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Viewing changes to src/formats/inchi/runichi.c

  • Committer: Bazaar Package Importer
  • Author(s): Michael Banck
  • Date: 2008-07-22 23:54:58 UTC
  • mfrom: (3.1.10 intrepid)
  • Revision ID: james.westby@ubuntu.com-20080722235458-3o606czluviz4akx
Tags: 2.2.0-2
* Upload to unstable.
* debian/control: Updated descriptions.
* debian/patches/gauss_cube_format.patch: New patch, makes the 
  gaussian cube format available again.
* debian/rules (DEB_DH_MAKESHLIBS_ARGS_libopenbabel3): Removed.
* debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Likewise.
* debian/libopenbabel3.install: Adjust formats directory to single 
  version hierarchy.

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src/formats/inchi/runichi.c
1
1
/*
2
 
 * International Union of Pure and Applied Chemistry (IUPAC)
3
2
 * International Chemical Identifier (InChI)
4
3
 * Version 1
5
 
 * Software version 1.01
6
 
 * May 16, 2006
 
4
 * Software version 1.02-beta
 
5
 * August 23, 2007
7
6
 * Developed at NIST
 
7
 *
 
8
 * The InChI library and programs are free software developed under the
 
9
 * auspices of the International Union of Pure and Applied Chemistry (IUPAC);
 
10
 * you can redistribute this software and/or modify it under the terms of 
 
11
 * the GNU Lesser General Public License as published by the Free Software 
 
12
 * Foundation:
 
13
 * http://www.opensource.org/licenses/lgpl-license.php
8
14
 */
9
15
 
 
16
 
10
17
#include <stdio.h>
11
18
#include <stdlib.h>
12
19
#include <string.h>
16
23
#include <errno.h>
17
24
#include <limits.h>
18
25
 
 
26
 
 
27
 
19
28
#include "mode.h"       /* moved from below, suggestion by David Mosenkis */
20
29
 
21
30
#include "ichitime.h"
32
41
#include "ichierr.h"
33
42
#include "ichimain.h"
34
43
#include "extr_ct.h"
 
44
#include "ichitaut.h"
35
45
 
36
46
#ifdef INCHI_LIB
37
47
#include "ichi_lib.h"
44
54
#include "debug.h"
45
55
#endif
46
56
 
 
57
 
47
58
/* for DisplayTheWholeStructure() */
48
59
 
49
60
#define COMP_ORIG_0_MAIN  0x0001
54
65
#define COMP_ORIG_1_RECN  0x0020
55
66
 
56
67
 
 
68
 
 
69
 
57
70
/* local prototypes */
58
71
int GetProcessingWarningsOneINChI(INChI *pINChI, INP_ATOM_DATA *inp_norm_data, char *pStrErrStruct);
59
72
int  GetProcessingWarnings(INChI *cur_INChI[], INP_ATOM_DATA **inp_norm_data, STRUCT_DATA *sd);
117
130
#endif /* } TEST_RENUMB_ATOMS */
118
131
 
119
132
 
120
 
#ifdef INCHI_LIBRARY
 
133
/*^^^ */
 
134
/*#ifdef INCHI_LIBRARY*/
 
135
#if ( defined(INCHI_LIBRARY) || defined(BUILD_CINCHI_WITH_INCHIKEY) )
 
136
 
121
137
/*****************************************************************
122
138
 *
123
139
 *  Estimate printf string length
359
375
#define INCHI_ADD_STR_LEN   32768
360
376
#endif /* INCHI_LIBRARY */
361
377
 
362
 
#ifdef INCHI_LIBRARY
 
378
/*^^^ */
 
379
/*#ifdef INCHI_LIBRARY*/
 
380
#if ( defined(INCHI_LIBRARY) || defined(BUILD_CINCHI_WITH_INCHIKEY) )
363
381
/*****************************************************************/
364
382
int inchi_print( INCHI_FILE* f, const char* lpszFormat, ... )
365
383
{
434
452
#endif
435
453
 
