rino 0.1.0 → 0.2.0

data/ext/src/mol2atom.h

@@ -0,0 +1,31 @@
+/*
+ * International Union of Pure and Applied Chemistry (IUPAC)
+ * International Chemical Identifier (InChI)
+ * Version 1
+ * Software version 1.01
+ * July 21, 2006
+ * Developed at NIST
+ */
+
+#ifndef __MOL2ATOM_H__
+#define __MOL2ATOM_H__
+
+#include "readmol.h"
+
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+extern "C" {
+#endif
+#endif
+
+void calculate_valences (MOL_DATA* mol_data, inp_ATOM* at, int *num_atoms, int bDoNotAddH, int *err, char *pStrErr);
+/* void WriteCoord( char *str, double x );*/
+
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+}
+#endif
+#endif
+
+
+#endif  /* __MOL2ATOM_H__ */

data/ext/src/readinch.c

@@ -0,0 +1,239 @@
+/*
+ * 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 <stdio.h>
+#include <stdlib.h>
+#include <limits.h>
+#include <math.h>
+#include <float.h>
+#include <string.h>
+#include <ctype.h>
+
+#include "mode.h"
+
+#include "inpdef.h"
+#include "util.h"
+#include "readmol.h"
+
+#include "ichicomp.h"
+#include "ichierr.h"
+#include "extr_ct.h"
+
+#define NO_ATOM          (-1) /* non-existent (central) atom */
+
+#define SB_PARITY_FLAG  0x38 /* disconnected structure has undef. parity */
+#define SB_PARITY_SHFT  3
+#define SB_PARITY_MASK  0x07
+#define SB_PARITY_1(X) (X & SB_PARITY_MASK)  /* refers to connected structure */
+#define SB_PARITY_2(X) (((X) >> SB_PARITY_SHFT) & SB_PARITY_MASK) /* refers to connected structure */
+
+/* 0D parity types */
+typedef enum tagINCHIStereoType0D {
+   INCHI_StereoType_None        = 0,
+   INCHI_StereoType_DoubleBond  = 1,
+   INCHI_StereoType_Tetrahedral = 2,
+   INCHI_StereoType_Allene      = 3
+} inchi_StereoType0D;
+
+/* 0D parities */
+typedef enum tagINCHIStereoParity0D {
+   INCHI_PARITY_NONE      = AB_PARITY_NONE,
+   INCHI_PARITY_ODD       = AB_PARITY_ODD ,  /* 'o' */
+   INCHI_PARITY_EVEN      = AB_PARITY_EVEN,  /* 'e' */
+   INCHI_PARITY_UNKNOWN   = AB_PARITY_UNKN,  /* 'u' */
+   INCHI_PARITY_UNDEFINED = AB_PARITY_UNDF   /* '?' -- should not be used; however, see Note above */
+} inchi_StereoParity0D;
+
+/* bond type definitions */
+typedef enum tagINCHIBondType {
+   INCHI_BOND_TYPE_NONE    =  0,
+   INCHI_BOND_TYPE_SINGLE  =  BOND_TYPE_SINGLE,
+   INCHI_BOND_TYPE_DOUBLE  =  BOND_TYPE_DOUBLE,
+   INCHI_BOND_TYPE_TRIPLE  =  BOND_TYPE_TRIPLE,
+   INCHI_BOND_TYPE_ALTERN  =  BOND_TYPE_ALTERN
+} inchi_BondType;
+
+/* 2D stereo definitions */
+typedef enum tagINCHIBondStereo2D {
+   /* stereocenter-related; positive: the sharp end points to this atom  */
+   INCHI_BOND_STEREO_NONE           =  0,
+   INCHI_BOND_STEREO_SINGLE_1UP     =  STEREO_SNGL_UP,
+   INCHI_BOND_STEREO_SINGLE_1EITHER =  STEREO_SNGL_EITHER,
+   INCHI_BOND_STEREO_SINGLE_1DOWN   =  STEREO_SNGL_DOWN,
+   /* stereocenter-related; negative: the sharp end points to the opposite atom  */
+   INCHI_BOND_STEREO_SINGLE_2UP     = -STEREO_SNGL_UP,
+   INCHI_BOND_STEREO_SINGLE_2EITHER = -STEREO_SNGL_EITHER,
+   INCHI_BOND_STEREO_SINGLE_2DOWN   = -STEREO_SNGL_DOWN,
+   /* stereobond-related */
+   INCHI_BOND_STEREO_DOUBLE_EITHER  =  STEREO_DBLE_EITHER
+} inchi_BondStereo2D;
+
+/****************************************************************************/
+typedef struct tagINCHIStereo0D {
+    S_SHORT  neighbor[4];    /* 4 atoms always */
+    S_SHORT  central_atom;   /* central tetrahedral atom or a central */
+                            /* atom of allene; otherwise NO_ATOM */
+    S_CHAR  type;           /* inchi_StereoType0D */
+    S_CHAR  parity;         /* inchi_StereoParity0D: may be a combination of two parities: */
+                            /* ParityOfConnected | (ParityOfDisconnected << 3), see Note above */
+}inchi_Stereo0D;
+/****************************************************************************/
+
+/* This contains executable code. Included in lReadAux.c, e_ReadINCH.c, ReadINCH.c,  */
+#include "aux2atom.h"
+
+
+int INChIToOrigAtom( FILE *inp_molfile, ORIG_ATOM_DATA *orig_at_data, int bMergeAllInputStructures,
+                       int bGetOrigCoord, int bDoNotAddH, INPUT_TYPE nInputType,
+                       char *pSdfLabel, char *pSdfValue, long *lSdfId,
+                       INCHI_MODE *pInpAtomFlags, int *err, char *pStrErr )
+{
+    /* inp_ATOM       *at = NULL; */
+    int            num_dimensions_new;
+    int            num_inp_bonds_new;
+    int            num_inp_atoms_new;
+    inp_ATOM      *at_new     = NULL;
+    inp_ATOM      *at_old     = NULL;
+    int            nNumAtoms  = 0;
+    MOL_COORD     *szCoordNew = NULL;
+    MOL_COORD     *szCoordOld = NULL;
+    int            i, j;
+
+    if ( pStrErr ) {
+        pStrErr[0] = '\0';
+    }
+
+    /*FreeOrigAtData( orig_at_data );*/
+    if ( lSdfId )
+        *lSdfId = 0;
+    do {
+        
+        at_old     = orig_at_data? orig_at_data->at      : NULL; /*  save pointer to the previous allocation */
+        szCoordOld = orig_at_data? orig_at_data->szCoord : NULL;
+        num_inp_atoms_new =
+            INChIToInpAtom( inp_molfile, (bGetOrigCoord && orig_at_data)? &szCoordNew : NULL,
+                          bDoNotAddH, nInputType, orig_at_data? &at_new:NULL,
+                          MAX_ATOMS,
+                          &num_dimensions_new, &num_inp_bonds_new,
+                          pSdfLabel, pSdfValue, lSdfId, pInpAtomFlags, err, pStrErr );
+        if ( num_inp_atoms_new <= 0 && !*err ) {
+            MOLFILE_ERR_SET (*err, 0, "Empty structure");
+            *err = 98;
+        } else
+        if ( orig_at_data && !num_inp_atoms_new && 10 < *err && *err < 20 && orig_at_data->num_inp_atoms > 0 && bMergeAllInputStructures ) {
+            *err = 0; /* end of file */
+            break;
+        } else
+        if ( num_inp_atoms_new > 0 && orig_at_data ) {
+            /*  merge pOrigDataTmp + orig_at_data => pOrigDataTmp; */
+            nNumAtoms = num_inp_atoms_new + orig_at_data->num_inp_atoms;
+            if ( nNumAtoms >= MAX_ATOMS ) {
+                MOLFILE_ERR_SET (*err, 0, "Too many atoms");
+                *err = 70;
+                orig_at_data->num_inp_atoms = -1;
+            } else
+            if ( !at_old ) {
+                /* the first structure */
+                orig_at_data->at      = at_new;
+                orig_at_data->szCoord = szCoordNew; 
+                at_new = NULL;
+                szCoordNew = NULL;
+                orig_at_data->num_inp_atoms  = num_inp_atoms_new;
+                orig_at_data->num_inp_bonds  = num_inp_bonds_new;
+                orig_at_data->num_dimensions = num_dimensions_new;
+            } else
+            if ( (orig_at_data->at = ( inp_ATOM* ) inchi_calloc( nNumAtoms, sizeof(inp_ATOM) )) &&
+                  (!szCoordNew || (orig_at_data->szCoord = (MOL_COORD *) inchi_calloc( nNumAtoms, sizeof(MOL_COORD) ))) ) {
+                /*  switch at_new <--> orig_at_data->at; */
+                if ( orig_at_data->num_inp_atoms ) {
+                    memcpy( orig_at_data->at, at_old, orig_at_data->num_inp_atoms * sizeof(orig_at_data->at[0]) );
+                    /*  adjust numbering in the newly read structure */
+                    for ( i = 0; i < num_inp_atoms_new; i ++ ) {
+                        for ( j = 0; j < at_new[i].valence; j ++ ) {
+                            at_new[i].neighbor[j] += orig_at_data->num_inp_atoms;
+                        }
+                        at_new[i].orig_at_number += orig_at_data->num_inp_atoms; /* 12-19-2003 */
+                    }
+                    if ( orig_at_data->szCoord && szCoordOld ) {
+                        memcpy( orig_at_data->szCoord, szCoordOld, orig_at_data->num_inp_atoms * sizeof(MOL_COORD) );
+                    }
+                }
+                if ( at_old ) {
+                    inchi_free( at_old );
+                    at_old = NULL;
+                }
+                if ( szCoordOld ) {
+                    inchi_free( szCoordOld );
+                    szCoordOld = NULL;
+                }
+                /*  copy newly read structure */
+                memcpy( orig_at_data->at + orig_at_data->num_inp_atoms,
+                        at_new,
+                        num_inp_atoms_new * sizeof(orig_at_data->at[0]) );
+                if ( orig_at_data->szCoord && szCoordNew ) {
+                    memcpy( orig_at_data->szCoord + orig_at_data->num_inp_atoms,
+                            szCoordNew,
+                            num_inp_atoms_new * sizeof(MOL_COORD) );
+                }
+                /*  add other things */
+                orig_at_data->num_inp_atoms += num_inp_atoms_new;
+                orig_at_data->num_inp_bonds += num_inp_bonds_new;
+                orig_at_data->num_dimensions = inchi_max(num_dimensions_new, orig_at_data->num_dimensions);
+            } else {
+                MOLFILE_ERR_SET (*err, 0, "Out of RAM");
+                *err = -1;
+            }
+        } else
+        if ( num_inp_atoms_new > 0 ) {
+            nNumAtoms += num_inp_atoms_new;
+        }
+        if ( at_new ) {
+            inchi_free( at_new );
+            at_new = NULL;
+        }
+
+    } while ( !*err && bMergeAllInputStructures );
+    /*
+    if ( !*err ) {
+        orig_at_data->num_components =
+            MarkDisconnectedComponents( orig_at_data );
+        if ( orig_at_data->num_components == 0 ) {
+            MOLFILE_ERR_SET (*err, 0, "No components found");
+            *err = 99;
+        }
+        if ( orig_at_data->num_components < 0 ) {
+            MOLFILE_ERR_SET (*err, 0, "Too many components");
+            *err = 99;
+        }
+    }
+    */
+    if ( szCoordNew ) {
+        inchi_free( szCoordNew );
+    }
+    if ( at_new ) {
+        inchi_free( at_new );
+    }
+    if ( !*err && orig_at_data ) { /* added testing (orig_at_data != NULL) */
+        if ( ReconcileAllCmlBondParities( orig_at_data->at, orig_at_data->num_inp_atoms, 0 ) ) {
+            MOLFILE_ERR_SET (*err, 0, "Cannot reconcile stereobond parities");  /*   <BRKPT> */
+            if (!orig_at_data->num_dimensions) {
+                *err = 1;
+            }
+        }
+    }
+    if ( *err ) {
+        FreeOrigAtData( orig_at_data );
+    }
+    if ( *err && !(10 < *err && *err < 20) && pStrErr && !pStrErr[0] ) {
+        MOLFILE_ERR_SET (*err, 0, "Unknown error");  /*   <BRKPT> */
+    }
+    return orig_at_data? orig_at_data->num_inp_atoms : nNumAtoms;
+}
+
+

