rino 0.1.0 → 0.2.0

data/ext/src/ichimake.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
  */
 
@@ -70,6 +70,8 @@
 #define iiEq2ISO     0x0080  /* isotopic */
 #define iiEq2INV     0x0100  /* equal to inverted (stereo sp3) or to numbering of inverted stereo */
 
+#define iiEmpty      0x0200  /* item is empty while in the preceding layer the item is not empty */
+
 /*********************** Printing strings external declarations *******************************/
 
 extern const char sCompDelim[];

data/ext/src/ichimap1.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
  */
 
@@ -38,18 +38,18 @@ int All_SC_Same(  AT_RANK canon_rank1, /*  canonical number */
     AT_RANK r1 = pRankStack1[0][n1];
     int     iMax1 = (int)r1;
     int     i1, s1;
-    int     bFound=0, stereo_atom_parity;
+    int     bFound=0, stereo_atom_parity=-1;
 
     /*  find one stereo atom such that canon_rank1 can be mapped on it */
     for ( i1 = 1; i1 <= iMax1 && r1 == pRankStack2[0][s1=(int)pRankStack2[1][iMax1-i1]]; i1++ ) {
         if ( at[s1].stereo_bond_neighbor[0] ) {
-            bFound=0; /* at[s1] is not sp3-stereogenic: it belongs to stereobond */
+            bFound=0; /* at[s1] is not sp3-stereogenic: it belongs to a stereobond */
             break;
         } else
         if ( i1 == 1 ) {
             stereo_atom_parity = PARITY_VAL(at[s1].stereo_atom_parity);
             if ( !ATOM_PARITY_KNOWN(stereo_atom_parity) ) {
-                bFound=0;  /* at[s1] does not have KNOWN parity */
+                bFound=0;  /* at[s1] does not have a KNOWN parity */
                 break;
             }
         } else

data/ext/src/ichimap2.c

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

data/ext/src/ichimap4.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
  */
 
@@ -67,7 +67,6 @@ int map_stereo_bonds4 (
                           */
     int tpos1;
     AT_STEREO_DBLE prevBond;
-
     tpos1 = CurTreeGetPos( cur_tree );
 
 total_restart:
@@ -604,29 +603,29 @@ repeat_all:
                 at_rank_canon_n1 = 0;
                 at_rank_canon_n2 = 0;
                 for ( i = 0; i < num1; i ++ ) {
-                    int at_from, at_to;
+                    int at_from_n1, at_to_n1, at_no_n1_num_success = 0;
                     istk2 = istk;
                     if ( num1 == 2 ) {
                         at_rank_canon_n1 = nCanonRankFrom[EN1[0].from_at];
                         /*  an additional neighbor mapping is necessary; */
                         /*  we need to map only one at_from1 neighbor to make all neighbors have different ranks */
 
-                        at_from = EN1[0].from_at;
-                        at_to   = EN1[0].to_at[i];
+                        at_from_n1 = EN1[0].from_at;
+                        at_to_n1   = EN1[0].to_at[i];
 
                         if ( tpos1 < CurTreeGetPos( cur_tree ) &&
                              1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n1 ) &&
-                             1 == CurTreeIsLastAtomEqu( cur_tree, at_to, nSymmStereo ) )
+                             1 == CurTreeIsLastAtomEqu( cur_tree, at_to_n1, nSymmStereo ) )
                             continue;
                         /*
                         if ( nSymmStereo && !pCS->bFirstCT ) {
-                            if ( i && nSymmStereo[at_to] == nSymmStereo[(int)EN1[0].to_at[0]] ) {
+                            if ( i && nSymmStereo[at_to_n1] == nSymmStereo[(int)EN1[0].to_at[0]] ) {
                                 continue; // do not test stereo equivalent atoms except the first one
                             }
                         }
                         */
                         /*  neighbors are tied. Untie them by breaking a tie on ONE of them. */
-                        ret1 = map_an_atom2( num_at_tg, num_max, at_from, at_to,
+                        ret1 = map_an_atom2( num_at_tg, num_max, at_from_n1, at_to_n1,
                                             nTempRank, nNumMappedRanks[istk2], &nNumMappedRanks[istk2+1], pCS,
                                             NeighList, pRankStack1+nStackPtr[istk2], pRankStack2+nStackPtr[istk2],
                                             &bAddStack );
@@ -644,7 +643,7 @@ repeat_all:
                                  0 == CurTreeIsLastRank( cur_tree, at_rank_canon_n1 ) ) {
                                 CurTreeAddRank( cur_tree, at_rank_canon_n1 );
                             }
-                            CurTreeAddAtom( cur_tree, at_to );
+                            CurTreeAddAtom( cur_tree, at_to_n1 );
                         }
 
 
@@ -668,27 +667,28 @@ repeat_all:
                     num2 = parity2 > 0? 1:2;
                     at_rank_canon_n2 = 0;
                     for ( j = 0; j < num2; j ++ ) {
+                        int at_from_n2, at_to_n2;
                         istk3 = istk2;
                         if ( num2 == 2 ) {
                             at_rank_canon_n2 = nCanonRankFrom[EN2[0].from_at];
                             /*  we need to map only one at_from2 neighbor to make its neighbors have different ranks */
-                            at_from = EN2[0].from_at;
-                            at_to   = EN2[0].to_at[j];
+                            at_from_n2 = EN2[0].from_at;
+                            at_to_n2   = EN2[0].to_at[j];
 
                             if ( tpos1 < CurTreeGetPos( cur_tree ) &&
                                  1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n2 ) &&
-                                 1 == CurTreeIsLastAtomEqu( cur_tree, at_to, nSymmStereo ) )
+                                 1 == CurTreeIsLastAtomEqu( cur_tree, at_to_n2, nSymmStereo ) )
                                 continue;
                             