436
454
 
437
 
#ifdef INCHI_LIBRARY
 
455
/*^^^ */
 
456
/*#ifdef INCHI_LIBRARY*/
 
457
#if ( defined(INCHI_LIBRARY) || defined(BUILD_CINCHI_WITH_INCHIKEY) )
 
458
 
438
459
/**********************************************************************/
439
460
/* This function's output should not be displayed in the output pane  */
440
461
/**********************************************************************/
503
524
    return ret? ret : ret2;
504
525
}
505
526
#endif
506
 
#ifdef INCHI_LIBRARY
 
527
 
 
528
/*^^^ #ifdef INCHI_LIBRARY */
 
529
#if ( defined(INCHI_LIBRARY) || defined(BUILD_CINCHI_WITH_INCHIKEY) )
507
530
/*****************************************************************/
508
531
int my_fprintf( INCHI_FILE* f, const char* lpszFormat, ... )
509
532
{
553
576
    int ret=0, ret2=0;
554
577
    va_list argList;
555
578
 
556
 
#ifndef INCHI_LIB
 
579
 
 
580
/*#ifndef INCHI_LIB*/
 
581
/*^^^ */
 
582
#if ( !defined(INCHI_LIB) && !defined(BUILD_CINCHI_WITH_INCHIKEY) )
557
583
    if ( f ) {
558
584
        if ( f == stderr && lpszFormat && lpszFormat[0] && '\r' == lpszFormat[strlen(lpszFormat)-1] ) {
559
585
#define CONSOLE_LINE_LEN 80
585
611
        va_end( argList );
586
612
    }
587
613
#else
 
614
 
 
615
/*^^^ */
 
616
#if ( !defined(BUILD_CINCHI_WITH_INCHIKEY) )
588
617
    if ( f ) {
589
618
        my_va_start( argList, lpszFormat );
590
619
        ret = vfprintf( f, lpszFormat, argList );
592
621
    }
593
622
#endif
594
623
 
595
 
    return ret? ret : ret2;
596
 
}
597
 
#endif
 
624
 
 
625
#endif
 
626
 
 
627
    return ret? ret : ret2;
 
628
}
 
629
#endif
 
630
 
 
631
 
 
632
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ */
 
633
 
 
634
int my_fileprintf( FILE* f, const char* lpszFormat, ... )
 
635
{
 
636
    int ret=0, ret2=0;
 
637
    va_list argList;
 
638
 
 
639
 
 
640
 
 
641
 
 
642
    if ( f ) {
 
643
        if ( f == stderr && lpszFormat && lpszFormat[0] && '\r' == lpszFormat[strlen(lpszFormat)-1] ) {
 
644
#define CONSOLE_LINE_LEN 80
 
645
 
 
646
#ifndef INCHI_ANSI_ONLY
 
647
            char szLine[CONSOLE_LINE_LEN];
 
648
            my_va_start( argList, lpszFormat );
 
649
            ret = _vsnprintf( szLine, CONSOLE_LINE_LEN-1, lpszFormat, argList );
 
650
            va_end( argList );
 
651
            if ( ret < 0 ) {
 
652
                /*  output is longer than the console line */
 
653
                strcpy(szLine+CONSOLE_LINE_LEN-4, "...\r");
 
654
            }
 
655
            fputs( szLine, f );
 
656
#else
 
657
            my_va_start( argList, lpszFormat );
 
658
            ret = vfprintf( f, lpszFormat, argList );
 
659
            va_end( argList );
 
660
#endif
 
661
 
 
662
#undef CONSOLE_LINE_LEN
 
663
        } else {
 
664
            my_va_start( argList, lpszFormat );
 
665
            ret = vfprintf( f, lpszFormat, argList );
 
666
            va_end( argList );
 
667
        }
 
668
    }
 
669
    if ( f && f != stderr ) { /* disabled stderr output in case f == NULL. 11-23-2005 */
 
