    if ( argc == 1 || argc==2 && ( argv[1][0]==INCHI_OPTION_PREFX ) &&
        (!strcmp(argv[1]+1, "?") || !stricmp(argv[1]+1, "help") ) ) 
    {
        HelpCommandLineParms(plog); 
        inchi_ios_flush(plog);
        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( szSdfDataValue    , 0, sizeof( szSdfDataValue    ) );
    

    plog->f = stderr;
    if ( 0 > ReadCommandLineParms( argc, (const char **)argv, ip, szSdfDataValue, &ulDisplTime, bReleaseVersion, plog) ) 
                                         /* explicitly cast to (const char **) to avoid a warning about "incompatible pointer type":*/    
    {
        goto exit_function;
    }


    if ( !OpenFiles( &(inp_file->f), &(pout->f), &(plog->f), &(pprb->f), 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;
    }


    inchi_ios_eprint( plog, "The command line used:\n\"");
    for(k=0; k<argc-1; k++)
        inchi_ios_eprint( plog, "%-s ",argv[k]);
    inchi_ios_eprint( plog, "%-s\"\n", argv[argc-1]);


    PrintInputParms(plog,ip);
    inchi_ios_flush2(plog, stderr);


    if ( !( pStr = (char*) inchi_malloc(nStrLen) ) ) 
    {
        inchi_ios_eprint( plog, "Cannot allocate output buffer. Terminating\n"); 
        inchi_ios_flush2(plog, stderr);
        goto exit_function;
    }
    pStr[0] = '\0';


#if ( READ_INCHI_STRING == 1 )
    if ( ip->nInputType == INPUT_INCHI ) {
        memset( sd, 0, sizeof(*sd) );
        ReadWriteInChI( inp_file, pout, plog, ip,  sd, NULL, NULL, NULL, 0, NULL);
        inchi_ios_flush2(plog, stderr);
        ulTotalProcessingTime = sd->ulStructTime;
        num_inp               = sd->fPtrStart;
        num_err               = sd->fPtrEnd;
        goto exit_function;
    }
#endif


    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;
        */
    }


    /**********************************************************************************************/
    /*  Main cycle : read input structures and create their INChI								  */
    /**********************************************************************************************/
    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, plog, pout, pprb,
                                orig_inp_data, &num_inp, pStr, nStrLen, pStructPtrs );
        inchi_ios_flush2(plog, stderr);


        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, plog, pout, pprb,
                                     orig_inp_data, prep_inp_data,
                                     num_inp, pStr, nStrLen,
                                     0 /* save_opt_bits */);        
        inchi_ios_flush2(plog, stderr);


#ifdef TARGET_EXE_STANDALONE
        /* correctly treat tabbed output with InChIKey */
        if ( ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT ) 
            if ( ip->bCalcInChIHash != INCHIHASH_NONE )
                if (pout->s.pStr)
                    if (pout->s.nUsedLength>0)
                        if (pout->s.pStr[pout->s.nUsedLength-1]=='\n')
                            /* replace LF with TAB */
                            pout->s.pStr[pout->s.nUsedLength-1] = '\t';
#endif

        /*  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;
        }


#ifdef TARGET_EXE_STANDALONE
        if ( ip->bCalcInChIHash != INCHIHASH_NONE )
        {
            char *buf = NULL;
            size_t slen = pout->s.nUsedLength;

            extract_inchi_substring(&buf, pout->s.pStr, slen);            

            if (NULL==buf)
            {
                ik_ret = INCHIKEY_NOT_ENOUGH_MEMORY;                     
            }
            else
            {
                xhash1 = xhash2 = 0;
                if ( ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1 ) ||
                     ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1_XTRA2 ) )
                     xhash1 = 1;
                if ( ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA2 ) ||
                     ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1_XTRA2 ) )
                     xhash2 = 1;
                ik_ret = GetINCHIKeyFromINCHI(buf, xhash1, xhash2, 
                                              ik_string, szXtra1, szXtra2); 
                inchi_free(buf);
            }
            