data/ext/src/readmol.c

@@ -0,0 +1,28 @@
+/*
+ * 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 <stdio.h>
+#include <stdlib.h>
+#include <limits.h>
+#include <math.h>
+#include <float.h>
+#include <string.h>
+#include <ctype.h>
+
+#include "mode.h"
+
+#include "comdef.h"
+#include "util.h"
+#include "readmol.h"
+
+#include "ichicomp.h"
+#include "inpdef.h"
+
+
+#include "lreadmol.h"

data/ext/src/{e_readmol.h → readmol.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
  */
 
@@ -77,7 +77,7 @@ typedef struct tagMOL_ATOM {
     double   fY;                       /* F10.5;       Generic */
     double   fZ;                       /* F10.5;       Generic */
     char     szAtomSymbol[6];          /* aaa;         Generic */ /* changed from 4 to 6 to match STDATA */
-    S_SHORT  cMassDifference;   /* dd;  (M_ISO) Generic: -3..+4 otherwise 0 or 127=most abund. isotope */
+    S_CHAR   cMassDifference;   /* dd;  (M_ISO) Generic: -3..+4 otherwise 0 or 127=most abund. isotope */
     S_CHAR   cCharge;           /* ccc; (M CHG), Generic: 1=+3,2=+2,3=+1,4=doublet,5=-1,6=-2,7=-3 */
     char     cRadical;                 /*      (M RAD) */
     char     cStereoParity;            /* sss;         Generic */
@@ -128,8 +128,8 @@ typedef struct tagMOL_BONDS {
 /****************************************************************************/
 typedef struct tagMOL_CTAB {
     /* Line #1: Counts line */
-    short nNumberOfAtoms;                  /* aaa; <= 999; Generic */
-    short nNumberOfBonds;                  /* bbb; <= 999; Generic */
+    short nNumberOfAtoms;                  /* aaa; <= 255; Generic */
+    short nNumberOfBonds;                  /* bbb; <= 255; Generic */
 #if ( MOL_QUERY == MOL_PRESENT )
     short nNumberOfAtomsLists;              /* lll; <=  30; Query   */
 #endif
@@ -162,15 +162,13 @@ extern "C" {
 #endif
 
 
-MOL_DATA* e_delete_mol_data( MOL_DATA* mol_data );
-
-MOL_DATA* e_read_sdfile_segment(FILE* inp, MOL_HEADER_BLOCK *OnlyHeaderBlock, MOL_CTAB *OnlyCtab,
+MOL_DATA* delete_mol_data( MOL_DATA* mol_data );
+MOL_DATA* read_sdfile_segment(FILE* inp, MOL_HEADER_BLOCK *OnlyHeaderBlock, MOL_CTAB *OnlyCtab,
                               int bGetOrigCoord,
                               char *pname, int lname,
                               long *Id, const char *pSdfLabel, char *pSdfValue,
                               int *err, char *pStrErr );
 
-
 #ifndef INCHI_ALL_CPP
 #ifdef __cplusplus
 }

data/ext/src/runichi.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
  */
 
@@ -58,7 +58,7 @@
 int GetProcessingWarningsOneINChI(INChI *pINChI, INP_ATOM_DATA *inp_norm_data, char *pStrErrStruct);
 int  GetProcessingWarnings(INChI *cur_INChI[], INP_ATOM_DATA **inp_norm_data, STRUCT_DATA *sd);
 int DisplayTheWholeStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, FILE *inp_file, INCHI_FILE *log_file,
-                              ORIG_ATOM_DATA *orig_inp_data, int num_inp, int iINChI, int bShowStruct, int bINCHI_LIB_Flag );
+                              ORIG_ATOM_DATA *orig_inp_data, long num_inp, int iINChI, int bShowStruct, int bINCHI_LIB_Flag );
 int DuplicateOrigAtom( ORIG_ATOM_DATA *new_orig_atom, ORIG_ATOM_DATA *orig_atom );
 int bCheckUnusualValences( ORIG_ATOM_DATA *orig_at_data, int bAddIsoH,  char *pStrErrStruct );
 int CreateCompositeNormAtom( COMP_ATOM_DATA *composite_norm_data, INP_ATOM_DATA2 *all_inp_norm_data,
@@ -86,7 +86,7 @@ typedef struct tagRenumbData {
     PINChI_Aux2     ren_INChI_Aux[1];
     INP_ATOM_DATA  orig_inp_cur_data;
     INP_ATOM_DATA  saved_inp_cur_data;
-#if( TEST_RENUMB_ATOMS_SAVE_LONGEST == 1 )
+#if( TEST_RENUMB_ATOMS_SAVE_LONGEST == 1 || TEST_RENUMB_SWITCH == 1 )
     INP_ATOM_DATA  longest_inp_cur_data;
 #endif
     INP_ATOM_DATA  ren_inp_norm_data1, ren_inp_norm_data2;
@@ -108,11 +108,11 @@ int RenumberingTestUninit( RENUMB_DATA *pRenumbData );
 int RenumberingTest( PINChI2 *pICh, PINChI_Aux2 *pINChI_Aux, ORIG_ATOM_DATA *orig_inp_data, int iINChI,
                      RENUMB_DATA *pRenumbData, INP_ATOM_DATA *inp_cur_data, INP_ATOM_DATA **inp_norm_data,
                      STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, INCHI_FILE *log_file, INCHI_FILE *prb_file,
-                     int i, int num_inp, NORM_CANON_FLAGS *pncFlags);
+                     int i, long num_inp, NORM_CANON_FLAGS *pncFlags);
 /*
 int RenumberingTest( INChI *pINChI[][TAUT_NUM], INChI_Aux *pINChI_Aux[][TAUT_NUM], int iINChI,
                      RENUMB_DATA *pRenumbData, INP_ATOM_DATA *inp_cur_data, INP_ATOM_DATA **inp_norm_data,
-                     STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, INCHI_FILE *log_file, int i, int num_inp);
+                     STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, INCHI_FILE *log_file, int i, long num_inp);
 */
 #endif /* } TEST_RENUMB_ATOMS */
 