                             /*
                             if ( nSymmStereo && !pCS->bFirstCT ) {
-                                if ( j && nSymmStereo[at_to] == nSymmStereo[(int)EN2[0].to_at[0]] ) {
+                                if ( j && nSymmStereo[at_to_n2] == nSymmStereo[(int)EN2[0].to_at[0]] ) {
                                     continue; // do not test stereo equivalent atoms except the first one
                                 }
                             }
                             */
                             /*  neighbors are tied. Untie them by breaking a tie on ONE of them. */
-                            ret1 = map_an_atom2( num_at_tg, num_max, at_from, at_to,
+                            ret1 = map_an_atom2( num_at_tg, num_max, at_from_n2, at_to_n2,
                                                 nTempRank, nNumMappedRanks[istk3], &nNumMappedRanks[istk3+1], pCS,
                                                 NeighList, pRankStack1+nStackPtr[istk3],
                                                 pRankStack2+nStackPtr[istk3],
@@ -704,7 +704,7 @@ repeat_all:
                                      0 == CurTreeIsLastRank( cur_tree, at_rank_canon_n2 ) ) {
                                     CurTreeAddRank( cur_tree, at_rank_canon_n2 );
                                 }
-                                CurTreeAddAtom( cur_tree, at_to );
+                                CurTreeAddAtom( cur_tree, at_to_n2 );
                             }
 
                             parity2 = parity_of_mapped_half_bond( at_from2, at_to2, at_from1, at_to1, at, &EN2[1],
@@ -749,7 +749,7 @@ repeat_all:
                             /*  remove failed atom2 from the tree */
                             if ( tpos1 < CurTreeGetPos( cur_tree ) &&
                                  1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n2 ) ) {
-                                CurTreeRemoveIfLastAtom( cur_tree, at_to );
+                                CurTreeRemoveIfLastAtom( cur_tree, at_to_n2 );
                                 CurTreeRemoveLastRankIfNoAtoms( cur_tree );
                             }
                             continue;  /*  Reject: not a minimal CT. */
@@ -801,6 +801,7 @@ repeat_all:
                                     CurTreeKeepLastAtomsOnly( cur_tree, tpos1, 1 );  /*  start over */
                                     nTotSuccess |= 2; /*  Obtained a smaller CT */
                                 }
+                                at_no_n1_num_success ++;
                             } else {
                                 if ( bStereoIsBetterWasSetHere ) {  /*  rollback */
                                     pCS->bStereoIsBetter = 0;
@@ -808,7 +809,7 @@ repeat_all:
                                 }
                                 if ( tpos1 < CurTreeGetPos( cur_tree ) &&
                                      1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n2 ) ) {
-                                    CurTreeRemoveIfLastAtom( cur_tree, at_to );
+                                    CurTreeRemoveIfLastAtom( cur_tree, at_to_n2 );
                                     CurTreeRemoveLastRankIfNoAtoms( cur_tree );
                                 }
                             }
@@ -819,6 +820,12 @@ repeat_all:
                          1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n2 ) ) {
                          CurTreeRemoveLastRank( cur_tree );
                     }
+                    /* added 2006-07-20 */
+                    if ( !at_no_n1_num_success && tpos1 < CurTreeGetPos( cur_tree ) &&
+                        1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n1 ) ) {
+                         CurTreeRemoveIfLastAtom( cur_tree, at_to_n1 );
+                    }
+                         
                 } /*  end choices in mapping neighbors of the 1st half-bond */
                 if (  tpos1 < CurTreeGetPos( cur_tree ) &&
                       1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n1 ) ) {
@@ -1174,7 +1181,7 @@ repeat_all:
             
             /*********************************************************************************
              *
-             *   Unknown Stereocenter Parity case: possibly need to map stereo bond neighbors
+             *   Unknown Stereocenter Parity case: possibly need to map stereo center neighbors
              */
             if ( stereo_center_parity == sb_parity_calc )
             {
@@ -1230,14 +1237,20 @@ repeat_all:
                     pCS->LinearCTStereoCarb[nNumMappedAtoms].parity = parity1;
                     pCS->LinearCTStereoCarb[nNumMappedAtoms].at_num = at_rank_canon1;
                     pCS->bRankUsedForStereo[at_from1] = 3;
-                    pCS->bAtomUsedForStereo[at_to1] -= STEREO_AT_MARK;
+#if( FIX_ChCh_STEREO_CANON_BUG == 1 )
+                    if ( !bAllParitiesIdentical )
+#endif
+                        pCS->bAtomUsedForStereo[at_to1] -= STEREO_AT_MARK;
 
                     ret = map_stereo_atoms4 ( at, num_atoms, num_at_tg, num_max, nCanonRankFrom, nAtomNumberCanonFrom, nCanonRankTo,
                                        nSymmRank, pRankStack1+nStackPtr[istk],  pRankStack2+nStackPtr[istk],
                                        nTempRank,  nMappedRanks[istk],  nSymmStereo,  NeighList,
                                        pCS, cur_tree, nNumMappedAtoms+1 );
                     pCS->bRankUsedForStereo[at_from1] = 0;
-                    pCS->bAtomUsedForStereo[at_to1] += STEREO_AT_MARK;
+#if( FIX_ChCh_STEREO_CANON_BUG == 1 )
+                    if ( !bAllParitiesIdentical )
+#endif
+                        pCS->bAtomUsedForStereo[at_to1] += STEREO_AT_MARK;
                     if ( ret == 4 ) {
                         return ret;
                     }