                
        
            if (ik_ret==INCHIKEY_OK)   
            {
                /* NB: correctly treat tabbed output with InChIKey & hash extensions */                
                char csep = '\n';
#ifdef TARGET_EXE_STANDALONE
                if ( ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT ) 
                    csep = '\t';
#endif                
                inchi_ios_print(pout, "InChIKey=%-s",ik_string);
                if ( xhash1 )
                    inchi_ios_print(pout, "%cXHash1=%-s",csep,szXtra1);
                if ( xhash2 )
                    inchi_ios_print(pout, "%cXHash2=%-s",csep,szXtra2);
                inchi_ios_print(pout, "\n");
            }
            else    
            {
                inchi_ios_print(plog, "Warning (Could not compute InChIKey: ", num_inp);
                switch(ik_ret)
                {
                    case INCHIKEY_UNKNOWN_ERROR:
                        inchi_ios_print(plog, "unresolved error)");
                        break;
                    case INCHIKEY_EMPTY_INPUT:
                        inchi_ios_print(plog,  "got an empty string)");
                        break;
                    case INCHIKEY_INVALID_INCHI_PREFIX:
                    case INCHIKEY_INVALID_INCHI:
                    case INCHIKEY_INVALID_STD_INCHI:
                        inchi_ios_print(plog, "got non-InChI string)");
                        break;
                    case INCHIKEY_NOT_ENOUGH_MEMORY:
                        inchi_ios_print(plog, "not enough memory to treat the string)");
                        break;
                    default:inchi_ios_print(plog, "internal program error)");
                        break;
                }
                inchi_ios_print(plog, " structure #%-lu.\n", num_inp);
                if ( ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT )
                    inchi_ios_print(pout, "\n");
            }
            inchi_ios_flush(pout);
            inchi_ios_flush2(plog, stderr);
        }

        else
            inchi_ios_flush(pout);


#endif

   /*   --- debug only ---
        if ( pStructPtrs->cur_fptr > 5 ) {
            pStructPtrs->cur_fptr = 5;
        }
   */


            
    } /* end of main cycle - while ( !sd->bUserQuit && !bInterrupted ) */



exit_function:
    if ( (ip->bINChIOutputOptions & INCHI_OUT_XML) && sd->bXmlStructStarted > 0 ) 
    {
            if ( !OutputINChIXmlStructEndTag( pout,  pStr, nStrLen, 1 ) ) 
            {
                inchi_ios_eprint( plog, "Cannot create end xml tag for structure #%ld.%s%s%s%s Terminating.\n", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
                inchi_ios_flush2(plog, stderr);
                sd->bXmlStructStarted = -1; /*  do not repeat same message */
        }
    }
    if ( (ip->bINChIOutputOptions & INCHI_OUT_XML) && ip->bXmlStarted ) 
    {
        OutputINChIXmlRootEndTag( pout ); 
        inchi_ios_flush(pout);
        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

    /* close output(s) */
    inchi_ios_close(inp_file);    
    inchi_ios_close(pout);    
    inchi_ios_close(pprb);
    {
        int hours, minutes, seconds, mseconds;
        SplitTime( ulTotalProcessingTime, &hours, &minutes, &seconds, &mseconds );
        inchi_ios_eprint( plog, "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);
        inchi_ios_flush2(plog, stderr);
    }
    inchi_ios_close(plog);
    if ( pStr )                             
        inchi_free( pStr );


    /* frees */
    for ( i = 0; i < MAX_NUM_PATHS; i ++ ) 
    {
        if ( ip->path[i] ) 
        {
            free( (void*) ip->path[i] ); /*  cast deliberately discards 'const' qualifier */
            ip->path[i] = NULL;
        }
    }
    SetBitFree( );

/* internal tests --- */
#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 )
    if ( num_repeat-- > 0 ) 
        goto repeat;
#endif
/* --- internal tests */

#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) )
    if ( inp_file->f && inp_file->f != stdin ) 
    {
        user_quit("Press Enter to exit ?", ulDisplTime);
    }
#endif

#if ( ( BUILD_WITH_AMI==1 ) && defined( _WIN32 ) && defined( _CONSOLE ) && !defined( COMPILE_ANSI_ONLY ) )
    if ( bInterrupted ) 
        return CTRL_STOP_EVENT;
#endif
	return 0;
}