IUPAC-InChI · nnuk · Aug 20, 2026 · Aug 17, 2026 · Aug 17, 2026 · Aug 19, 2026
diff --git a/INCHI-1-DOC/CHANGELOG.md b/INCHI-1-DOC/CHANGELOG.md
@@ -7,6 +7,10 @@
 - Molecular Inorganics preprocessing now follows the revised bond-disconnection decision tree, preserving stereo-indicated metal bonds, linked-metal structures, and qualifying metal-containing chelate ring systems while applying the Group 1/2 and terminal-metal exceptions.
 - The generated InChI for qualifying chelate complexes may intentionally change from a disconnected representation to a connected representation. In particular, the Ti bis-flavonoid regression case is now represented as connected `C30H18O14Ti` instead of disconnected `2C15H10O7.Ti` components.
 
+### Fixed
+
+- GHI #252: Explicit H/D/T atoms used as polymer crossing-bond end groups are now preserved during terminal-H processing when the `Polymers` option is enabled. This allows valid SRU/CRU structures with explicit hydrogen leaving groups to be processed instead of being rejected as unsupported. The retained H/D/T atom is represented explicitly as a numbered atom in the `/c` layer rather than being converted to an implicit hydrogen.
+
 ## v1.07.5 2026-02-17
 
 ### Changed

diff --git a/INCHI-1-SRC/INCHI_API/libinchi/src/inchi_dll_a2.c b/INCHI-1-SRC/INCHI_API/libinchi/src/inchi_dll_a2.c
@@ -167,6 +167,7 @@ int  Normalization_step( CANON_GLOBALS *pCG,
                          inp_ATOM *inp_at,
                          INP_ATOM_DATA *out_norm_data[2],
                          int num_inp_at,
+                         const unsigned char *keep_explicit_HDT,
                          struct tagInchiTime *ulMaxTime,
                          INCHI_MODE *pbTautFlags,
                          INCHI_MODE *pbTautFlagsDone,
@@ -340,37 +341,37 @@ int NormOneStructureINChI( CANON_GLOBALS *pCG,
     /* assign values to sd->num_components[]                                                  */
 
     /* djb-rwth: MYREALLOC2( PINChI2, PINChI_Aux2, pINChI2[iINChI], pINChI_Aux2[iINChI], sd->num_components[iINChI], cur_prep_inp_data->num_components, k ) has been replaced and the whole block rewritten to address memory leaks and reading from freed memory locations */
-    do 
-    { 
-        if( (sd->num_components[iINChI]) <= (cur_prep_inp_data->num_components) ) 
+    do
+    {
+        if( (sd->num_components[iINChI]) <= (cur_prep_inp_data->num_components) )
         {
             PINChI2* newPTR1 = (PINChI2 *)inchi_calloc( (long long)cur_prep_inp_data->num_components + 1, sizeof(PINChI2) );
             PINChI_Aux2* newPTR2 = (PINChI_Aux2*)inchi_calloc( (long long)cur_prep_inp_data->num_components + 1, sizeof(PINChI_Aux2) );
             if ( newPTR1 && newPTR2 )
-            { 
+            {
                 if (pINChI2[iINChI] && sd->num_components[iINChI] > 0)
                     memcpy( newPTR1, pINChI2[iINChI], (sd->num_components[iINChI]) * sizeof(PINChI2) );
                 if (pINChI_Aux2[iINChI] && sd->num_components[iINChI] > 0)
                     memcpy( newPTR2, pINChI_Aux2[iINChI], (sd->num_components[iINChI]) * sizeof(PINChI_Aux2) );
-                if (pINChI2[iINChI]) 
+                if (pINChI2[iINChI])
                     inchi_free(pINChI2[iINChI]);
                 if (pINChI_Aux2[iINChI])
                     inchi_free(pINChI_Aux2[iINChI]);
                 pINChI2[iINChI] = newPTR1;
                 pINChI_Aux2[iINChI] = newPTR2;
                 sd->num_components[iINChI] = cur_prep_inp_data->num_components;
                 k  = 0;
-            } 
-            else 
-            {        
-                inchi_free(newPTR1); 
-                inchi_free(newPTR2); 
+            }
+            else
+            {
+                inchi_free(newPTR1);
+                inchi_free(newPTR2);
                 k = 1;
-            }             
-        } 
-        else 
-        { 
-            k = 0; 
+            }
+        }
+        else
+        {
+            k = 0;
         }
     } while (0);
 