data/ext/src/ichinorm.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
  */
 
@@ -122,7 +122,10 @@ int MarkRingSystemsInp( inp_ATOM *at, int num_atoms )
     do {
         /* advance */
 advance_block:
-        if ( (int)at[i=nStackAtom[nTopStackAtom]].valence > (j = (int)cNeighNumb[i]) ) {
+        /*if ( (int)at[i=nStackAtom[nTopStackAtom]].valence > (j = (int)cNeighNumb[i]) )*/
+        /* replaced due to missing sequence point */
+        if ( i=(int)nStackAtom[nTopStackAtom], j = (int)cNeighNumb[i], (int)at[i].valence > j )
+        {
             cNeighNumb[i] ++;
             u = (int)at[i].neighbor[j];
             if ( !nDfsNumber[u] ) {
@@ -199,7 +202,10 @@ advance_block:
     do {
         /* advance */
 advance_ring:
-        if ( (int)at[i=nStackAtom[nTopStackAtom]].valence > (j = (int)cNeighNumb[i]) ) {
+        /*if ( (int)at[i=nStackAtom[nTopStackAtom]].valence > (j = (int)cNeighNumb[i]) )*/
+        /* replaced due to missing sequence point */
+        if ( i=(int)nStackAtom[nTopStackAtom], j = (int)cNeighNumb[i], (int)at[i].valence > j )
+        {
             cNeighNumb[i] ++;
             u = (int)at[i].neighbor[j];
             if ( !nDfsNumber[u] ) {
@@ -523,7 +529,7 @@ int remove_terminal_HDT( int num_atoms, inp_ATOM *at )
         at[i].component = i; /*  temporarily save original numbering */
         /*  get k = temp. hydrogen isotope/non-hydrogen atom type: */
         /*  k=0:H, k=2:D, k=3:T, k=4=kMax: not a hydrogen */
-        k = at[i].elname[1]? kMax : (p=strchr(szHDT, at[i].elname[0]))? p-szHDT : kMax;
+        k = at[i].elname[1]? kMax : (p=(char*)strchr(szHDT, at[i].elname[0]))? p-szHDT : kMax;
         /*  set hydrogen isotope atw differences */
         /*  Notes: k-value of isotopic H is incremented to correct iso_atw_diff value later. */
         /*         1H isotope cannot be detected here. */

data/ext/src/ichinorm.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
  */
 
@@ -47,6 +47,7 @@ int free_t_group_info( T_GROUP_INFO *t_group_info );
 int make_a_copy_of_t_group_info( T_GROUP_INFO *t_group_info, T_GROUP_INFO *t_group_info_orig );
 int set_tautomer_iso_sort_keys( T_GROUP_INFO *t_group_info );
 int CountTautomerGroups( sp_ATOM *at, int num_atoms, T_GROUP_INFO *t_group_info );
+int CountTautomerGroupsInpAt( inp_ATOM *at, int num_atoms, T_GROUP_INFO *t_group_info );
 int SortTautomerGroupsAndEndpoints( T_GROUP_INFO *t_group_info, int num_atoms, int num_at_tg, AT_RANK *nRank );
 int FillIsotopicAtLinearCT( int num_atoms, sp_ATOM* at, const AT_RANK *nAtomNumber,
                             AT_ISOTOPIC *LinearCTIsotopic, int nMaxLenLinearCTIsotopic, int *pnLenLinearCTIsotopic );

data/ext/src/ichiparm.c

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

data/ext/src/ichiparm.h

@@ -2,8 +2,8 @@
  * International Union of Pure and Applied Chemistry (IUPAC)
  * International Chemical Identifier (InChI)
  * Version 1
- * Software version 1.00
- * April 13, 2005
+ * Software version 1.01
+ * July 21, 2006
  * Developed at NIST
  */
 
@@ -62,7 +62,12 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
     int           bDisplay = 0;
     int           bNoStructLabels = 0;
     int           bOutputMolfileOnly = 0;
+    int           bOutputMolfileDT = 0;
+    int           bOutputMolfileSplit = 0;
     int           bForcedChiralFlag = 0;
+#if( READ_INCHI_STRING == 1 )
+    int           bDisplayIfRestoreWarnings = 0;
+#endif
 #ifdef INCHI_LIB
     int           bXml = INCHI_OUT_XML;
 #else
@@ -73,6 +78,16 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
 #ifdef STEREO_WEDGE_ONLY
     int bPointedEdgeStereo = STEREO_WEDGE_ONLY; /*   NEWPS TG_FLAG_POINTED_EDGE_STEREO*/
 #endif
+#if( FIX_ADJ_RAD == 1 )
+    int bFixAdjacentRad = 0;
+#endif
+#if( ADD_PHOSPHINE_STEREO == 1 )
+    int bAddPhosphineStereo = 0;
+#endif
+#if( ADD_ARSINE_STEREO == 1 )
+    int bAddArsineStereo = 0;
+#endif
+    int bFixSp3bug        = 0;
 