670
        my_va_start( argList, lpszFormat );
 
671
        ret2 = vfprintf( stderr, lpszFormat, argList );
 
672
        va_end( argList );
 
673
    }
 
674
 
 
675
 
 
676
    return ret? ret : ret2;
 
677
}
 
678
 
598
679
#ifndef INCHI_ANSI_ONLY
599
680
/********************************************************************/
600
681
void FillTableParms( SET_DRAW_PARMS *sdp, INChI **cur_INChI, INChI_Aux **cur_INChI_Aux,
746
827
#ifndef INCHI_ANSI_ONLY
747
828
#ifndef INCHI_LIB
748
829
/*******************************************************************/
749
 
int DisplayStructure( inp_ATOM *at, int num_at, int num_removed_H,
 
830
int DisplayStructure( inp_ATOM *at, int num_at, int num_removed_H, int bAdd_DT_to_num_H,
750
831
                      int nNumRemovedProtons, NUM_H *nNumRemovedProtonsIsotopic,
751
832
                      int bIsotopic, int j /*bTautomeric*/,
752
833
                      INChI **cur_INChI, INChI_Aux **cur_INChI_Aux,
756
837
    int err = -1;
757
838
    if ( CreateInfoAtomData( &inf_data, num_at, 1 ) ) {
758
839
        err = 0;
759
 
        FillOutInfAtom( at, &inf_data, num_at, num_removed_H, nNumRemovedProtons,
760
 
                        nNumRemovedProtonsIsotopic, bIsotopic,
 
840
        FillOutInfAtom( at, &inf_data, num_at, num_removed_H, bAdd_DT_to_num_H,
 
841
                        nNumRemovedProtons, nNumRemovedProtonsIsotopic, bIsotopic,
761
842
                        cur_INChI?cur_INChI[j]:NULL,
762
843
                        cur_INChI_Aux?cur_INChI_Aux[j]:NULL, bAbcNumbers, nMode);
763
844
        FillTableParms( &dp->sdp, cur_INChI, cur_INChI_Aux, nMode, bIsotopic, j );
786
867
        if ( bTautomeric == TAUT_INI ) {
787
868
            /*
788
869
            FillOutInfAtom( (composite_norm_data+bTautomeric)->at, &inf_data, (composite_norm_data+bTautomeric)->num_at,
789
 
                            (composite_norm_data+bTautomeric)->num_removed_H,
 
870
                            (composite_norm_data+bTautomeric)->num_removed_H, bAdd_DT_to_num_H,
790
871
                            (composite_norm_data+bTautomeric)->nNumRemovedProtons,
791
872
                            (composite_norm_data+bTautomeric)->nNumRemovedProtonsIsotopic, bIsotopic,
792
873
                            NULL, NULL, bAbcNumbers, nMode);
838
919
        case CT_CALC_STEREO_ERR:     p = "CALC_STEREO_ERR";       break;
839
920
        case CT_STEREO_CANON_ERR:    p = "STEREO_CANON_ERR";      break;
840
921
        case CT_CANON_ERR:           p = "CANON_ERR";             break;
841
 
        case CT_WRONG_FORMULA:       p = "Wrong or missing chemical formula"; break;
 
922
        case CT_WRONG_FORMULA:       p = "Wrong or missing chemical formula";  break;
842
923
        /*case CT_CANON_ERR2:          p = "CT_CANON_ERR2";         break;*/
843
924
        case CT_UNKNOWN_ERR:         p = "UNKNOWN_ERR";           break;
844
 
        case BNS_RADICAL_ERR:        p = "Cannot process free radical center";      break;
 
925
        case BNS_RADICAL_ERR:        p = "Cannot process free radical center"; break;
 
926
        case BNS_ALTBOND_ERR:        p = "Cannot process aromatic bonds";      break;
845
927
 