@@ -416,7 +416,7 @@ int inchi_print( INCHI_FILE* f, const char* lpszFormat, ... )
     } else {
         /* printf( "\r" ); */
         my_va_start( argList, lpszFormat );
-        //ret2 = vfprintf( stdout, lpszFormat, argList );
+        ret2 = vfprintf( stdout, lpszFormat, argList );
         /* ret2 = vprintf( lpszFormat, argList ); */
         va_end( argList );
     }
@@ -508,8 +508,10 @@ int inchi_print_nodisplay( INCHI_FILE* f, const char* lpszFormat, ... )
 int my_fprintf( INCHI_FILE* f, const char* lpszFormat, ... )
 {
     if ( f ) {
-        int ret=0, max_len;
+        int ret=0, max_len, nAddLength = 0;
+        char *new_str = NULL;
         va_list argList;
+
         my_va_start( argList, lpszFormat );
         max_len = GetMaxPrintfLength( lpszFormat, argList);
         va_end( argList );
@@ -517,8 +519,8 @@ int my_fprintf( INCHI_FILE* f, const char* lpszFormat, ... )
         if ( max_len >= 0 ) {
             if ( f->nAllocatedLength - f->nUsedLength <= max_len ) {
                 /* enlarge output string */
-                int  nAddLength = inchi_max( INCHI_ADD_STR_LEN, max_len );
-                char *new_str = (char *)inchi_calloc( f->nAllocatedLength + nAddLength, sizeof(new_str[0]) );
+                nAddLength = inchi_max( INCHI_ADD_STR_LEN, max_len );
+                new_str = (char *)inchi_calloc( f->nAllocatedLength + nAddLength, sizeof(new_str[0]) );
                 if ( new_str ) {
                     if ( f->pStr ) {
                         if ( f->nUsedLength > 0 ) {
@@ -577,9 +579,9 @@ int my_fprintf( INCHI_FILE* f, const char* lpszFormat, ... )
             va_end( argList );
         }
     }
-    if ( f != stderr ) {
+    if ( f && f != stderr ) { /* disabled stderr output in case f == NULL. 11-23-2005 */
         my_va_start( argList, lpszFormat );
-        //ret2 = vfprintf( stderr, lpszFormat, argList );
+        ret2 = vfprintf( stderr, lpszFormat, argList );
         va_end( argList );
     }
 #else
@@ -603,8 +605,9 @@ void FillTableParms( SET_DRAW_PARMS *sdp, INChI **cur_INChI, INChI_Aux **cur_INC
     int  i, j;
     INChI_Stereo *Stereo;
     int          bShowTaut = (cur_INChI && cur_INChI[indx]->lenTautomer > 0)? 1 : 0;
+#if( REL_RAC_STEREO_IGN_1_SC == 1 )
     int bRelRac = 0 != (nMode & (REQ_MODE_RELATIVE_STEREO | REQ_MODE_RACEMIC_STEREO ));
-
+#endif
     if ( !cur_INChI || !cur_INChI_Aux ) {
         sdp->tdp->bDrawTbl = 0;
         sdp->bOrigAtom     = 1;
@@ -743,7 +746,7 @@ void FillCompositeTableParms( SET_DRAW_PARMS *sdp, AT_NUMB StereoFlags,
 #ifndef INCHI_ANSI_ONLY
 #ifndef INCHI_LIB
 /*******************************************************************/
-int DisplayStructure( inp_ATOM *at, int num_at, int num_removed_H,
+int DisplayStructure( inp_ATOM *at, int num_at, int num_removed_H, int bAdd_DT_to_num_H,
                       int nNumRemovedProtons, NUM_H *nNumRemovedProtonsIsotopic,
                       int bIsotopic, int j /*bTautomeric*/,
                       INChI **cur_INChI, INChI_Aux **cur_INChI_Aux,
@@ -753,8 +756,8 @@ int DisplayStructure( inp_ATOM *at, int num_at, int num_removed_H,
     int err = -1;
     if ( CreateInfoAtomData( &inf_data, num_at, 1 ) ) {
         err = 0;
-        FillOutInfAtom( at, &inf_data, num_at, num_removed_H, nNumRemovedProtons,
-                        nNumRemovedProtonsIsotopic, bIsotopic,
+        FillOutInfAtom( at, &inf_data, num_at, num_removed_H, bAdd_DT_to_num_H,
+                        nNumRemovedProtons, nNumRemovedProtonsIsotopic, bIsotopic,
                         cur_INChI?cur_INChI[j]:NULL,
                         cur_INChI_Aux?cur_INChI_Aux[j]:NULL, bAbcNumbers, nMode);
         FillTableParms( &dp->sdp, cur_INChI, cur_INChI_Aux, nMode, bIsotopic, j );
@@ -783,7 +786,7 @@ int DisplayCompositeStructure( COMP_ATOM_DATA *composite_norm_data, int bIsotopi
         if ( bTautomeric == TAUT_INI ) {
             /*
             FillOutInfAtom( (composite_norm_data+bTautomeric)->at, &inf_data, (composite_norm_data+bTautomeric)->num_at,
-                            (composite_norm_data+bTautomeric)->num_removed_H,
+                            (composite_norm_data+bTautomeric)->num_removed_H, bAdd_DT_to_num_H,
                             (composite_norm_data+bTautomeric)->nNumRemovedProtons,
                             (composite_norm_data+bTautomeric)->nNumRemovedProtonsIsotopic, bIsotopic,
                             NULL, NULL, bAbcNumbers, nMode);
@@ -835,9 +838,11 @@ const char *ErrMsg( int nErrorCode )
         case CT_CALC_STEREO_ERR:     p = "CALC_STEREO_ERR";       break;
         case CT_STEREO_CANON_ERR:    p = "STEREO_CANON_ERR";      break;
         case CT_CANON_ERR:           p = "CANON_ERR";             break;
+        case CT_WRONG_FORMULA:       p = "Wrong or missing chemical formula";  break;
         /*case CT_CANON_ERR2:          p = "CT_CANON_ERR2";         break;*/
         case CT_UNKNOWN_ERR:         p = "UNKNOWN_ERR";           break;
-        case BNS_RADICAL_ERR:        p = "Cannot process free radical center";      break;
+        case BNS_RADICAL_ERR:        p = "Cannot process free radical center"; break;
+        case BNS_ALTBOND_ERR:        p = "Cannot process aromatic bonds";      break;
 
         default:
             if ( nErrorCode > CT_UNKNOWN_ERR ) {
@@ -970,7 +975,7 @@ int SaveEquComponentsInfoAndSortOrder ( int iINChI, INCHI_SORT *pINChISort[TAUT_
 }
 
 /************************************************************************************************/
-int DisplayTheWholeCompositeStructure( INPUT_PARMS *ip, STRUCT_DATA *sd, int num_inp, int iINChI,
+int DisplayTheWholeCompositeStructure( INPUT_PARMS *ip, STRUCT_DATA *sd, long num_inp, int iINChI,
                                        PINChI2 *pINChI2, PINChI_Aux2 *pINChI_Aux2,
                                        ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data,
                                        COMP_ATOM_DATA composite_norm_data[TAUT_NUM+1] )
@@ -1021,7 +1026,7 @@ int DisplayTheWholeCompositeStructure( INPUT_PARMS *ip, STRUCT_DATA *sd, int num
             for ( k = 0; k <= composite_norm_data[j].bHasIsotopicLayer && !sd->bUserQuitComponentDisplay; k ++ ) {
                 /*  added number of components, added another format for a single component case - DCh */
                 int bMobileH = (bDisplayTaut>0 && nNumTautComponents);
-                sprintf( szTitle, "%s Structure #%d%s%s.%s%s%s%s%s",
+                sprintf( szTitle, "%s Structure #%ld%s%s.%s%s%s%s%s",
                               j == TAUT_INI? "Preprocessed":"Result for", num_inp,
                               bMobileH? ", mobile H":
                               bDisplayTaut==0?", fixed H":"",
@@ -1050,7 +1055,7 @@ int DisplayTheWholeCompositeStructure( INPUT_PARMS *ip, STRUCT_DATA *sd, int num
                     int             bDisplaySaved = ip->bDisplay;
                     /****** Display Equ Sets of composite Result structure **************/
                     for ( nEquSet = 1; nEquSet <= inp_data->nNumEquSets; nEquSet ++ ) {
-                        sprintf( szTitle, "Equ set %d of %d, %s Structure #%d%s%s.%s%s%s%s%s",
+                        sprintf( szTitle, "Equ set %d of %d, %s Structure #%ld%s%s.%s%s%s%s%s",
                                       nEquSet, inp_data->nNumEquSets,
                                       j == TAUT_INI? "Preprocessed":"Result for",
                                       num_inp,
@@ -1178,7 +1183,7 @@ int DisplayTheWholeCompositeStructure( INPUT_PARMS *ip, STRUCT_DATA *sd, int num
 /*                  num_components[INCHI_BAS] > 0 if there was input structure      */
 /***********************************************************************************/
 /* pINChI[INCHI_REC] refers to the reconnected structure,                            */
-/*                  and only if the inpur structure has been disconnected, that is,*/
+/*                  and only if the input structure has been disconnected, that is,*/
 /*                  num_components[INCHI_REC] > 0                                   */
 /***********************************************************************************/
 int SortAndPrintINChI( INCHI_FILE *output_file, char *pStr, int nStrLen, INCHI_FILE *log_file,
@@ -1187,7 +1192,7 @@ int SortAndPrintINChI( INCHI_FILE *output_file, char *pStr, int nStrLen, INCHI_F
                       ORIG_STRUCT *pOrigStruct, int num_components[INCHI_NUM],
                       int num_non_taut[INCHI_NUM], int num_taut[INCHI_NUM],
                       INCHI_MODE bTautFlags[INCHI_NUM], INCHI_MODE bTautFlagsDone[INCHI_NUM],
-                      NORM_CANON_FLAGS *pncFlags, int num_inp,
+                      NORM_CANON_FLAGS *pncFlags, long num_inp,
                       PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM], int *pSortPrintINChIFlags )
 {
     INCHI_SORT *pINChISort[INCHI_NUM][TAUT_NUM];
@@ -1195,7 +1200,11 @@ int SortAndPrintINChI( INCHI_FILE *output_file, char *pStr, int nStrLen, INCHI_F
     INCHI_MODE nMode;
     int       bDisconnectedCoord = (0 != (bTautFlagsDone[0] & TG_FLAG_DISCONNECT_COORD_DONE));
     int bINChIOutputOptions0, bCurOption, bINChIOutputOptionsCur, bEmbedReconnected, bAnnInXmlBrackets;
-    static char szAnnHdr[] = "InChI ANNOTATED CONTENTS";
+#if( SPECIAL_BUILD == 1 )
+    static const char szAnnHdr[] = "MoChI ANNOTATED CONTENTS";
+#else
+    static const char szAnnHdr[] = "InChI ANNOTATED CONTENTS";
+#endif
 