 
     ext[0] = ".mol";
@@ -207,10 +222,10 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
             } else
 #endif
             if ( !memicmp( pArg, "START:", 6 ) ) {
-                ip->first_struct_number = (int)strtol(pArg+6, NULL, 10);
+                ip->first_struct_number = strtol(pArg+6, NULL, 10);
             } else
             if ( !memicmp( pArg, "END:", 4 ) ) {
-                ip->last_struct_number = (int)strtol(pArg+4, NULL, 10);
+                ip->last_struct_number = strtol(pArg+4, NULL, 10);
             } else /*  RSB: */
             if ( !memicmp( pArg, "RSB:", 4 ) ) {
                 mdbr = (int)strtol(pArg+4, NULL, 10);
@@ -371,11 +386,28 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
             if ( !stricmp( pArg, "NoADP" ) ) {
                  bTgFlagHardAddRenProtons = 0;
             } else
+            if ( !stricmp( pArg, "FixSp3bug" ) ) {
+                 bFixSp3bug = 1;
+            } else
+            if ( !stricmp( pArg, "FB" ) ) {
+                 bFixSp3bug = 1; /* fix all known v1 bugs */
+            } else
 #ifdef STEREO_WEDGE_ONLY
             if ( !stricmp( pArg, "NEWPS" ) ) {
                  bPointedEdgeStereo = 1;
             } else
 #endif
+#if( ADD_PHOSPHINE_STEREO == 1 )
+            if ( !stricmp( pArg, "SPXYZ" ) ) {
+                 bAddPhosphineStereo = 1;
+            } else
+#endif
+#if( ADD_ARSINE_STEREO == 1 )
+            if ( !stricmp( pArg, "SASXYZ" ) ) {
+                 bAddArsineStereo = 1;
+            } else
+#endif
+
             if ( !stricmp( pArg, "PW" ) ) {
                 ip->bSaveWarningStructsAsProblem = 1;
             } else {
@@ -517,10 +549,26 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
             if ( !stricmp( pArg, "SUU" ) ) {       /* include omitted undef/unkn stereo */
                 bVer1DefaultMode &= ~(REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU);
             } else
+            if ( !stricmp( pArg, "FixSp3bug" ) ) {
+                 bFixSp3bug = 1;
+            } else
+            if ( !stricmp( pArg, "FB" ) ) {
+                 bFixSp3bug = 1; /* fix all known v1 bugs */
+            } else
 #ifdef STEREO_WEDGE_ONLY
             if ( !stricmp( pArg, "NEWPS" ) ) {
                  bPointedEdgeStereo = 1;
             } else
+#endif
+#if( ADD_PHOSPHINE_STEREO == 1 )
+            if ( !stricmp( pArg, "SPXYZ" ) ) {
+                 bAddPhosphineStereo = 1;
+            } else
+#endif
+#if( ADD_ARSINE_STEREO == 1 )
+            if ( !stricmp( pArg, "SASXYZ" ) ) {
+                 bAddArsineStereo = 1;
+            } else
 #endif
             if ( !stricmp( pArg, "RECMET" ) ) {    /* do reconnect metals */
                 bReconnectCoord = 1;
@@ -542,6 +590,12 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
             if ( !stricmp( pArg, "D" ) ) {          /* display the structures */
                 bDisplay |= 1;
             } else
+#if( READ_INCHI_STRING == 1 )
+            if ( !stricmp( pArg, "DDSRC" ) ) {
+                bDisplayIfRestoreWarnings = 1;  /* InChI->Structure debugging: Display Debug Structure Restore Components */
+            }
+            else
+#endif
             if ( !stricmp( pArg, "NOLABELS" ) ) {
                  bNoStructLabels = 1;
             } else
@@ -578,7 +632,32 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
                 bXml                |= INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS;
                 bXml                &= ~(INCHI_OUT_XML | INCHI_OUT_XML_TEXT_COMMENTS);
             } else
-            if ( INPUT_NONE == ip->nInputType &&
+#if( READ_INCHI_STRING == 1 )
+            if ( !stricmp( pArg, "InChI2InChI" )  ) {
+                 /* Read InChI Identifiers and output InChI Identifiers */
+                ip->nInputType = INPUT_INCHI;
+                ip->bReadInChIOptions |= READ_INCHI_OUTPUT_INCHI;
+                ip->bReadInChIOptions &= ~READ_INCHI_TO_STRUCTURE;
+            } else
+            if ( !stricmp( pArg, "SplitInChI" )  ) {
+                 /* Split InChI Identifiers into components */
+                ip->bReadInChIOptions |= READ_INCHI_SPLIT_OUTPUT;
+            } else
+            if ( !stricmp( pArg, "InChI2Struct" )  ) {
+                 /* Split InChI Identifiers into components */
+                ip->bReadInChIOptions |= READ_INCHI_TO_STRUCTURE;
+                ip->bReadInChIOptions &= ~READ_INCHI_OUTPUT_INCHI;
+                ip->nInputType = INPUT_INCHI;
+            } else
+            if ( !stricmp( pArg, "KeepBalanceP" )  ) {
+                 /* When spliting InChI Identifiers into components: */
+                 /* If MobileH output then add p to each component;  */
+                 /* Otherwise add one more component containing balance */
+                 /* of protons and exchangeable isotopic H */
+                ip->bReadInChIOptions |= READ_INCHI_KEEP_BALANCE_P;
+            } else
+#endif
+            if ( /* INPUT_NONE == ip->nInputType &&*/
                 !memicmp( pArg, "SDF:", 4 )  ) {
                  /* SDfile label */
                 k = 0;
@@ -587,11 +666,15 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
                 if ( k ) {
                     ip->pSdfLabel  = ip->szSdfDataHeader;
                     ip->pSdfValue  = szSdfDataValue;
-                    ip->nInputType = INPUT_SDFILE;
+                    if ( INPUT_NONE == ip->nInputType ) {
+                        ip->nInputType = INPUT_SDFILE;
+                    }
                 } else {
                     ip->pSdfLabel  = NULL;
                     ip->pSdfValue  = NULL;
-                    ip->nInputType = INPUT_MOLFILE;
+                    if ( INPUT_NONE == ip->nInputType ) {
+                        ip->nInputType = INPUT_MOLFILE;
+                    }
                 }
             } else
 #if( ADD_CMLPP == 1 )
@@ -604,15 +687,26 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
             if ( !stricmp( pArg, "RECMET-" ) ) {     /* do not reconnect metals (default) */
                 bReconnectCoord = 0;
             } else
-            if ( !stricmp( pArg, "OUTPUTSDF" ) ) {  /* ourput SDfile */
+            if ( !stricmp( pArg, "OUTPUTSDF" ) ) {  /* output SDfile */
                 bOutputMolfileOnly = 1;
             } else
+            if ( !stricmp( pArg, "SdfAtomsDT" ) ) {  /* output isotopes H as D and T in SDfile */
+                bOutputMolfileDT = 1;
+            } else                                    
+            if ( !stricmp( pArg, "SdfSplit" ) ) {  /* Split single Molfiles into disconnected components */
+                bOutputMolfileSplit = 1;
+            } else
             if ( !stricmp( pArg, "STDIO" ) ) {
                 bNameSuffix = 0;
             } else
             if ( !stricmp( pArg, "DCR" ) ) {
                 bDisplayCompositeResults = 1;
             } else
+#if( FIX_ADJ_RAD == 1 )
+            if ( !stricmp( pArg, "FixRad" ) ) {
+                bFixAdjacentRad = 1;
+            } else
+#endif
             /*============= Additional options ==========*/
             /* Tautomer perception off */
             if ( !stricmp( pArg, "EXACT" ) ) {
@@ -662,10 +756,10 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
                 bDisconnectSalts = 0;
             } else
             if ( !memicmp( pArg, "START:", 6 ) ) {
-                ip->first_struct_number = (int)strtol(pArg+6, NULL, 10);
+                ip->first_struct_number = strtol(pArg+6, NULL, 10);
             } else
             if ( !memicmp( pArg, "END:", 4 ) ) {
-                ip->last_struct_number = (int)strtol(pArg+4, NULL, 10);
+                ip->last_struct_number = strtol(pArg+4, NULL, 10);
             } else /*  RSB: */
             if ( !memicmp( pArg, "RSB:", 4 )) {
                 mdbr = (int)strtol(pArg+4, NULL, 10);
@@ -734,7 +828,7 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
                 szOutputPath[len++] = INCHI_PATH_DELIM;
                 szOutputPath[len]   = '\0';
             }
-            if ( len > 0 && (r = strrchr( p, INCHI_PATH_DELIM ) ) && r[1] ) {
+            if ( len > 0 && (r = (char *)strrchr( p, INCHI_PATH_DELIM ) ) && r[1] ) {
                 strcat( szOutputPath, r+1 );
                 p = szOutputPath;
             }
@@ -757,7 +851,33 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
         }
     }
 