846
928
        default:
847
929
            if ( nErrorCode > CT_UNKNOWN_ERR ) {
1283
1365
#ifndef INCHI_ANSI_ONLY
1284
1366
/* find equivalent and wINChI display order; use requested in ip->bCompareComponents comparison */
1285
1367
        ret = SaveEquComponentsInfoAndSortOrder ( iINChI, pINChISort[j], num_components, orig_inp_data, prep_inp_data,
1286
 
                                                  composite_norm_data[j], ip->bCompareComponents );
 
1368
#if( FIX_DALKE_BUGS == 1 )
 
1369
                                                  composite_norm_data? composite_norm_data[j]:NULL,
 
1370
#else
 
1371
                                                  composite_norm_data[j],
 
1372
#endif
 
1373
                                                  ip->bCompareComponents );
1287
1374
        if ( RETURNED_ERROR( ret ) ) {
1288
1375
            ret = 0;
1289
1376
            goto exit_function;
1328
1415
        
1329
1416
        /* print inchi string(s) */
1330
1417
 
 
1418
 
1331
1419
        bINChIOutputOptions0 = ip->bINChIOutputOptions & ~INCHI_OUT_PRINT_OPTIONS;
1332
1420
 
1333
1421
        bEmbedReconnected    = ip->bINChIOutputOptions & INCHI_OUT_EMBED_REC;
1414
1502
        }
1415
1503
    }
1416
1504
    ret = ret? 0 : _IS_FATAL;
 
1505
 
 
1506
 
 
1507
 
1417
1508
    return ret;
1418
1509
}
1419
1510
/**********************************************************************************/
1690
1781
#endif
1691
1782
/*****************************************************************************************************/
1692
1783
int TreatReadTheStructureErrors(  STRUCT_DATA *sd, INPUT_PARMS *ip, int nLogMask,
1693
 
                                  FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
 
1784
                                  FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, 
 
1785
                                  FILE *prb_file, /*^^^ was: INCHI_FILE */
1694
1786
                                  ORIG_ATOM_DATA *orig_inp_data, long *num_inp, char *pStr, int nStrLen )
1695
1787
{
1696
1788
    int nRet = _IS_OKAY;
1708
1800
 
1709
1801
    /*  Skipping the structures */
1710
1802
    if ( *num_inp < ip->first_struct_number ) {
1711
 
#ifndef INCHI_LIBRARY
 
1803
 
 
1804
#if ( !defined(INCHI_LIBRARY) && !defined(BUILD_CINCHI_WITH_INCHIKEY) )
 
1805
/*^^^ #ifndef INCHI_LIBRARY */
1712
1806
        if ( log_file != stderr ) {
1713
1807
            my_fprintf( stderr, "\rSkipping structure #%ld.%s%s%s%s...", *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue));
1714
1808
        }
1752
1846
    if ( sd->nErrorType == _IS_ERROR ) {  /*  70 => too many atoms */
1753
1847
        if ( nLogMask & LOG_MASK_ERR )
1754
1848
            my_fprintf( log_file, "Error %d (no %s; %s) inp structure #%ld.%s%s%s%s\n",
1755
 
                    sd->nStructReadError, INCHI_NAME, sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
 
1849
                    sd->nStructReadError, (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY)?"Molfile":INCHI_NAME,
 
1850
                    sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
1756
1851
#if( bRELEASE_VERSION == 1 || EXTR_FLAGS == 0 )
1757
1852
        if ( prb_file && 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd && !ip->bSaveAllGoodStructsAsProblem) {
1758
1853
            CopyMOLfile(inp_file, sd->fPtrStart, sd->fPtrEnd, prb_file, *num_inp);
1910
2005
    sd->ulStructTime += lElapsedTime;
1911
2006
 
1912
2007
 
1913
 
#if( !defined( INCHI_LIB ) && !defined( INCHI_LIBRARY ) )
 