@@ -790,7 +791,7 @@ int NormOneComponentINChI( CANON_GLOBALS *pCG,
     {
         num_at = Normalization_step(pCG, ic,
             cur_INChI, cur_INChI_Aux,
-            inp_cur_data->at, inp_norm_data, inp_cur_data->num_at,
+            inp_cur_data->at, inp_norm_data, inp_cur_data->num_at, inp_cur_data->keep_explicit_HDT,
             pulTEnd, &bTautFlags, &bTautFlagsDone, cti);
 
         SetConnectedComponentNumber(inp_cur_data->at, inp_cur_data->num_at, i + 1); /*  normalization alters structure component number */
@@ -1142,6 +1143,7 @@ int  Normalization_step( CANON_GLOBALS *pCG,
                          inp_ATOM *inp_at,
                          INP_ATOM_DATA *out_norm_data[2],
                          int num_inp_at,
+                         const unsigned char *keep_explicit_HDT,
                          struct tagInchiTime *ulMaxTime,
                          INCHI_MODE *pbTautFlags,
                          INCHI_MODE *pbTautFlagsDone,
@@ -1182,7 +1184,7 @@ int  Normalization_step( CANON_GLOBALS *pCG,
 
     memset( z->s, 0, sizeof( z->s ) ); /* djb-rwth: memset_s C11/Annex K variant? */
 
-    if (pBCN) 
+    if (pBCN)
         memset( pBCN, 0, sizeof( pBCN[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */
 
     memset( t_group_info, 0, sizeof( *t_group_info ) ); /* djb-rwth: memset_s C11/Annex K variant? */
@@ -1251,7 +1253,7 @@ int  Normalization_step( CANON_GLOBALS *pCG,
     }
     else
     {
-        z->num_at_tg = z->num_atoms = remove_terminal_HDT( num_inp_at, z->out_at, z->fix_termhchrg );
+        z->num_at_tg = z->num_atoms = remove_terminal_HDT( num_inp_at, z->out_at, z->fix_termhchrg, keep_explicit_HDT);
 
         z->num_deleted_H = num_inp_at - z->num_atoms;
         t_group_info->tni.nNumRemovedExplicitH = z->num_deleted_H;

diff --git a/INCHI-1-SRC/INCHI_BASE/src/ichimake.c b/INCHI-1-SRC/INCHI_BASE/src/ichimake.c
@@ -3712,6 +3712,7 @@ int  Create_INChI(CANON_GLOBALS* pCG,
     inp_ATOM* inp_at,
     INP_ATOM_DATA* out_norm_data[2],
     int num_inp_at,
+    const unsigned char* keep_explicit_HDT,
     INCHI_MODE nUserMode,
     INCHI_MODE* pbTautFlags,
     INCHI_MODE* pbTautFlagsDone,
@@ -3893,7 +3894,7 @@ int  Create_INChI(CANON_GLOBALS* pCG,
     }
     else
     {
-        num_at_tg = num_atoms = remove_terminal_HDT(num_inp_at, out_at, bFixTermHChrg);
+        num_at_tg = num_atoms = remove_terminal_HDT(num_inp_at, out_at, bFixTermHChrg, keep_explicit_HDT);
         num_removed_H = num_inp_at - num_atoms;
         t_group_info->tni.nNumRemovedExplicitH = num_removed_H;
         add_DT_to_num_H(num_atoms, out_at);

diff --git a/INCHI-1-SRC/INCHI_BASE/src/ichinorm.c b/INCHI-1-SRC/INCHI_BASE/src/ichinorm.c
@@ -5805,7 +5805,7 @@ int OAD_Edit_Underivatize( struct tagINCHI_CLOCK *ic,
     /*set_R2C_el_numbers( );*/
 