-#endif  /* } ACD_LABS_VERSION */
+#endif  /* } NOT ACD_LABS_VERSION */
+
+
+#if( READ_INCHI_STRING == 1 )
+    if ( INPUT_INCHI == ip->nInputType ) {
+        bCompareComponents                 = 0;
+        /*bDisplayCompositeResults           = 0;*/
+        bOutputMolfileOnly                 = 0;
+        /*bNoStructLabels                    = 1;*/
+        bINChIOutputOptions  |= INCHI_OUT_NO_AUX_INFO;
+        bINChIOutputOptions  &= ~INCHI_OUT_SHORT_AUX_INFO;
+        bINChIOutputOptions  &= ~INCHI_OUT_ONLY_AUX_INFO;
+        ip->bDisplayIfRestoreWarnings = bDisplayIfRestoreWarnings;
+
+        if ( !(bINChIOutputOptions &
+            
+             (INCHI_OUT_SDFILE_ONLY          |
+              INCHI_OUT_XML                  |
+              INCHI_OUT_PLAIN_TEXT           |
+              INCHI_OUT_PLAIN_TEXT_COMMENTS  |
+              INCHI_OUT_XML_TEXT_COMMENTS    
+                                             ) ) ) {
+
+            bINChIOutputOptions |= INCHI_OUT_PLAIN_TEXT;
+        }
+    }
+#endif
 
 
     if ( bVer1Options ) {
@@ -834,6 +954,10 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
     if ( bOutputMolfileOnly ) {
         bXml &= ~(INCHI_OUT_XML                 | INCHI_OUT_PLAIN_TEXT |
                   INCHI_OUT_PLAIN_TEXT_COMMENTS | INCHI_OUT_XML_TEXT_COMMENTS | INCHI_OUT_TABBED_OUTPUT);
+#if( SDF_OUTPUT_DT == 1 )
+        ip->bINChIOutputOptions |= bOutputMolfileDT?    INCHI_OUT_SDFILE_ATOMS_DT : 0;
+        ip->bINChIOutputOptions |= bOutputMolfileSplit? INCHI_OUT_SDFILE_SPLIT : 0;
+#endif
     }
     if ( bXml & INCHI_OUT_XML ) {
         bXml &= ~(INCHI_OUT_PLAIN_TEXT | INCHI_OUT_XML_TEXT_COMMENTS | INCHI_OUT_TABBED_OUTPUT);
@@ -882,6 +1006,17 @@ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *s
 #ifdef STEREO_WEDGE_ONLY
     ip->bTautFlags  |= bPointedEdgeStereo?      TG_FLAG_POINTED_EDGE_STEREO  : 0;
 #endif
+#if( FIX_ADJ_RAD == 1 )
+    ip->bTautFlags  |= bFixAdjacentRad?         TG_FLAG_FIX_ADJ_RADICALS : 0;
+#endif
+#if( ADD_PHOSPHINE_STEREO == 1 )
+    ip->bTautFlags  |= bAddPhosphineStereo?     TG_FLAG_PHOSPHINE_STEREO : 0;
+#endif
+#if( ADD_ARSINE_STEREO == 1 )
+    ip->bTautFlags  |= bAddArsineStereo?        TG_FLAG_ARSINE_STEREO : 0;
+#endif
+    ip->bTautFlags  |= bFixSp3bug?              TG_FLAG_FIX_SP3_BUG   : 0;
+
     if ( !ip->nInputType ) {
         ip->nInputType = INPUT_MOLFILE;
     }
@@ -898,7 +1033,8 @@ int PrintInputParms( INCHI_FILE *log_file, INPUT_PARMS *ip )
 