2008
/*^^^#if( !defined( INCHI_LIB ) && !defined( INCHI_LIBRARY ) ) */
 
2009
#if( !defined( INCHI_LIB ) && !defined( INCHI_LIBRARY ) && !defined(BUILD_CINCHI_WITH_INCHIKEY) )
1914
2010
#if( TEST_RENUMB_ATOMS != 1 )
1915
2011
    /*  log file / console output */
1916
2012
    if ( log_file && log_file != stderr ) { /* NULL log_file now ignored. 11-23-2005 */
2061
2157
/****************************************************************************************************/
2062
2158
int TreatCreateOneComponentINChIError(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data,
2063
2159
                                     int i, long num_inp,
2064
 
                                     FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
 
2160
                                     FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, 
 
2161
                                     FILE *prb_file, /*^^^ was: INCHI_FILE */
2065
2162
                                     char *pStr, int nStrLen )
2066
2163
{
2067
2164
    if ( sd->nErrorCode ) {
2087
2184
            }
2088
2185
        }
2089
2186
    }
2090
 
#ifndef INCHI_LIBRARY
 
2187
/*^^^ #ifndef INCHI_LIBRARY */
 
2188
#if( !defined( INCHI_LIBRARY ) && !defined(BUILD_CINCHI_WITH_INCHIKEY) )
2091
2189
    /*  print the logfile record */
2092
2190
    if ( log_file && log_file != stderr && (sd->ulStructTime >= 1000 || sd->nErrorCode) ) {
2093
2191
        fprintf( log_file, "%10lu msec structure #%ld.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n",
2100
2198
}
2101
2199
/****************************************************************************************************/
2102
2200
int TreatCreateINChIWarning(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, long num_inp,
2103
 
                                     FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
 
2201
                                     FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, 
 
2202
                                     FILE *prb_file, /*^^^ was: INCHI_FILE */
2104
2203
                                     char *pStr, int nStrLen )
2105
2204
{
2106
2205
#if( bRELEASE_VERSION == 0 && (EXTR_FLAGS || EXTR_MASK) )
2222
2321
#ifndef INCHI_LIBRARY
2223
2322
/*******************************************************************************************/
2224
2323
int GetOneStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
2225
 
                     FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
 
2324
                     FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, 
 
2325
                     FILE *prb_file, /*^^^ was: INCHI_FILE */
2226
2326
                     ORIG_ATOM_DATA *orig_inp_data, long *num_inp, char *pStr, int nStrLen, STRUCT_FPTRS *struct_fptrs )
2227
2327
{
2228
2328
    int nRet, inp_index, out_index, bUseFptr = (NULL != struct_fptrs);
2579
2679
    if ( /*ip->bDisplayEachComponentINChI &&*/ !pRenumbData->nRet2 ) {
2580
2680
        int err, len;
2581
2681
        /*
2582
 
        err = DisplayStructure( inp_cur_data->at, inp_cur_data->num_at, 0, 0, NULL. 1, 0, NULL, NULL,
 
2682
        err = DisplayStructure( inp_cur_data->at, inp_cur_data->num_at, 0, 1, 0, NULL. 1, 0, NULL, NULL,
2583
2683
                                            ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
2584
2684
        */
2585
 
        err = DisplayStructure( inp_cur_data->at, inp_cur_data->num_at, 0, 0, NULL, 1/*isotopic*/, 0/*taut*/, NULL, NULL,
 
2685
        err = DisplayStructure( inp_cur_data->at, inp_cur_data->num_at, 0, 1, 0, NULL, 1/*isotopic*/, 0/*taut*/, NULL, NULL,
2586
2686
                                            ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
2587
2687
        if ( pRenumbData->c1 || pRenumbData->c2 ) {
2588
2688
            len = strlen(szTitle);
2589
2689
            strcat( szTitle, " (Renumbered)" );
2590
2690
            err = DisplayStructure( pRenumbData->longest_inp_cur_data.at, pRenumbData->longest_inp_cur_data.num_at,
2591
 