     ret = 1;
     for ( i = 0; i < INCHI_NUM; i ++ ) {
@@ -1225,7 +1234,7 @@ int SortAndPrintINChI( INCHI_FILE *output_file, char *pStr, int nStrLen, INCHI_F
             }
         } else {
             for ( k1 = 0; k1 < TAUT_NUM; k1 ++ ) {
-                pINChISort[j][k1] = NULL;
+                pINChISort[j][k1] = NULL; /* keep BC happy */
             }
         }
     }
@@ -1284,83 +1293,115 @@ int SortAndPrintINChI( INCHI_FILE *output_file, char *pStr, int nStrLen, INCHI_F
         }
 #endif
     }
-
-    bINChIOutputOptions0 = ip->bINChIOutputOptions &
-                                         ~(INCHI_OUT_EMBED_REC |
-                                           INCHI_OUT_XML |
-                                           INCHI_OUT_PLAIN_TEXT |
-                                           INCHI_OUT_PLAIN_TEXT_COMMENTS |
-                                           INCHI_OUT_XML_TEXT_COMMENTS);
-    bEmbedReconnected    = ip->bINChIOutputOptions & INCHI_OUT_EMBED_REC;
-
-    for ( i = 0; i < 4; i ++ ) {
-        switch( i ) {
-        case 0:
-            bCurOption = INCHI_OUT_XML;
-            break;
-        case 1:
-            bCurOption = INCHI_OUT_PLAIN_TEXT;
-            break;
-        case 2:
-            bCurOption = INCHI_OUT_PLAIN_TEXT_COMMENTS;
-            break;
-        case 3:
-            bCurOption = INCHI_OUT_XML_TEXT_COMMENTS;
-            break;
-        default:
-            continue;
-        }
-        if ( ip->bINChIOutputOptions & bCurOption ) {
-            bAnnInXmlBrackets = 0;
-            if ( i == 1 ) {
-                ;/*bEmbedReconnected = 0;*/
+    
+    if ( !( ip->bINChIOutputOptions & INCHI_OUT_PRINT_OPTIONS ) ) {
+        /* prepare InChI from the structures obtained by reversing InChI for returning to the caller */
+        for ( j = 0; j < INCHI_NUM; j ++ ) {
+            if ( !num_components[j] ) {
+                continue;
             }
-            if ( i == 3 ) {
-                bCurOption = INCHI_OUT_XML; /* xml output as annotation */
+            /* pINChI[iINCHI][iComponent][bTaut] */
+            /* j  = disconnected/connected */
+            /* k1 = sort order for Mobile or Fixed H */
+            k1 = TAUT_YES; /* in Mobile H order */
+            /* store components in Mobile H order */
+            
+            for ( i = 0; i < num_components[j]; i ++ ) {
+
+                if ( pINChISort[j][k1][i].pINChI[TAUT_NON] &&
+                    !pINChISort[j][k1][i].pINChI[TAUT_YES] ) {
+                    /* make sure Mobile-H is always present */
+                    for ( k = 0; k < TAUT_NUM; k ++ ) {
+                        pINChI[j][i][k]     = pINChISort[j][k1][i].pINChI[ALT_TAUT(k)];
+                        pINChI_Aux[j][i][k] = pINChISort[j][k1][i].pINChI_Aux[ALT_TAUT(k)];
+                    }
+                } else {
+
+                    for ( k = 0; k < TAUT_NUM; k ++ ) {
+                        pINChI[j][i][k]     = pINChISort[j][k1][i].pINChI[k];
+                        pINChI_Aux[j][i][k] = pINChISort[j][k1][i].pINChI_Aux[k];
+                    }
+                }
             }
-            bINChIOutputOptionsCur = bINChIOutputOptions0 | bCurOption;
-            switch ( i ) {
+        }
+
+    } else {
+        
+        /* print inchi string(s) */
+
+        bINChIOutputOptions0 = ip->bINChIOutputOptions & ~INCHI_OUT_PRINT_OPTIONS;
+
+        bEmbedReconnected    = ip->bINChIOutputOptions & INCHI_OUT_EMBED_REC;
+
+        for ( i = 0; i < 4; i ++ ) {
+            switch( i ) {
             case 0:
+                bCurOption = INCHI_OUT_XML;
+                break;
             case 1:
-                /* output INChI */
-                bINChIOutputOptionsCur |= bEmbedReconnected;
+                bCurOption = INCHI_OUT_PLAIN_TEXT;
                 break;
             case 2:
+                bCurOption = INCHI_OUT_PLAIN_TEXT_COMMENTS;
+                break;
             case 3:
-                /* output annotation */
-                bAnnInXmlBrackets = (i == 2 && (ip->bINChIOutputOptions & INCHI_OUT_XML ));
-                if ( bAnnInXmlBrackets ) {
-                    inchi_print( output_file, "\n<%s>\n", szAnnHdr );
-                } else {
-                    inchi_print( output_file, "\n==== %s ====\n", szAnnHdr );
-                }
-                bINChIOutputOptionsCur |= bEmbedReconnected;
-                bINChIOutputOptionsCur &= ~INCHI_OUT_TABBED_OUTPUT;
+                bCurOption = INCHI_OUT_XML_TEXT_COMMENTS;
                 break;
             default:
                 continue;
             }
+            if ( ip->bINChIOutputOptions & bCurOption ) {
+                bAnnInXmlBrackets = 0;
+                if ( i == 1 ) {
+                    ;/*bEmbedReconnected = 0;*/
+                }
+                if ( i == 3 ) {
+                    bCurOption = INCHI_OUT_XML; /* xml output as annotation */
+                }
+                bINChIOutputOptionsCur = bINChIOutputOptions0 | bCurOption;
+                switch ( i ) {
+                case 0:
+                case 1:
+                    /* output INChI */
+                    bINChIOutputOptionsCur |= bEmbedReconnected;
+                    break;
+                case 2:
+                case 3:
+                    /* output annotation */
+                    bAnnInXmlBrackets = (i == 2 && (ip->bINChIOutputOptions & INCHI_OUT_XML ));
+                    if ( bAnnInXmlBrackets ) {
+                        inchi_print( output_file, "\n<%s>\n", szAnnHdr );
+                    } else {
+                        inchi_print( output_file, "\n==== %s ====\n", szAnnHdr );
+                    }
+                    bINChIOutputOptionsCur |= bEmbedReconnected;
+                    bINChIOutputOptionsCur &= ~INCHI_OUT_TABBED_OUTPUT;
+                    break;
+                default:
+                    continue;
+                }
 
-            ret &= OutputINChI2( pStr, nStrLen, pINChISort, INCHI_BAS /*iINChI*/, pOrigStruct,
-                                bDisconnectedCoord, OUT_TN, bINChIOutputOptionsCur, 0 != (bINChIOutputOptionsCur & INCHI_OUT_XML),
-                                ip->bAbcNumbers, ip->bCtPredecessors, ip->bNoStructLabels,
-                                num_components, num_non_taut, num_taut,
-                                output_file, log_file, num_inp,
-                                ip->pSdfLabel,ip->pSdfValue, ip->lSdfId, pSortPrintINChIFlags );
-
-            if ( ret &&  !(bINChIOutputOptionsCur & INCHI_OUT_EMBED_REC) ) {
-                ret &= OutputINChI2( pStr, nStrLen, pINChISort, INCHI_REC /*iINChI*/, pOrigStruct,
+                ret &= OutputINChI2( pStr, nStrLen, pINChISort, INCHI_BAS /*iINChI*/, pOrigStruct,
                                     bDisconnectedCoord, OUT_TN, bINChIOutputOptionsCur, 0 != (bINChIOutputOptionsCur & INCHI_OUT_XML),
                                     ip->bAbcNumbers, ip->bCtPredecessors, ip->bNoStructLabels,
                                     num_components, num_non_taut, num_taut,
                                     output_file, log_file, num_inp,
                                     ip->pSdfLabel,ip->pSdfValue, ip->lSdfId, pSortPrintINChIFlags );
-            }
-            if ( bAnnInXmlBrackets ) {
-                inchi_print( output_file, "</%s>\n\n", szAnnHdr );
-            }
-            if ( !ret ) {
-                break;
+
+                if ( ret &&  !(bINChIOutputOptionsCur & INCHI_OUT_EMBED_REC) ) {
+                    ret &= OutputINChI2( pStr, nStrLen, pINChISort, INCHI_REC /*iINChI*/, pOrigStruct,
+                                        bDisconnectedCoord, OUT_TN, bINChIOutputOptionsCur, 0 != (bINChIOutputOptionsCur & INCHI_OUT_XML),
+                                        ip->bAbcNumbers, ip->bCtPredecessors, ip->bNoStructLabels,
+                                        num_components, num_non_taut, num_taut,
+                                        output_file, log_file, num_inp,
+                                        ip->pSdfLabel,ip->pSdfValue, ip->lSdfId, pSortPrintINChIFlags );
+                }
+                if ( bAnnInXmlBrackets ) {
+                    inchi_print( output_file, "</%s>\n\n", szAnnHdr );
+                }
+                if ( !ret ) {
+                    break;
+                }
             }
         }
     }
@@ -1428,10 +1469,11 @@ void FreeINChIArrays( PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, int num_componen
  * output " L=V" or " L missing" or ""
  * The fprintf format string must contain %s%s%s%s
  */
-char gsMissing[] = "is missing";
-char gsEmpty[]   = "";
-char gsSpace[]   = " ";
-char gsEqual[]   = "=";
+
+const char gsMissing[] = "is missing";
+const char gsEmpty[]   = "";
+const char gsSpace[]   = " ";
+const char gsEqual[]   = "=";
 