     /* SDfile output */
     if ( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY ) {
-        my_fprintf( log_file, "Output SDfile only\n" );
+        my_fprintf( log_file, "Output SDfile only%s\n",
+            (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ATOMS_DT)? " (write H isotopes as D, T)":"" );
         return 0;
     }
     /* tautomerism */
@@ -919,6 +1055,11 @@ int PrintInputParms( INCHI_FILE *log_file, INPUT_PARMS *ip )
          }
     }
     my_fprintf( log_file, "\n");
+#if( FIX_ADJ_RAD == 1 )
+    if ( ip->bTautFlags & TG_FLAG_FIX_ADJ_RADICALS ) {
+        my_fprintf( log_file, "Fix Adjacent Radicals\n" );
+    }
+#endif
     i = 0;
     /* isotopic */
     if ( nMode & REQ_MODE_ISO ) {
@@ -960,11 +1101,27 @@ int PrintInputParms( INCHI_FILE *log_file, INPUT_PARMS *ip )
             }
             i = 0;
         }
+#endif
         if ( TG_FLAG_POINTED_EDGE_STEREO & ip->bTautFlags ) {
             my_fprintf( log_file, "%sOnly narrow end of wedge points to stereocenter\n", i? "\n":"" );
             i = 0;
         }
+#if( ADD_PHOSPHINE_STEREO == 1 )
+        if ( TG_FLAG_PHOSPHINE_STEREO & ip->bTautFlags ) {
+            my_fprintf( log_file, "%sInclude phoshine stereochemistry\n", i? "\n":"" );
+            i = 0;
+        }
+#endif
+#if( ADD_ARSINE_STEREO == 1 )
+        if ( TG_FLAG_ARSINE_STEREO & ip->bTautFlags ) {
+            my_fprintf( log_file, "%sInclude arsine stereochemistry\n", i? "\n":"" );
+            i = 0;
+        }
 #endif
+        if ( TG_FLAG_FIX_SP3_BUG & ip->bTautFlags ) {
+            my_fprintf( log_file, "%sFix bug leading to missing or undefined sp3 parity\n", i? "\n":"" );
+            i = 0;
+        }
     } else {
         my_fprintf( log_file, ", Stereo OFF");
     }
@@ -1036,8 +1193,16 @@ int PrintInputParms( INCHI_FILE *log_file, INPUT_PARMS *ip )
             ip->nInputType == INPUT_MOLFILE?     "MOLfile"       :
             ip->nInputType == INPUT_SDFILE?      "SDfile"        :
             ip->nInputType == INPUT_CMLFILE?     "CMLfile"       :
+#if( READ_INCHI_STRING == 1 )
+            ip->nInputType == INPUT_INCHI?       "InChI (plain identifier)" :
+#endif
+#if( SPECIAL_BUILD == 1 )
+            ip->nInputType == INPUT_INCHI_XML?   "MoChI (xml)"   :
+            ip->nInputType == INPUT_INCHI_PLAIN? "MoChI (plain)" : "Unknown" );
+#else
             ip->nInputType == INPUT_INCHI_XML?   "InChI (xml)"   :
             ip->nInputType == INPUT_INCHI_PLAIN? "InChI (plain)" : "Unknown" );
+#endif
         if ( (ip->nInputType == INPUT_MOLFILE || ip->nInputType == INPUT_SDFILE) &&
              ip->bGetMolfileNumber ) {
             my_fprintf( log_file, "  (attempting to read Molfile number)" );
@@ -1066,10 +1231,10 @@ int PrintInputParms( INCHI_FILE *log_file, INPUT_PARMS *ip )
     my_fprintf( log_file, "%sUp to %d atoms per structure\n", i?"; ":"", MAX_ATOMS);
     i = 0;
     if ( ip->first_struct_number > 1 ) {
-        my_fprintf( log_file, "Skipping %d structure%s\n", ip->first_struct_number-1, ip->first_struct_number==2? "":"s" );
+        my_fprintf( log_file, "Skipping %ld structure%s\n", ip->first_struct_number-1, ip->first_struct_number==2? "":"s" );
     }
     if ( ip->last_struct_number > 0 ) {
-        my_fprintf( log_file, "Terminate after structure #%d\n", ip->last_struct_number );
+        my_fprintf( log_file, "Terminate after structure #%ld\n", ip->last_struct_number );
     }
     if ( ip->bSaveWarningStructsAsProblem && ip->path[3] && ip->path[3][0] ) {
         my_fprintf( log_file, "Saving warning structures into the problem file\n");
@@ -1144,8 +1309,7 @@ void HelpCommandLineParms( INCHI_FILE *f )
 
 #if ( bRELEASE_VERSION == 1 )
 
-    inchi_print_nodisplay( f, "%s ver %s.\n\nUsage:\ncInChI-1 inputFile [outputFile [logFile [problemFile]]] [%coption[ %coption...]]\n", INCHI_NAME, INCHI_VERSION, INCHI_OPTION_PREFX, INCHI_OPTION_PREFX);
-
+    inchi_print_nodisplay( f, "%s ver %s%s.\n\nUsage:\nc%s-%s inputFile [outputFile [logFile [problemFile]]] [%coption[ %coption...]]\n", INCHI_NAME, INCHI_VERSION, SPECIAL_BUILD_STRING, INCHI_NAME, INCHI_VERSION, INCHI_OPTION_PREFX, INCHI_OPTION_PREFX);
     inchi_print_nodisplay( f, "\nOptions:\n");
     inchi_print_nodisplay( f, "  SNon        Exclude stereo (Default: Include Absolute stereo)\n");
     inchi_print_nodisplay( f, "  SRel        Relative stereo\n");
@@ -1153,6 +1317,12 @@ void HelpCommandLineParms( INCHI_FILE *f )
     inchi_print_nodisplay( f, "  SUCF        Use Chiral Flag: On means Absolute stereo, Off - Relative\n"); 
     inchi_print_nodisplay( f, "  SUU         Include omitted unknown/undefined stereo\n");
     inchi_print_nodisplay( f, "  NEWPS       Narrow end of wedge points to stereocenter (default: both)\n");
+#if( ADD_PHOSPHINE_STEREO == 1 )
+    inchi_print_nodisplay( f, "  SPXYZ       Include Phosphines Stereochemistry\n");
+#endif
+#if( ADD_ARSINE_STEREO == 1 )
+    inchi_print_nodisplay( f, "  SAsXYZ      Include Arsines Stereochemistry\n");
+#endif
     inchi_print_nodisplay( f, "  RecMet      Include reconnected metals results\n");
     inchi_print_nodisplay( f, "  FixedH      Mobile H Perception Off (Default: On)\n");
     inchi_print_nodisplay( f, "  AuxNone     Omit auxiliary information (default: Include)\n");
@@ -1171,14 +1341,29 @@ void HelpCommandLineParms( INCHI_FILE *f )
     inchi_print_nodisplay( f, "  Wnumber     Set time-out per structure in seconds; W0 means unlimited\n");
     inchi_print_nodisplay( f, "  SDF:DataHeader Read from the input SDfile the ID under this DataHeader\n");
 #if( ADD_CMLPP == 1 )
-    inchi_print_nodisplay( f, "  CML         Input in CML format (default for input file .CML extension) \n");
+    inchi_print_nodisplay( f, "  CML         Input in CML format (default for input file .CML extension)\n");
 #endif
     inchi_print_nodisplay( f, "  NoLabels    Omit structure number, DataHeader and ID from %s output\n", INCHI_NAME);
     inchi_print_nodisplay( f, "  Tabbed      Separate structure number, %s, and AuxIndo with tabs\n", INCHI_NAME);
     inchi_print_nodisplay( f, "  OutputSDF   Convert %s created with default aux. info to SDfile\n", INCHI_NAME);
+#ifdef INCHI_MAIN
+    inchi_print_nodisplay( f, "  InChI2Struct Test mode: Mol/SDfile->%s->Structure->%s and a structure in AuxInfo format\n", INCHI_NAME, INCHI_NAME);
+#else
+    /*
+    inchi_print_nodisplay( f, "  InChI2Struct Convert %s string into a structure in AuxInfo format and its %s\n", INCHI_NAME, INCHI_NAME);
+    */
+#endif
+    inchi_print_nodisplay( f, "  InChI2InChI  Convert %s string into %s string for validation purposes\n", INCHI_NAME, INCHI_NAME);
+#if ( SDF_OUTPUT_DT == 1 )
+    inchi_print_nodisplay( f, "  SdfAtomsDT  Output Hydrogen Isotopes to SDfile as Atoms D and T\n");
+#endif
     inchi_print_nodisplay( f, "  STDIO       Use standard input/output streams\n");
+    inchi_print_nodisplay( f, "  FB          (or FixSp3Bug) Fix bug leading to missing or undefined sp3 parity\n" );
     inchi_print_nodisplay( f, "  WarnOnEmptyStructure Warn and produce empty %s for empty structure\n", INCHI_NAME);
-
+#if( FIX_ADJ_RAD == 1 )
+    inchi_print_nodisplay( f, "  FixRad      Fix Adjacent Radicals\n");
+#endif
+       
 #else
 