 #ifndef UNDERIV_ADD_EXPLICIT_H
-    num_atoms = remove_terminal_HDT( orig_inp_data->num_inp_atoms, at, 1 );
+    num_atoms = remove_terminal_HDT( orig_inp_data->num_inp_atoms, at, 1, NULL );
     /*^^^^^ always accomodate accomodate FIX_TERM_H_CHRG_BUG - IPl, July 2008*/
     num_removed_H = orig_inp_data->num_inp_atoms - num_atoms;
     orig_inp_data->num_inp_atoms = num_atoms;
@@ -5833,7 +5833,7 @@ int OAD_Edit_Underivatize( struct tagINCHI_CLOCK *ic,
         }
 
 #ifdef UNDERIV_ADD_EXPLICIT_H
-        num_atoms = remove_terminal_HDT(inp_cur_data[i_component].num_at, inp_cur_data[i_component].at, 1);
+        num_atoms = remove_terminal_HDT(inp_cur_data[i_component].num_at, inp_cur_data[i_component].at, 1, NULL);
         inp_cur_data[i_component].num_removed_H = inp_cur_data[i_component].num_at - num_atoms;
         inp_cur_data[i_component].num_at = num_atoms;
 #endif
@@ -7184,7 +7184,7 @@ int Ring2Chain( struct tagINCHI_CLOCK *ic,
 
     /*set_R2C_el_numbers( );*/
 
-    num_atoms = remove_terminal_HDT( orig_inp_data->num_inp_atoms, at, 1 );
+    num_atoms = remove_terminal_HDT( orig_inp_data->num_inp_atoms, at, 1, NULL );
     /*^^^^^ always accomodate accomodate FIX_TERM_H_CHRG_BUG - IPl, July 2008*/
     orig_inp_data->num_inp_atoms = num_atoms;
 

diff --git a/INCHI-1-SRC/INCHI_BASE/src/ichinorm.h b/INCHI-1-SRC/INCHI_BASE/src/ichinorm.h
@@ -110,7 +110,8 @@ int MakeIsotopicHGroup( inp_ATOM *at,
 
 int remove_terminal_HDT( int num_atoms,
                          inp_ATOM *at,
-                         int bFixTermHChrg );
+                         int bFixTermHChrg,
+                         const unsigned char* keep_explicit_HDT);
 int RemoveExcessiveImplicitH( int num_atoms,
                               int num_removed_H,
                               inp_ATOM *at );

diff --git a/INCHI-1-SRC/INCHI_BASE/src/ichirvr1.c b/INCHI-1-SRC/INCHI_BASE/src/ichirvr1.c
@@ -5332,6 +5332,7 @@ int MakeOneInChIOutOfStrFromINChI( struct tagCANON_GLOBALS *pCG,
                            inp_cur_data->at,
                            inp_norm_data,
                            inp_cur_data->num_at + inp_cur_data->num_removed_H,
+                           NULL,
                            ip->nMode,
                            &bTautFlags,
                            &bTautFlagsDone,

diff --git a/INCHI-1-SRC/INCHI_BASE/src/inpdef.h b/INCHI-1-SRC/INCHI_BASE/src/inpdef.h
@@ -568,6 +568,7 @@ typedef struct tagInfoAtomData
  *
  * @param at                   Array of input atoms
  * @param at_fixed_bonds       Array of input atoms with fixed bonds (tautomeric case, added or removed H)
+ * @param keep_explicit_HDT    Component-local polymer crossing-bond endpoint mask used to prevent explicit H/D/T removal
  * @param num_at               Number of atoms
  * @param num_removed_H        Number of removed hydrogens
  * @param num_bonds            Number of bonds
@@ -588,6 +589,7 @@ typedef struct tagInputAtomData
 {
     inp_ATOM *at;
     inp_ATOM *at_fixed_bonds; /* tautomeric case, added or removed H  */
+    unsigned char *keep_explicit_HDT;
     int num_at;
     int num_removed_H;
     int num_bonds;

diff --git a/INCHI-1-SRC/INCHI_BASE/src/mol2atom.c b/INCHI-1-SRC/INCHI_BASE/src/mol2atom.c
@@ -1183,6 +1183,14 @@ void FreeInpAtomData(INP_ATOM_DATA *inp_at_data)
     {
         FreeInpAtom(&inp_at_data->at);
         FreeInpAtom(&inp_at_data->at_fixed_bonds);
+
+        /*@nnuk*/
+        if (inp_at_data->keep_explicit_HDT)
+        {
+            inchi_free(inp_at_data->keep_explicit_HDT);
+            inp_at_data->keep_explicit_HDT = NULL;
+        }
+
         memset(inp_at_data, 0, sizeof(*inp_at_data)); /* djb-rwth: memset_s C11/Annex K variant? */
     }
 