 #ifndef INCHI_LIBRARY
 /*********************************************************************************************************/
@@ -1650,15 +1692,15 @@ int ReadTheStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, FILE *inp_file, ORIG_ATO
 /*****************************************************************************************************/
 int TreatReadTheStructureErrors(  STRUCT_DATA *sd, INPUT_PARMS *ip, int nLogMask,
                                   FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
-                                  ORIG_ATOM_DATA *orig_inp_data, int *num_inp, char *pStr, int nStrLen )
+                                  ORIG_ATOM_DATA *orig_inp_data, long *num_inp, char *pStr, int nStrLen )
 {
     int nRet = _IS_OKAY;
     /*  End of file */
     if ( 10 < sd->nStructReadError && sd->nStructReadError < 20 ) {
         if ( sd->pStrErrStruct[0] ) {
-            my_fprintf( log_file, "%s inp structure #%d: End of file.%s%s%s%s    \n", sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+            my_fprintf( log_file, "%s inp structure #%ld: End of file.%s%s%s%s    \n", sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
         }
-        my_fprintf( log_file, "End of file detected after structure #%d.   \n", *num_inp-1 );
+        //my_fprintf( log_file, "End of file detected after structure #%ld.   \n", *num_inp-1 );
         nRet = _IS_EOF;
         goto exit_function; /*  end of file */
     }
@@ -1669,7 +1711,7 @@ int TreatReadTheStructureErrors(  STRUCT_DATA *sd, INPUT_PARMS *ip, int nLogMask
     if ( *num_inp < ip->first_struct_number ) {
 #ifndef INCHI_LIBRARY
         if ( log_file != stderr ) {
-            my_fprintf( stderr, "\rSkipping structure #%d.%s%s%s%s...", *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue));
+            //my_fprintf( stderr, "\rSkipping structure #%ld.%s%s%s%s...", *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue));
         }
 #endif
         nRet = sd->nErrorType = _IS_SKIP;
@@ -1687,7 +1729,7 @@ int TreatReadTheStructureErrors(  STRUCT_DATA *sd, INPUT_PARMS *ip, int nLogMask
     if ( (ip->bINChIOutputOptions & INCHI_OUT_XML) && !sd->bXmlStructStarted ) {
         if ( !OutputINChIXmlStructStartTag( output_file, pStr, 1, nStrLen, ip->bNoStructLabels,
                                            *num_inp, ip->pSdfLabel, ip->pSdfValue ) ) {
-            my_fprintf( log_file, "Cannot create start xml tag for structure #%d.%s%s%s%s Terminating.\n", *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+            my_fprintf( log_file, "Cannot create start xml tag for structure #%ld.%s%s%s%s Terminating.\n", *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
             sd->bXmlStructStarted = -1;
             nRet = _IS_FATAL;
             goto exit_function;
@@ -1698,7 +1740,7 @@ int TreatReadTheStructureErrors(  STRUCT_DATA *sd, INPUT_PARMS *ip, int nLogMask
     /*  Fatal error */
     if ( sd->nErrorType == _IS_FATAL ) {
         if ( nLogMask & LOG_MASK_FATAL )
-            my_fprintf( log_file, "Fatal Error %d (aborted; %s) inp structure #%d.%s%s%s%s\n",
+            my_fprintf( 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 && 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd && !ip->bSaveAllGoodStructsAsProblem ) {
@@ -1710,7 +1752,7 @@ int TreatReadTheStructureErrors(  STRUCT_DATA *sd, INPUT_PARMS *ip, int nLogMask
     /*  Non-fatal errors: do not produce INChI */
     if ( sd->nErrorType == _IS_ERROR ) {  /*  70 => too many atoms */
         if ( nLogMask & LOG_MASK_ERR )
-            my_fprintf( log_file, "Error %d (no %s; %s) inp structure #%d.%s%s%s%s\n",
+            my_fprintf( log_file, "Error %d (no %s; %s) inp structure #%ld.%s%s%s%s\n",
                     sd->nStructReadError, INCHI_NAME, sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
 #if( bRELEASE_VERSION == 1 || EXTR_FLAGS == 0 )
         if ( prb_file && 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd && !ip->bSaveAllGoodStructsAsProblem) {
@@ -1722,7 +1764,7 @@ int TreatReadTheStructureErrors(  STRUCT_DATA *sd, INPUT_PARMS *ip, int nLogMask
     /*  Warnings: try to produce INChI */
     if ( sd->nErrorType == _IS_WARNING ) {
         if ( nLogMask & LOG_MASK_WARN )
-            my_fprintf( log_file, "Warning: (%s) inp structure #%d.%s%s%s%s\n",
+            my_fprintf( log_file, "Warning: (%s) inp structure #%ld.%s%s%s%s\n",
                     sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
     }
 
@@ -1747,7 +1789,7 @@ exit_function:
 /******************************************************************************************************/
 int GetOneComponent( STRUCT_DATA *sd, INPUT_PARMS *ip, INCHI_FILE *log_file, INCHI_FILE *output_file,
                      INP_ATOM_DATA *inp_cur_data,
-                     ORIG_ATOM_DATA *orig_inp_data, int i, int num_inp, char *pStr, int nStrLen )
+                     ORIG_ATOM_DATA *orig_inp_data, int i, long num_inp, char *pStr, int nStrLen )
 {
     inchiTime ulTStart;
     InchiTimeGet( &ulTStart );
@@ -1759,7 +1801,7 @@ int GetOneComponent( STRUCT_DATA *sd, INPUT_PARMS *ip, INCHI_FILE *log_file, INC
     if ( inp_cur_data->num_at <= 0 || orig_inp_data->nCurAtLen[i] != inp_cur_data->num_at ) {
         /*  log error message */
         AddMOLfileError(sd->pStrErrStruct, "Cannot extract Component");
-        my_fprintf( log_file, "%s #%d structure #%d.%s%s%s%s\n", sd->pStrErrStruct, i+1, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue));
+        my_fprintf( log_file, "%s #%d structure #%ld.%s%s%s%s\n", sd->pStrErrStruct, i+1, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue));
         sd->nErrorCode = inp_cur_data->num_at < 0? inp_cur_data->num_at : (orig_inp_data->nCurAtLen[i] != inp_cur_data->num_at)? CT_ATOMCOUNT_ERR : CT_UNKNOWN_ERR;
         /* num_err ++; */
         sd->nErrorType = _IS_ERROR;
@@ -1778,14 +1820,12 @@ int GetOneComponent( STRUCT_DATA *sd, INPUT_PARMS *ip, INCHI_FILE *log_file, INC
 /*******************************************************************************************/
 int GetProcessingWarningsOneINChI(INChI *pINChI, INP_ATOM_DATA *inp_norm_data, char *pStrErrStruct)
 {
-    int i, j;
+    int j;
     int nAmbiguousStereoAtoms, nAmbiguousStereoBonds;
     nAmbiguousStereoAtoms = 0;
     nAmbiguousStereoBonds = 0;
 