     inchi_print_nodisplay( f, "%s ver %s. Special testing version 12-12-2002.\n", INCHI_NAME, INCHI_VERSION);
@@ -1245,27 +1430,30 @@ int OpenFiles( FILE **inp_file, FILE **output_file, FILE **log_file, FILE **prb_
 */
     /*  logfile -- open es early as possible */
     if ( !ip->path[2] || !ip->path[2][0] ) {
-        my_fprintf( stderr, "%s version %s%s\n", INCHI_NAME, INCHI_VERSION, bRELEASE_VERSION? "":" (For pre-release testing)" );
+        my_fprintf( stderr, "%s version %s%s%s\n", INCHI_NAME, INCHI_VERSION, SPECIAL_BUILD_STRING, bRELEASE_VERSION? "":" (For pre-release testing)" );
         my_fprintf( stderr, "Log file not specified. Using standard error output.\n");
         *log_file = stderr;
     } else
     if ( !(*log_file = fopen( ip->path[2], "w" ) ) ) {
-        //my_fprintf( stderr, "%s version %s%s\n", INCHI_NAME, INCHI_VERSION, bRELEASE_VERSION? "":" (For pre-release testing)" );
-        //my_fprintf( stderr, "Cannot open log file '%s'. Using standard error output.\n", ip->path[2] );
+        my_fprintf( stderr, "%s version %s%s%s\n", INCHI_NAME, INCHI_VERSION, SPECIAL_BUILD_STRING, bRELEASE_VERSION? "":" (For pre-release testing)" );
+        my_fprintf( stderr, "Cannot open log file '%s'. Using standard error output.\n", ip->path[2] );
         *log_file = stderr;
     } else {
-        my_fprintf( *log_file, "%s version %s%s\n", INCHI_NAME, INCHI_VERSION, bRELEASE_VERSION? "":" (For pre-release testing)" );
+        //my_fprintf( *log_file, "%s version %s%s%s\n", INCHI_NAME, INCHI_VERSION, SPECIAL_BUILD_STRING, bRELEASE_VERSION? "":" (For pre-release testing)" );
         //my_fprintf( *log_file, "Opened log file '%s'\n", ip->path[2] );
     }
     /* input file */
-    if ( (ip->nInputType == INPUT_MOLFILE || ip->nInputType == INPUT_SDFILE || ip->nInputType == INPUT_CMLFILE) && ip->num_paths > 0 ) {
+    if ( (ip->nInputType == INPUT_MOLFILE || ip->nInputType == INPUT_SDFILE ||
+         ip->nInputType == INPUT_CMLFILE  || ip->nInputType == INPUT_INCHI) && ip->num_paths > 0 ) {
         const char *fmode = NULL;
 #if( defined(_MSC_VER)&&defined(_WIN32) || defined(__BORLANDC__)&&defined(__WIN32__) || defined(__GNUC__)&&defined(__MINGW32__)&&defined(_WIN32) )
         /* compilers that definitely allow fopen "rb" (binary read) mode */
+        fmode = "rb";
         if ( !ip->path[0] || !ip->path[0][0] || !(*inp_file = fopen( ip->path[0], "rb" ) ) ) {
             my_fprintf( *log_file, "Cannot open input file '%s'. Terminating.\n", ip->path[0]? ip->path[0] : "<No name>" );
             goto exit_function;
-        } else {
+        } else
+        if ( ip->nInputType == INPUT_CMLFILE ) {
             int c;
 #ifdef CML_DEBUG
             printf ("cr %d lf %d ret %d\n", (int) '\r', (int) '\f', (int) '\n');
@@ -1280,7 +1468,7 @@ int OpenFiles( FILE **inp_file, FILE **output_file, FILE **log_file, FILE **prb_
                     my_fprintf( *log_file, "Cannot open input file '%s' (2nd attempt). Terminating.\n", ip->path[0] );
                     goto exit_function;
                 }
-                //my_fprintf( *log_file, "Opened input file '%s'\n", ip->path[0] );
+                my_fprintf( *log_file, "Opened input file '%s'\n", ip->path[0] );
                 fmode = "r";
             } else {
                 fclose( *inp_file );
@@ -1303,7 +1491,7 @@ int OpenFiles( FILE **inp_file, FILE **output_file, FILE **log_file, FILE **prb_
 #endif
         DetectInputINChIFileType( inp_file, ip, fmode );
     } else
-    if ( (ip->nInputType != INPUT_MOLFILE && ip->nInputType != INPUT_SDFILE && ip->nInputType != INPUT_CMLFILE) ) {
+    if ( (ip->nInputType != INPUT_MOLFILE && ip->nInputType != INPUT_SDFILE && ip->nInputType != INPUT_CMLFILE && ip->nInputType != INPUT_INCHI) ) {
         my_fprintf( *log_file, "Input file type not specified. Terminating.\n");
         goto exit_function;
     } else {
@@ -1331,7 +1519,13 @@ int OpenFiles( FILE **inp_file, FILE **output_file, FILE **log_file, FILE **prb_
     }
     /*  problem file */
     if ( ip->path[3] && ip->path[3][0] ) {
-        if (  !(*prb_file = fopen( ip->path[3], "w" ) ) ) {
+        const char *fmode = "w";
+#if( defined(_MSC_VER)&&defined(_WIN32) || defined(__BORLANDC__)&&defined(__WIN32__) || defined(__GNUC__)&&defined(__MINGW32__)&&defined(_WIN32) )
+        if ( ip->nInputType != INPUT_CMLFILE ) {
+            fmode = "wb";
+        }
+#endif
+        if (  !(*prb_file = fopen( ip->path[3], fmode ) ) ) {
             my_fprintf( *log_file, "Cannot open problem file '%s'. Terminating.\n", ip->path[3] );
             goto exit_function;
         } else {
@@ -1344,7 +1538,7 @@ exit_function:
     return 0; /*  failed */
 