                                    0, 0, NULL, 1, 0, NULL, NULL, ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
 
2691
                                    0, 1, 0, NULL, 1, 0, NULL, NULL, ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
2592
2692
            szTitle[len] = '\0';
2593
2693
        }
2594
2694
        sd->bUserQuitComponentDisplay = (err==ESC_KEY);
2962
3062
    /******************************************************
2963
3063
     * Display the whole input structure in console app
2964
3064
     */
2965
 
#ifndef INCHI_LIB
 
3065
/*^^^ #ifndef INCHI_LIB */
 
3066
#if( !defined( INCHI_LIB ) && !defined(BUILD_CINCHI_WITH_INCHIKEY) )
2966
3067
    if ( bShowStruct && ip->bDisplay ) {
2967
3068
        if ( bDisplayEqu ) {
2968
3069
            sprintf( szTitle, " Equ Set %d of %d, Input Structure #%ld.%s%s%s%s%s",
2971
3072
        } else {
2972
3073
            sprintf( szTitle, "Input Structure #%ld.%s%s%s%s%s", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue), lpszType);
2973
3074
        }
2974
 
        err = DisplayStructure( orig_inp_data->at, orig_inp_data->num_inp_atoms, 0, 0, NULL, 1/*isotopic*/, 0/*taut*/, NULL, NULL,
 
3075
        err = DisplayStructure( orig_inp_data->at, orig_inp_data->num_inp_atoms, 0, 1, 0, NULL, 1/*isotopic*/, 0/*taut*/, NULL, NULL,
2975
3076
                                            ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
2976
3077
        sd->bUserQuitComponent = (err==ESC_KEY);
2977
3078
        if ( !err ) {
3036
3137
                    return -1;
3037
3138
                }
3038
3139
                vDrawData.pWindowData = CreateWinData_( orig_inp_data->at, orig_inp_data->num_inp_atoms,
3039
 
                                                        0, 0, NULL, 1, 0, NULL, NULL,
 
3140
                                                        0, 1 /* bAdd_DT_to_num_H */, 0, NULL, 1, 0, NULL, NULL,
3040
3141
                                                        ip->bAbcNumbers, &ip->dp, ip->nMode );
3041
3142
                if( vDrawData.pWindowData != NULL )
3042
3143
                {
3071
3172
/************************************************************************************************/
3072
3173
int ProcessOneStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
3073
3174
                         PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM],
3074
 
                         FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
 
3175
                         FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, 
 
3176
                         FILE *prb_file, /*^^^ was: INCHI_FILE */
3075
3177
                         ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data,
3076
3178
                         long num_inp, char *pStr, int nStrLen )
3077
3179
{
3082
3184
        ORIG_STRUCT      OrigStruct;
3083
3185
        ORIG_STRUCT      *pOrigStruct = NULL;
3084
3186
        int bSortPrintINChIFlags   = 0;
3085
 
 
 
3187
#if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 )
 
3188
        int ret1=0, ret2=0;
 
3189
#endif
3086
3190
        sd->bUserQuitComponent = 0;
3087
3191
        sd->bUserQuitComponentDisplay = 0;
3088
3192
        memset( composite_norm_data, 0, sizeof(composite_norm_data) );
3094
3198
        fix_odd_things( orig_inp_data->num_inp_atoms, orig_inp_data->at, 0 );
3095
3199
#endif
3096
3200
 
 
3201
#if( UNDERIVATIZE == 1 )  /***** post v.1 feature *****/
 
3202
        if ( ip->bUnderivatize && 0 > (ret2=underivatize( orig_inp_data )) ) {
 
3203
            long num_inp2 = num_inp;
 
3204
            AddMOLfileError(sd->pStrErrStruct, "Underivatization error");
 
3205
            sd->nStructReadError =  99;
 
3206
            sd->nErrorType = _IS_ERROR;
 