-    for ( i = 0; i < 2; i ++ ) {
-        if ( !inp_norm_data->at )
-            continue;
+    if ( inp_norm_data->at ) {
         for ( j = 0; j < pINChI->nNumberOfAtoms; j ++ ) {
             if ( inp_norm_data->at[j].bAmbiguousStereo & (AMBIGUOUS_STEREO_ATOM | AMBIGUOUS_STEREO_ATOM_ISO) ) {
                 nAmbiguousStereoAtoms ++;
@@ -1794,14 +1834,14 @@ int GetProcessingWarningsOneINChI(INChI *pINChI, INP_ATOM_DATA *inp_norm_data, c
                 nAmbiguousStereoBonds ++;
             }
         }
-    }
-    if ( nAmbiguousStereoAtoms ) {
-        AddMOLfileError(pStrErrStruct, "Ambiguous stereo:");
-        AddMOLfileError(pStrErrStruct, "center(s)");
-    }
-    if ( nAmbiguousStereoBonds ) {
-        AddMOLfileError(pStrErrStruct, "Ambiguous stereo:");
-        AddMOLfileError(pStrErrStruct, "bond(s)");
+        if ( nAmbiguousStereoAtoms ) {
+            AddMOLfileError(pStrErrStruct, "Ambiguous stereo:");
+            AddMOLfileError(pStrErrStruct, "center(s)");
+        }
+        if ( nAmbiguousStereoBonds ) {
+            AddMOLfileError(pStrErrStruct, "Ambiguous stereo:");
+            AddMOLfileError(pStrErrStruct, "bond(s)");
+        }
     }
     return (nAmbiguousStereoAtoms || nAmbiguousStereoBonds);
 }
@@ -1820,7 +1860,7 @@ int  GetProcessingWarnings(INChI *cur_INChI[], INP_ATOM_DATA **inp_norm_data, ST
 /*******************************************************************************************/
 int CreateOneComponentINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, INP_ATOM_DATA *inp_cur_data, ORIG_ATOM_DATA *orig_inp_data,
                             PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, int iINChI,
-                            int i, int num_inp, INP_ATOM_DATA **inp_norm_data, NORM_CANON_FLAGS *pncFlags, INCHI_FILE *log_file )
+                            int i, long num_inp, INP_ATOM_DATA **inp_norm_data, NORM_CANON_FLAGS *pncFlags, INCHI_FILE *log_file )
 {
     inchiTime     ulTStart, ulTEnd, *pulTEnd = NULL;
     int           k, num_at, ret = 0;
@@ -1874,11 +1914,11 @@ int CreateOneComponentINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, INP_ATOM_DATA *in
 #if( !defined( INCHI_LIB ) && !defined( INCHI_LIBRARY ) )
 #if( TEST_RENUMB_ATOMS != 1 )
     /*  log file / console output */
-    if ( log_file != stderr ) {
+    if ( log_file && log_file != stderr ) { /* NULL log_file now ignored. 11-23-2005 */
         if ( ip->bDisplay )
-            my_fprintf( log_file, "Component #%d structure #%d.%s%s%s%s...\n", i+1, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
-        else
-            //my_fprintf( stderr, "Component #%d structure #%d.%s%s%s%s...\r", i+1, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+            my_fprintf( log_file, "Component #%d structure #%ld.%s%s%s%s...\n", i+1, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+        //else
+            //my_fprintf( stderr, "Component #%d structure #%ld.%s%s%s%s...\r", i+1, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
     }
 #endif
 #endif
@@ -1902,10 +1942,10 @@ int CreateOneComponentINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, INP_ATOM_DATA *in
             InchiTimeAddMsec( pulTEnd, ip->msec_LeftTime );
         }
     }
-    num_at = Create_INChI( cur_INChI, cur_INChI_Aux, orig_inp_data, inp_cur_data->at,
+    num_at = Create_INChI( cur_INChI, cur_INChI_Aux, orig_inp_data/* not used */, inp_cur_data->at,
                           inp_norm_data,
                           inp_cur_data->num_at,
-                          ip->nMode, &bTautFlags, &bTautFlagsDone, pulTEnd, sd->pStrErrStruct);
+                          ip->nMode, &bTautFlags, &bTautFlagsDone, pulTEnd, NULL, sd->pStrErrStruct);
     SetConnectedComponentNumber( inp_cur_data->at, inp_cur_data->num_at, i+1 ); /*  normalization alters structure component number */
     for ( k = 0; k < TAUT_NUM; k ++ ) {
         if ( cur_INChI_Aux[k] && cur_INChI_Aux[k]->nNumberOfAtoms > 0 ) {
@@ -2021,13 +2061,13 @@ int CreateOneComponentINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, INP_ATOM_DATA *in
 }
 /****************************************************************************************************/
 int TreatCreateOneComponentINChIError(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data,
-                                     int i, int num_inp,
+                                     int i, long num_inp,
                                      FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
                                      char *pStr, int nStrLen )
 {
     if ( sd->nErrorCode ) {
         AddMOLfileError(sd->pStrErrStruct, ErrMsg(sd->nErrorCode) );
-        my_fprintf( log_file, "Error %d (%s) structure #%d component %d.%s%s%s%s\n",
+        my_fprintf( log_file, "Error %d (%s) structure #%ld component %d.%s%s%s%s\n",
             sd->nErrorCode, sd->pStrErrStruct, num_inp, i+1, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
         sd->nErrorType = (sd->nErrorCode==CT_OUT_OF_RAM || sd->nErrorCode==CT_USER_QUIT_ERR)? _IS_FATAL : _IS_ERROR;
         if ( (ip->bINChIOutputOptions & INCHI_OUT_XML)
@@ -2051,7 +2091,7 @@ int TreatCreateOneComponentINChIError(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATO
 #ifndef INCHI_LIBRARY
     /*  print the logfile record */
     if ( log_file && log_file != stderr && (sd->ulStructTime >= 1000 || sd->nErrorCode) ) {
-        fprintf( log_file, "%10lu msec structure #%d.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n",
+        fprintf( log_file, "%10lu msec structure #%ld.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n",
                 sd->ulStructTime, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue),
                 orig_inp_data->num_components, orig_inp_data->num_components==1?"":"s",
                 orig_inp_data->num_inp_atoms, orig_inp_data->num_inp_atoms==1?"":"s", sd->nErrorCode );
@@ -2060,7 +2100,7 @@ int TreatCreateOneComponentINChIError(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATO
     return sd->nErrorType;
 }
 /****************************************************************************************************/
-int TreatCreateINChIWarning(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, int num_inp,
+int TreatCreateINChIWarning(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, long num_inp,
                                      FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
                                      char *pStr, int nStrLen )
 {
@@ -2072,7 +2112,7 @@ int TreatCreateINChIWarning(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *or
     }
 #endif
     if ( !sd->nErrorCode && sd->pStrErrStruct[0] ) {
-        my_fprintf( log_file, "Warning (%s) structure #%d.%s%s%s%s\n",
+        my_fprintf( log_file, "Warning (%s) structure #%ld.%s%s%s%s\n",
             sd->pStrErrStruct, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
         sd->nErrorType = _IS_WARNING;
         if ( (ip->bINChIOutputOptions & INCHI_OUT_XML)
@@ -2100,14 +2140,14 @@ int TreatCreateINChIWarning(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *or
 #if( bRELEASE_VERSION != 1 && bOUTPUT_ONE_STRUCT_TIME == 1 )
 #ifndef INCHI_LIBRARY
     if ( log_file && log_file != stderr ) {
-        fprintf( log_file, "%10lu msec structure %1dD #%d.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n",
+        fprintf( log_file, "%10lu msec structure %1dD #%ld.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n",
                 sd->ulStructTime, orig_inp_data->num_dimensions, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue),
                 orig_inp_data->num_components, orig_inp_data->num_components==1?"":"s",
                 orig_inp_data->num_inp_atoms, orig_inp_data->num_inp_atoms==1?"":"s", sd->nErrorCode );
     }
 #else
     if ( log_file ) {
-        my_fprintf( log_file, "%10lu msec structure %1dD #%d.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n",
+        my_fprintf( log_file, "%10lu msec structure %1dD #%ld.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n",
                 sd->ulStructTime, orig_inp_data->num_dimensions, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue),
                 orig_inp_data->num_components, orig_inp_data->num_components==1?"":"s",
                 orig_inp_data->num_inp_atoms, orig_inp_data->num_inp_atoms==1?"":"s", sd->nErrorCode );
@@ -2184,7 +2224,7 @@ int DuplicateOrigAtom( ORIG_ATOM_DATA *new_orig_atom, ORIG_ATOM_DATA *orig_atom
 /*******************************************************************************************/
 int GetOneStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
                      FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
-                     ORIG_ATOM_DATA *orig_inp_data, int *num_inp, char *pStr, int nStrLen, STRUCT_FPTRS *struct_fptrs )
+                     ORIG_ATOM_DATA *orig_inp_data, long *num_inp, char *pStr, int nStrLen, STRUCT_FPTRS *struct_fptrs )
 {
     int nRet, inp_index, out_index, bUseFptr = (NULL != struct_fptrs);
 
@@ -2380,7 +2420,7 @@ int RenumberingTestUninit( RENUMB_DATA *pRenumbData )
 int RenumberingTest( PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, ORIG_ATOM_DATA *orig_inp_data, int iINChI,
                      RENUMB_DATA *pRenumbData, INP_ATOM_DATA *inp_cur_data, INP_ATOM_DATA **inp_norm_data,
                      STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, INCHI_FILE *log_file, INCHI_FILE *prb_file,
-                     int i, int num_inp, NORM_CANON_FLAGS *pncFlags)
+                     int i, long num_inp, NORM_CANON_FLAGS *pncFlags)
 {
     int k, bLongerTime;
     CopyInpAtomData( &pRenumbData->saved_inp_cur_data, inp_cur_data );
@@ -2391,7 +2431,7 @@ int RenumberingTest( PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, ORIG_ATOM_DATA *o
     while ( -- pRenumbData->ren_counter >= 0 && !pRenumbData->nRet2 ) {
         pRenumbData->nComp ++;
         MakeNewOrd( pRenumbData->orig_inp_cur_data.num_at, pRenumbData->new_ord );
-        RenumbInpAtomData( inp_cur_data, &pRenumbData->orig_inp_cur_data, pRenumbData->new_ord );
+        RenumbInpAtomData( inp_cur_data /* output*/, &pRenumbData->orig_inp_cur_data/* input*/, pRenumbData->new_ord/* input*/ );
 #if( TEST_RENUMB_ATOMS_SAVE_LONGEST == 1 )
         CopyInpAtomData( &pRenumbData->longest_inp_cur_data, inp_cur_data );
 #endif
@@ -2425,13 +2465,21 @@ int RenumberingTest( PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, ORIG_ATOM_DATA *o
                 my_fprintf( log_file, "\n" );
                 pRenumbData->ren_counter = 0; /* force exit */
                 pRenumbData->bRenumbErr = 1000*pRenumbData->c2 + pRenumbData->c1;
+#if( TEST_RENUMB_SWITCH == 1 )
+                CopyInpAtomData( &pRenumbData->longest_inp_cur_data, inp_cur_data );
+                if ( pRenumbData->longest_inp_cur_data.at ) {
+                    for ( k = 0; k < pRenumbData->longest_inp_cur_data.num_at; k ++ ) {
+                        pRenumbData->longest_inp_cur_data.at[k].orig_at_number = k+1; /* display new atom numbers */
+                    }
+                }
+#endif
             }
 #if( TEST_RENUMB_ATOMS_SAVE_LONGEST == 1 )
             /*  output time per this component */
-            my_fprintf( stderr, "\rComp#%d str#%d/%d%s%s%s%s Ren %d/%d n(%lu:%lu)c(%lu:%lu)...\r",
-                                i+1, num_inp, iINChI, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue), pRenumbData->nComp, pRenumbData->ren_counter+pRenumbData->nComp,
-                                pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulNormTime, pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulCanonTime,
-                                pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulNormTime, pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulCanonTime);
+            //my_fprintf( stderr, "\rComp#%d str#%ld/%d%s%s%s%s Ren %d/%d n(%lu:%lu)c(%lu:%lu)...\r",
+            //                    i+1, num_inp, iINChI, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue), pRenumbData->nComp, pRenumbData->ren_counter+pRenumbData->nComp,
+            //                    pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulNormTime, pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulCanonTime,
+            //                    pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulNormTime, pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulCanonTime);
 #endif
             /*  make sure the max. time is not overwritten */
             pRenumbData->ulCurTime0 = pRenumbData->ren_INChI_Aux[0][TAUT_NON]?
@@ -2464,20 +2512,24 @@ int RenumberingTest( PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, ORIG_ATOM_DATA *o
                 pRenumbData->ulMaxTimeCanon = pRenumbData->ulCurTimeCanon;
                 bLongerTime = 1;
             }
-#if( TEST_RENUMB_ATOMS_SAVE_LONGEST == 1 )
-            if ( bLongerTime ) {
+#if( TEST_RENUMB_ATOMS_SAVE_LONGEST == 1 || TEST_RENUMB_SWITCH == 1 )
+            if ( bLongerTime || TEST_RENUMB_SWITCH == 1 && (pRenumbData->c1 || pRenumbData->c2 || pRenumbData->nRet2) ) {
                 char szLine[512];
                 char szValue[512];
                 //my_fprintf( stderr, "\n" );
-                sprintf( szLine, "Comp#%d str#%d/%d%s%s%s%s Ren %d/%d n=%lu:%lu c=%lu:%lu",
+                sprintf( szLine, "Comp#%d str#%ld/%d%s%s%s%s Ren %d/%d n=%lu:%lu c=%lu:%lu",
                                 i+1, num_inp, iINChI, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue), pRenumbData->nComp, pRenumbData->ren_counter+pRenumbData->nComp,
-                                pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulNormTime, pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulCanonTime,
-                                pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulNormTime, pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulCanonTime);
-                sprintf( szValue, "%s (c%d/s%d/i%d, r%d/%d n=%lu:%lu c=%lu:%lu)",
+                                pRenumbData->ren_INChI_Aux[0][TAUT_NON]? pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulNormTime:0,
+                                pRenumbData->ren_INChI_Aux[0][TAUT_NON]? pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulCanonTime:0,
+                                pRenumbData->ren_INChI_Aux[0][TAUT_YES]? pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulNormTime:0,
+                                pRenumbData->ren_INChI_Aux[0][TAUT_YES]? pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulCanonTime:0);
+                sprintf( szValue, "%s (c%d/s%ld/i%d, r%d/%d n=%lu:%lu c=%lu:%lu)",
                                   (ip->pSdfValue && ip->pSdfValue[0])? ip->pSdfValue:"unk",
                                 i+1, num_inp, iINChI, pRenumbData->nComp, pRenumbData->ren_counter+pRenumbData->nComp,
-                                pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulNormTime, pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulCanonTime,
-                                pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulNormTime, pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulCanonTime);
+                                pRenumbData->ren_INChI_Aux[0][TAUT_NON]? pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulNormTime:0,
+                                pRenumbData->ren_INChI_Aux[0][TAUT_NON]? pRenumbData->ren_INChI_Aux[0][TAUT_NON]->ulCanonTime:0,
+                                pRenumbData->ren_INChI_Aux[0][TAUT_YES]? pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulNormTime:0,
+                                pRenumbData->ren_INChI_Aux[0][TAUT_YES]? pRenumbData->ren_INChI_Aux[0][TAUT_YES]->ulCanonTime:0);
 