 }
-#define NUM_VERSIONS 4
+#define NUM_VERSIONS 6
 #define LEN_VERSIONS 64
 /*******************************************************************/
 static int bMatchOnePrefix( int len, char *str, int lenPrefix[],
@@ -1382,7 +1576,7 @@ int DetectInputINChIFileType( FILE **inp_file, INPUT_PARMS *ip, const char *fmod
     static int  lenXmlMsgFatal;
     static int  bInitilized = 0;
     int  bINChI_plain = 0, bINChI_xml = 0, len, i;
-    if ( ip->nInputType == INPUT_INCHI_XML || ip->nInputType == INPUT_INCHI_PLAIN ) {
+    if ( ip->nInputType == INPUT_INCHI_XML || ip->nInputType == INPUT_INCHI_PLAIN || ip->nInputType == INPUT_INCHI ) {
         return 1;
     }
     if ( !bInitilized ) {
@@ -1390,18 +1584,26 @@ int DetectInputINChIFileType( FILE **inp_file, INPUT_PARMS *ip, const char *fmod
         lenPlnVersion[1]  = sprintf( szPlnVersion[1],  "INChI=1.12Beta/" );
         lenPlnVersion[2]  = sprintf( szPlnVersion[2],  "INChI=1.0RC/" );
         lenPlnVersion[3]  = sprintf( szPlnVersion[3],  "InChI=1.0RC/" );
+        lenPlnVersion[4]  = sprintf( szPlnVersion[4],  "InChI=1/" );
+        lenPlnVersion[5]  = sprintf( szPlnVersion[5],  "MoChI=1a/" );
         lenPlnAuxVer[0]   = sprintf( szPlnAuxVer[0],   "AuxInfo=%s/", INCHI_VERSION );
         lenPlnAuxVer[1]   = sprintf( szPlnAuxVer[1],   "AuxInfo=1.12Beta/" );
         lenPlnAuxVer[2]   = sprintf( szPlnAuxVer[2],   "AuxInfo=1.0RC/" );
         lenPlnAuxVer[3]   = sprintf( szPlnAuxVer[3],   "AuxInfo=1.0RC/" );
+        lenPlnAuxVer[4]   = sprintf( szPlnAuxVer[4],   "AuxInfo=1/" );
+        lenPlnAuxVer[5]   = sprintf( szPlnAuxVer[5],   "AuxInfo=1a/" );
         lenXmlVersion[0]  = sprintf( szXmlVersion[0],  "<%s version=\"%s\">", INCHI_NAME, INCHI_VERSION );
         lenXmlVersion[1]  = sprintf( szXmlVersion[1],  "<INChI version=\"1.12Beta\">" );
         lenXmlVersion[2]  = sprintf( szXmlVersion[2],  "<INChI version=\"1.0RC\">" );
         lenXmlVersion[3]  = sprintf( szXmlVersion[3],  "<InChI version=\"1.0RC\">" );
+        lenXmlVersion[4]  = sprintf( szXmlVersion[4],  "<InChI version=\"1\">" );
+        lenXmlVersion[5]  = sprintf( szXmlVersion[5],  "<MoChI version=\"1a\">" );
         lenXmlIdentVer[0] = sprintf( szXmlIdentVer[0], "<identifier version=\"%s\"", INCHI_VERSION );
         lenXmlIdentVer[1] = sprintf( szXmlIdentVer[1], "<identifier version=\"1.12Beta\"" );
         lenXmlIdentVer[2] = sprintf( szXmlIdentVer[2], "<identifier version=\"1.0RC\"" );
         lenXmlIdentVer[3] = sprintf( szXmlIdentVer[3], "<identifier version=\"1.0RC\"" );
+        lenXmlIdentVer[4] = sprintf( szXmlIdentVer[4], "<identifier version=\"1\"" );
+        lenXmlIdentVer[5] = sprintf( szXmlIdentVer[5], "<identifier version=\"1a\"" );
         lenXmlMsgError    = sprintf( szXmlMsgError,    "<message type=\"error (no %s)\"", INCHI_NAME );
         lenXmlStruct      = strlen(szXmlStruct);
         lenXmlMsgFatal    = strlen(szXmlMsgFatal);