3207
            nRet = _IS_ERROR;
 
3208
            TreatReadTheStructureErrors( sd, ip, LOG_MASK_ALL, inp_file, log_file, output_file, prb_file,
 
3209
                                        prep_inp_data, &num_inp2, pStr, nStrLen );
 
3210
            goto exit_function; /* output only if derivatives found */
 
3211
        }
 
3212
#endif /* UNDERIVATIZE == 1 */
 
3213
#if( RING2CHAIN == 1 )  /***** post v.1 feature *****/
 
3214
        if ( ip->bRing2Chain && 0 > (ret1 = Ring2Chain( orig_inp_data )) ) {
 
3215
            long num_inp2 = num_inp;
 
3216
            AddMOLfileError(sd->pStrErrStruct, "Ring to chain error");
 
3217
            sd->nStructReadError =  99;
 
3218
            sd->nErrorType = _IS_ERROR;
 
3219
            nRet = _IS_ERROR;
 
3220
            TreatReadTheStructureErrors( sd, ip, LOG_MASK_ALL, inp_file, log_file, output_file, prb_file,
 
3221
                                        prep_inp_data, &num_inp2, pStr, nStrLen );
 
3222
            goto exit_function; /* output only if derivatives found */
 
3223
        }
 
3224
#endif /* RING2CHAIN == 1 */
 
3225
#if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 )  /***** post v.1 feature *****/
 
3226
        if ( ip->bIngnoreUnchanged && !ret1 && !ret2 ) {
 
3227
            goto exit_function; /* output only if derivatives or ring/chain found */
 
3228
        }
 
3229
#endif /* RING2CHAIN == 1 || UNDERIVATIZE == 1 */
 
3230
 
 
3231
 
3097
3232
        /***** output MOLfile ***************/
3098
3233
        if ( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY  ) {
3099
3234
            char szNumber[32];
3100
 
#if ( !defined( INCHI_LIB ) && !defined( INCHI_LIBRARY ) )
 
3235
            int ret1a=0, ret2a=0; /* for derivatives and ring-chain */
 
3236
/*^^^ #if ( !defined( INCHI_LIB ) && !defined( INCHI_LIBRARY ) ) */
 
3237
#if( !defined( INCHI_LIB ) && !defined( INCHI_LIBRARY ) && !defined(BUILD_CINCHI_WITH_INCHIKEY) )
3101
3238
#if( TEST_RENUMB_ATOMS != 1 )
3102
3239
            /*  log file / console output */
3103
3240
            if ( log_file != stderr ) {
3108
3245
            }
3109
3246
#endif
3110
3247
#endif
3111
 
            sprintf( szNumber, "Structure #%ld", num_inp );
3112
 
            WriteOrigAtomDataToSDfile( orig_inp_data, output_file, szNumber, NULL,
 
3248
            ret1a = sprintf( szNumber, "Structure #%ld", num_inp );
 
3249
            ret2a = WriteOrigAtomDataToSDfile( orig_inp_data, output_file, szNumber, NULL,
3113
3250
                (sd->bChiralFlag & FLAG_INP_AT_CHIRAL)? 1:0,
3114
3251
                (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ATOMS_DT)? 1:0, ip->pSdfLabel, ip->pSdfValue );
3115
3252
            goto exit_function;
3347
3484
/************************************************************************************************/
3348
3485
int CreateOneStructureINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
3349
3486
                         PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], int iINChI,
3350
 
                         FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
 
3487
                         FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, 
 
3488
                         FILE *prb_file, /*^^^ was: INCHI_FILE */
3351
3489
                         ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data,
3352
3490
                         COMP_ATOM_DATA composite_norm_data2[][TAUT_NUM+1],
3353
3491
                         long num_inp, char *pStr, int nStrLen, NORM_CANON_FLAGS *pncFlags )
3754
3892
            }
3755
3893
#ifndef INCHI_LIB
3756
3894
            err = DisplayStructure( inp_cur_data->at, inp_cur_data->num_at,
3757
 