                 WriteToSDfile( &pRenumbData->longest_inp_cur_data, prb_file, szLine, NULL, ip->pSdfLabel, szValue );
             }
@@ -2516,7 +2568,7 @@ int RenumberingTest( PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, ORIG_ATOM_DATA *o
     sd->num_taut[iINChI]     = pRenumbData->num_taut0;
     sd->num_non_taut[iINChI] = pRenumbData->num_non_taut0;
     if ( pRenumbData->num_taut % pRenumbData->nComp || pRenumbData->num_non_taut % pRenumbData->nComp ) {
-        my_fprintf( log_file, "Compare (%d,%d) %d (err=%d) %s structure #%d component %d.%s%s%s%s\n",
+        my_fprintf( log_file, "Compare (%d,%d) %d (err=%d) %s structure #%ld component %d.%s%s%s%s\n",
                     pRenumbData->num_non_taut % pRenumbData->nComp, pRenumbData->num_taut % pRenumbData->nComp,
                     pRenumbData->nComp, 333, INCHI_NAME, num_inp, i+1, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
     }
@@ -2526,9 +2578,20 @@ int RenumberingTest( PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, ORIG_ATOM_DATA *o
     /*  renumbered input structure */
 #ifndef INCHI_ANSI_ONLY /* { */
     if ( /*ip->bDisplayEachComponentINChI &&*/ !pRenumbData->nRet2 ) {
-        int err;
-        err = DisplayStructure( inp_cur_data->at, inp_cur_data->num_at, 0, 0, 0, 0, NULL, NULL,
+        int err, len;
+        /*
+        err = DisplayStructure( inp_cur_data->at, inp_cur_data->num_at, 0, 1, 0, NULL. 1, 0, NULL, NULL,
                                             ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
+        */
+        err = DisplayStructure( inp_cur_data->at, inp_cur_data->num_at, 0, 1, 0, NULL, 1/*isotopic*/, 0/*taut*/, NULL, NULL,
+                                            ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
+        if ( pRenumbData->c1 || pRenumbData->c2 ) {
+            len = strlen(szTitle);
+            strcat( szTitle, " (Renumbered)" );
+            err = DisplayStructure( pRenumbData->longest_inp_cur_data.at, pRenumbData->longest_inp_cur_data.num_at,
+                                    0, 1, 0, NULL, 1, 0, NULL, NULL, ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
+            szTitle[len] = '\0';
+        }
         sd->bUserQuitComponentDisplay = (err==ESC_KEY);
         if ( !err ) {
             my_fprintf( stderr, "Cannot display the structure\n");
@@ -2541,7 +2604,9 @@ int RenumberingTest( PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, ORIG_ATOM_DATA *o
     FreeInpAtomData( &pRenumbData->saved_inp_cur_data );
     FreeInpAtomData( pRenumbData->ren_inp_norm_data[TAUT_NON] );
     FreeInpAtomData( pRenumbData->ren_inp_norm_data[TAUT_YES] );
-
+#if( TEST_RENUMB_ATOMS_SAVE_LONGEST == 1 || TEST_RENUMB_SWITCH == 1 )
+    FreeInpAtomData( &pRenumbData->longest_inp_cur_data );
+#endif
     return pRenumbData->nRet2;
 }
 #endif  /* } TEST_RENUMB_ATOMS  */
@@ -2604,13 +2669,20 @@ int PreprocessOneStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *or
     /* 2. fix odd things in prep_inp_data            */
     /*************************************************/
 
-    if ( 0 < fix_odd_things( prep_inp_data->num_inp_atoms, prep_inp_data->at ) ) {
+    if ( 0 < fix_odd_things( prep_inp_data->num_inp_atoms, prep_inp_data->at, 0 ) ) {
         AddMOLfileError(sd->pStrErrStruct, "Charges were rearranged");
         if ( sd->nErrorType < _IS_WARNING ) {
             sd->nErrorType = _IS_WARNING;
         }
         sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE;
     }
+#if( FIX_ADJ_RAD == 1 )
+    if ( ip->bTautFlags & TG_FLAG_FIX_ADJ_RADICALS ) {
+        if ( 0 < FixAdjacentRadicals( prep_inp_data->num_inp_atoms, prep_inp_data->at ) ) {
+            sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ADJ_RADICALS_DONE;
+        }
+    }
+#endif
 #if( bRELEASE_VERSION == 0 && (EXTR_FLAGS & EXTR_HAS_FEATURE) )
     if ( bFoundFeature( prep_inp_data->at, prep_inp_data->num_inp_atoms ) ) {
         sd->bExtract |= EXTR_HAS_FEATURE;
@@ -2855,7 +2927,7 @@ exit_function:
 #ifndef INCHI_ANSI_ONLY  /* { */
 /************************************************************************************************/
 int DisplayTheWholeStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, FILE *inp_file, INCHI_FILE *log_file,
-                              ORIG_ATOM_DATA *orig_inp_data, int num_inp, int iINChI, int bShowStruct, int bINCHI_LIB_Flag )
+                              ORIG_ATOM_DATA *orig_inp_data, long num_inp, int iINChI, int bShowStruct, int bINCHI_LIB_Flag )
 {
 
     int bDisplayEqu = 0;
@@ -2894,13 +2966,13 @@ int DisplayTheWholeStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, F
 #ifndef INCHI_LIB
     if ( bShowStruct && ip->bDisplay ) {
         if ( bDisplayEqu ) {
-            sprintf( szTitle, " Equ Set %d of %d, Input Structure #%d.%s%s%s%s%s",
+            sprintf( szTitle, " Equ Set %d of %d, Input Structure #%ld.%s%s%s%s%s",
                      ip->dp.nCurEquLabel, ip->dp.nNumEquSets,
                      num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue), lpszType);
         } else {
-            sprintf( szTitle, "Input Structure #%d.%s%s%s%s%s", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue), lpszType);
+            sprintf( szTitle, "Input Structure #%ld.%s%s%s%s%s", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue), lpszType);
         }
-        err = DisplayStructure( orig_inp_data->at, orig_inp_data->num_inp_atoms, 0, 0, NULL, 1/*isotopic*/, 0/*taut*/, NULL, NULL,
+        err = DisplayStructure( orig_inp_data->at, orig_inp_data->num_inp_atoms, 0, 1, 0, NULL, 1/*isotopic*/, 0/*taut*/, NULL, NULL,
                                             ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
         sd->bUserQuitComponent = (err==ESC_KEY);
         if ( !err ) {
@@ -2912,14 +2984,14 @@ int DisplayTheWholeStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, F
         if ( ip->bDisplay && !sd->bUserQuitComponent ) {
             if ( iINChI == 1 ) {
                 if ( ip->bDisplay )
-                    my_fprintf( log_file, "Processing (rec) structure #%d.%s%s%s%s...\n", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+                    my_fprintf( log_file, "Processing (rec) structure #%ld.%s%s%s%s...\n", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
                 else
-                    my_fprintf( stderr, "Processing (rec) structure #%d.%s%s%s%s...\r", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+                    my_fprintf( stderr, "Processing (rec) structure #%ld.%s%s%s%s...\r", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
             } else {
                 if ( ip->bDisplay )
-                    my_fprintf( log_file, "Processing structure #%d.%s%s%s%s...\n", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+                    my_fprintf( log_file, "Processing structure #%ld.%s%s%s%s...\n", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
                 else
-                    my_fprintf( stderr, "Processing structure #%d.%s%s%s%s...\r", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+                    my_fprintf( stderr, "Processing structure #%ld.%s%s%s%s...\r", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
             }
         }
     }
@@ -2949,7 +3021,7 @@ int DisplayTheWholeStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, F
             nComponent    = k/4;
             bPreprocessed = ((k/2)%2);
 
-            sprintf( szTitle, "%s Structure #%d.%s%s%s%s",
+            sprintf( szTitle, "%s Structure #%ld.%s%s%s%s",
                               bPreprocessed? "Preprocessed" : bReconnected? "Reconnected" : "Input",
                               num_inp,
                               SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue));
@@ -2965,7 +3037,7 @@ int DisplayTheWholeStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, F
                     return -1;
                 }
                 vDrawData.pWindowData = CreateWinData_( orig_inp_data->at, orig_inp_data->num_inp_atoms,
-                                                        0, 0, NULL, 1, 0, NULL, NULL,
+                                                        0, 1 /* bAdd_DT_to_num_H */, 0, NULL, 1, 0, NULL, NULL,
                                                         ip->bAbcNumbers, &ip->dp, ip->nMode );
                 if( vDrawData.pWindowData != NULL )
                 {
@@ -3002,7 +3074,7 @@ int ProcessOneStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
                          PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM],
                          FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
                          ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data,
-                         int num_inp, char *pStr, int nStrLen )
+                         long num_inp, char *pStr, int nStrLen )
 {
         int nRet = 0, nRet1, i, k, maxINChI=0;
         COMP_ATOM_DATA composite_norm_data[INCHI_NUM][TAUT_NUM+1]; /* [0]:non-taut, [1]:taut, [2]:intermediate taut struct */
@@ -3020,7 +3092,7 @@ int ProcessOneStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
 