@@ -1557,12 +1565,10 @@ int SetExtOrigAtDataByMolfileExtInput(MOL_FMT_DATA *mfdata,
                     ia2 = mfdata->ctab.bonds[ib - 1].atnum2;
                     unitk->blist[2 * m] = ia1;
                     unitk->blist[2 * m + 1] = ia2;
-                    if (!strcmp(mfdata->ctab.atoms[ia1 - 1].symbol, "H") ||
-                        !strcmp(mfdata->ctab.atoms[ia2 - 1].symbol, "H"))
-                    {
-                        TREAT_ERR(err, 9002, "Hydrogen as polymer end group is not supported");
-                        goto exit_function;
-                    }
+
+                    /**
+                     *@nnuk: GHI#252 addressed and redundant logic removed
+                     */
                 }
             }
             else

diff --git a/INCHI-1-SRC/INCHI_BASE/src/runichi.c b/INCHI-1-SRC/INCHI_BASE/src/runichi.c
@@ -327,26 +327,13 @@ int ProcessOneStructure(INCHI_CLOCK* ic,
             goto exit_function;
         }
 
-        /*// Debugging: Print atom structure after disconnections
-        for (int i = 0; i < orig_inp_data->num_inp_atoms; i++)
-        {
-            printf("Atom %d: Element %s, Valence: %d, Charge: %d, Num of Implicit H: %d, Neighbors: ",
-                i + 1, orig_inp_data->at[i].elname, orig_inp_data->at[i].valence, orig_inp_data->at[i].charge, orig_inp_data->at[i].num_H);
-            for (int j = 0; j < orig_inp_data->at[i].valence; j++)
-            {
-                printf("%d ", orig_inp_data->at[i].neighbor[j] + 1);
-            }
-            printf("\n");
-        }*/
-
         /* Preserve SDF output in Molecular Inorganics mode if requested */
         ret1 = OrigAtData_SaveMolfile(orig_inp_data, sd, ip, num_inp, out_file);
         if (ret1)
         {
             goto exit_function;
         }
 
-        /*printf("Molecular inorganics preprocessing completed successfully.\n");*/
         nRet1 = CreateOneStructureINChI(pCG, ic, sd, ip, szTitle,
             pINChI, pINChI_Aux, INCHI_BAS,
             inp_file, log_file, out_file, prb_file,
@@ -361,7 +348,6 @@ int ProcessOneStructure(INCHI_CLOCK* ic,
             (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE) &&
             (ip->bTautFlags & TG_FLAG_RECONNECT_COORD) )
         {
-            /*printf("Generating reconnected InChI due to retained bonds.\n");*/
 
             nRet1 = CreateOneStructureINChI(pCG, ic, sd, ip, szTitle,
                 pINChI, pINChI_Aux, INCHI_REC,
@@ -391,10 +377,9 @@ int ProcessOneStructure(INCHI_CLOCK* ic,
         /*
          * InChI is already generated via the Molecular Inorganics-specific path.
          * Skip the standard structure-generation path to prevent duplicate
-         * CreateOneStructureINChI() calls, which previously caused redundant
-         * allocations and AddressSanitizer-reported memory leaks.
+         * CreateOneStructureINChI() calls and redundant allocations.
          *
-         * pOrigStruct was populated above from the native input, so the shared
+         * pOrigStruct and OrigStruct were populated above from the native input, so the shared
          * cleanup path (SortAndPrintINChI + OrigStruct_Free) emits the AuxInfo
          * reversibility layers (/rA, /rB, /rC), including atom coordinates, and
          * releases it.
@@ -1978,6 +1963,7 @@ int CreateOneComponentINChI(CANON_GLOBALS* pCG,
         cur_INChI, cur_INChI_Aux,
         orig_inp_data/* not used */,
         inp_cur_data->at, inp_norm_data, inp_cur_data->num_at,
+        inp_cur_data->keep_explicit_HDT,
         ip->nMode,
         &bTautFlags, &bTautFlagsDone,
         pulTEnd, NULL, sd->pStrErrStruct);