                                    0, 0, NULL, 1/*isotopic*/, 0/*taut*/, NULL, NULL,
 
3895
                                    0, 1, 0, NULL, 1/*isotopic*/, 0/*taut*/, NULL, NULL,
3758
3896
                                    ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
3759
3897
            sd->bUserQuitComponentDisplay = (err==ESC_KEY);
3760
3898
            if ( !err ) {
 
3899
#if( !defined(BUILD_CINCHI_WITH_INCHIKEY) )
3761
3900
                my_fprintf( stderr, "Cannot display the structure\n");
 
3901
#endif
3762
3902
            }
3763
3903
#else
3764
3904
            if(DRAWDATA && DRAWDATA_EXISTS)
3766
3906
                struct DrawData vDrawData;
3767
3907
                int    nType = COMPONENT_ORIGINAL;
3768
3908
                vDrawData.pWindowData = CreateWinData_( inp_cur_data->at, inp_cur_data->num_at,
3769
 
                                                        0, 0, NULL,
 
3909
                                                        0, 1 /* bAdd_DT_to_num_H */, 0, NULL,
3770
3910
                                                        1 /* display isotopic if present */, 0, NULL, NULL,
3771
3911
                                                        ip->bAbcNumbers, &ip->dp, ip->nMode );
3772
3912
                if( vDrawData.pWindowData != NULL )
3888
4028
                                continue;
3889
4029
                            if ( bFixedBondsTaut ) {
3890
4030
                                err = DisplayStructure( inp_norm_data[j]->at_fixed_bonds, inp_norm_data[j]->num_at,
3891
 
                                                        inp_norm_data[j]->num_removed_H,
 
4031
                                                        inp_norm_data[j]->num_removed_H, 0 /*bAdd_DT_to_num_H*/,
3892
4032
                                                        inp_norm_data[j]->nNumRemovedProtons,
3893
4033
                                                        inp_norm_data[j]->nNumRemovedProtonsIsotopic,
3894
4034
                                                        bHasIsotopicLayer, j, NULL,  NULL,
3895
4035
                                                        ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
3896
4036
                            } else {
3897
4037
                                err = DisplayStructure( inp_norm_data[j]->at, inp_norm_data[j]->num_at,
3898
 
                                                        0, 0, NULL,
 
4038
                                                        0, 0 /*bAdd_DT_to_num_H*/, 0, NULL,
3899
4039
                                                        k, j, pINChI[i], pINChI_Aux[i],
3900
4040
                                                        ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
3901
4041
                            }
3907
4047
                            {
3908
4048
                                struct DrawData vDrawData;
3909
4049
                                vDrawData.pWindowData = CreateWinData_( inp_norm_data[j]->at, inp_norm_data[j]->num_at,
3910
 
                                                        0, 0, NULL,
 
4050
                                                        0, 0 /* bAdd_DT_to_num_H */, 0, NULL,
3911
4051
                                                        k, j, pINChI[i], pINChI_Aux[i],
3912
4052
                                                        ip->bAbcNumbers, &ip->dp, ip->nMode );
3913
4053
                                if( vDrawData.pWindowData != NULL )
3935
4075
                                    vDrawData.pWindowData =
3936
4076
                                         CreateWinData_( inp_norm_data[j]->at_fixed_bonds, inp_norm_data[j]->num_at,
3937
4077
                                                         inp_norm_data[j]->num_removed_H,
 
4078
                                                         0 /* bAdd_DT_to_num_H */,
3938
4079
                                                         inp_norm_data[j]->nNumRemovedProtons,
3939
4080
                                                         inp_norm_data[j]->nNumRemovedProtonsIsotopic,
3940
4081
                                                         k, j, NULL, NULL,
4249
4390
    return ret;
4250
4391
}
4251
4392
#endif /* } INCHI_ANSI_ONLY */
 
4393
 
 
4394