         /* for testing only */
 #if( REMOVE_ION_PAIRS_ORIG_STRU == 1 )
-        fix_odd_things( orig_inp_data->num_inp_atoms, orig_inp_data->at );
+        fix_odd_things( orig_inp_data->num_inp_atoms, orig_inp_data->at, 0 );
 #endif
 
         /***** output MOLfile ***************/
@@ -3031,15 +3103,16 @@ int ProcessOneStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
             /*  log file / console output */
             if ( log_file != stderr ) {
                 if ( ip->bDisplay )
-                    my_fprintf( log_file, "Writing structure #%d.%s%s%s%s...\n", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
-                else
-                    my_fprintf( stderr, "Writing structure #%d.%s%s%s%s...\r", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+                    my_fprintf( log_file, "Writing structure #%ld.%s%s%s%s...\n", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+                //else
+                    //my_fprintf( stderr, "Writing structure #%ld.%s%s%s%s...\r", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
             }
 #endif
 #endif
-            sprintf( szNumber, "Structure #%d", num_inp );
+            sprintf( szNumber, "Structure #%ld", num_inp );
             WriteOrigAtomDataToSDfile( orig_inp_data, output_file, szNumber, NULL,
-                (sd->bChiralFlag & FLAG_INP_AT_CHIRAL)? 1:0, ip->pSdfLabel, ip->pSdfValue );
+                (sd->bChiralFlag & FLAG_INP_AT_CHIRAL)? 1:0,
+                (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ATOMS_DT)? 1:0, ip->pSdfLabel, ip->pSdfValue );
             goto exit_function;
         }
 
@@ -3198,7 +3271,7 @@ exit_loop:;
         /* XML struct end tag */
         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 #%d.%s%s%s%s Terminating.\n", num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+                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 */
                 nRet = _IS_FATAL;
             } else {
@@ -3278,7 +3351,7 @@ int CreateOneStructureINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
                          FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
                          ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data,
                          COMP_ATOM_DATA composite_norm_data2[][TAUT_NUM+1],
-                         int num_inp, char *pStr, int nStrLen, NORM_CANON_FLAGS *pncFlags )
+                         long num_inp, char *pStr, int nStrLen, NORM_CANON_FLAGS *pncFlags )
 {
     int i, j, k, /*m,*/ nRet = 0;
 #ifndef INCHI_LIB
@@ -3596,9 +3669,9 @@ int CreateOneStructureINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
         }
 #ifndef INCHI_LIB  /* { */
 #if( bREUSE_INCHI == 1 )
-        if ( iINChI == INCHI_REC && (!ip->bDisplay && !(ip->bCompareComponents & CMP_COMPONENTS) ||
+        if ( iINChI == INCHI_REC && (!ip->bDisplay && !ip->bDisplayCompositeResults && !(ip->bCompareComponents & CMP_COMPONENTS) ||
                                    sd->bUserQuitComponentDisplay) ) {
-            /* reconnected structure */
+            /* reconnected structure (06-20-2005: added "&& !ip->bDisplayCompositeResults" to display composite structure) */
             int m = iINChI-1;
             /* find whether we have already calculated this INChI in basic (disconnected) layer */
             for ( j = n = 0; j < prep_inp_data[m].num_components; j ++ ) {
@@ -3672,17 +3745,17 @@ int CreateOneStructureINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
         /*  b) Display the extracted original component structure */
         if ( inp_cur_data->at && ip->bDisplay && !sd->bUserQuitComponentDisplay ) {
             if ( cur_prep_inp_data->num_components == 1 ) {
-                sprintf( szTitle, "%sInput Structure #%d.%s%s%s%s%s",
+                sprintf( szTitle, "%sInput Structure #%ld.%s%s%s%s%s",
                                   bStructurePreprocessed? "Preprocessed ":"",
                                   num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue), iINChI? " (Reconnected)":"");
             } else {
-                sprintf( szTitle, "Component #%d of %d, Input Structure #%d.%s%s%s%s%s",
+                sprintf( szTitle, "Component #%d of %d, Input Structure #%ld.%s%s%s%s%s",
                                   i+1, cur_prep_inp_data->num_components,
                                   num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue), iINChI? " (Reconnected)":"");
             }
 #ifndef INCHI_LIB
             err = DisplayStructure( inp_cur_data->at, inp_cur_data->num_at,
-                                    0, 0, NULL, 1/*isotopic*/, 0/*taut*/, NULL, NULL,
+                                    0, 1, 0, NULL, 1/*isotopic*/, 0/*taut*/, NULL, NULL,
                                     ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
             sd->bUserQuitComponentDisplay = (err==ESC_KEY);
             if ( !err ) {
@@ -3694,7 +3767,7 @@ int CreateOneStructureINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
                 struct DrawData vDrawData;
                 int    nType = COMPONENT_ORIGINAL;
                 vDrawData.pWindowData = CreateWinData_( inp_cur_data->at, inp_cur_data->num_at,
-                                                        0, 0, NULL,
+                                                        0, 1 /* bAdd_DT_to_num_H */, 0, NULL,
                                                         1 /* display isotopic if present */, 0, NULL, NULL,
                                                         ip->bAbcNumbers, &ip->dp, ip->nMode );
                 if( vDrawData.pWindowData != NULL )
@@ -3721,9 +3794,9 @@ int CreateOneStructureINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
         RenumberingTestInit( pRenumbData, inp_cur_data );
         if ( log_file != stderr ) {
             if ( ip->bDisplay )
-                my_fprintf( log_file, "Component #%d structure #%d.%s%s%s%s...\n", i+1, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+                my_fprintf( log_file, "Component #%d structure #%ld.%s%s%s%s...\n", i+1, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
             else
-                my_fprintf( stderr, "Component #%d structure #%d.%s%s%s%s...\r", i+1, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+                my_fprintf( stderr, "Component #%d structure #%ld.%s%s%s%s...\r", i+1, num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
         }
         /****************************************************************************/
         /*     R E N U M B E R I N G (testing only) Part I  ENDS here               */
@@ -3797,14 +3870,14 @@ int CreateOneStructureINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
                             nNumDisplayedFixedBondTaut += bFixedBondsTaut; /* display only one time */
                             /*  added number of components, added another format for a single component case - DCh */
                             if ( cur_prep_inp_data->num_components > 1 ) {
-                                sprintf( szTitle, "%s Component #%d of %d, Structure #%d%s%s.%s%s%s%s%s",
+                                sprintf( szTitle, "%s Component #%d of %d, Structure #%ld%s%s.%s%s%s%s%s",
                                               bFixedBondsTaut? "Preprocessed":"Result for",
                                               i+1, cur_prep_inp_data->num_components, num_inp,
                                               bDisplayTaut==1? ", mobile H": bDisplayTaut==0?", fixed H":"",
                                               bIsotopic? ", isotopic":"",
                                               SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue), iINChI? " (Reconnected)":"");
                             } else {
-                                sprintf( szTitle, "%s Structure #%d%s%s.%s%s%s%s%s",
+                                sprintf( szTitle, "%s Structure #%ld%s%s.%s%s%s%s%s",
                                               bFixedBondsTaut? "Preprocessed":"Result for",
                                               num_inp,
                                               bDisplayTaut==1? ", mobile H": bDisplayTaut==0?", fixed H":"",
@@ -3816,14 +3889,14 @@ int CreateOneStructureINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
                                 continue;
                             if ( bFixedBondsTaut ) {
                                 err = DisplayStructure( inp_norm_data[j]->at_fixed_bonds, inp_norm_data[j]->num_at,
-                                                        inp_norm_data[j]->num_removed_H,
+                                                        inp_norm_data[j]->num_removed_H, 0 /*bAdd_DT_to_num_H*/,
                                                         inp_norm_data[j]->nNumRemovedProtons,
                                                         inp_norm_data[j]->nNumRemovedProtonsIsotopic,
                                                         bHasIsotopicLayer, j, NULL,  NULL,
                                                         ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
                             } else {
                                 err = DisplayStructure( inp_norm_data[j]->at, inp_norm_data[j]->num_at,
-                                                        0, 0, NULL,
+                                                        0, 0 /*bAdd_DT_to_num_H*/, 0, NULL,
                                                         k, j, pINChI[i], pINChI_Aux[i],
                                                         ip->bAbcNumbers, &ip->dp, ip->nMode, szTitle );
                             }
@@ -3835,7 +3908,7 @@ int CreateOneStructureINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
                             {
                                 struct DrawData vDrawData;
                                 vDrawData.pWindowData = CreateWinData_( inp_norm_data[j]->at, inp_norm_data[j]->num_at,
-                                                        0, 0, NULL,
+                                                        0, 0 /* bAdd_DT_to_num_H */, 0, NULL,
                                                         k, j, pINChI[i], pINChI_Aux[i],
                                                         ip->bAbcNumbers, &ip->dp, ip->nMode );
                                 if( vDrawData.pWindowData != NULL )
@@ -3863,6 +3936,7 @@ int CreateOneStructureINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
                                     vDrawData.pWindowData =
                                          CreateWinData_( inp_norm_data[j]->at_fixed_bonds, inp_norm_data[j]->num_at,
                                                          inp_norm_data[j]->num_removed_H,
+                                                         0 /* bAdd_DT_to_num_H */,
                                                          inp_norm_data[j]->nNumRemovedProtons,
                                                          inp_norm_data[j]->nNumRemovedProtonsIsotopic,
                                                          k, j, NULL, NULL,