rino 0.1.0 → 0.2.0

data/ext/src/strutil.h

@@ -2,39 +2,170 @@
  * 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
  */
 
 #ifndef __STRUTIL_H__
 #define __STRUTIL_H__
 
-
 #ifndef INCHI_ALL_CPP
 #ifdef __cplusplus
 extern "C" {
 #endif
 #endif
 
+/* forward declaration */
+struct tagTautomerGroupsInfo;
+
 int ExtractConnectedComponent(  inp_ATOM *at, int num_at, int component_number, inp_ATOM *component_at );
 int SetConnectedComponentNumber( inp_ATOM *at, int num_at, int component_number );
 INChI     *Alloc_INChI( inp_ATOM *at, int num_at, int *found_num_bonds, int *found_num_isotopic, int nAllocMode );
 int       Free_INChI(INChI **ppINChI);
+int       Free_INChI_Members(INChI *pINChI);
+int       Free_INChI_Stereo( INChI_Stereo *pINChI_Stereo );
+
 INChI_Aux *Alloc_INChI_Aux( int num_at, int num_isotopic_atoms, int nAllocMode, int bOrigData );
 int       Free_INChI_Aux( INChI_Aux **ppINChI_Aux );
 int  Create_INChI( INChI **ppINChI, INChI_Aux **ppINChI_Aux, ORIG_ATOM_DATA *orig_inp_data,
                   inp_ATOM *inp_at, INP_ATOM_DATA *inp_norm_data[2],
                   int num_inp_at, INCHI_MODE nUserMode,
                   INCHI_MODE *pbTautFlags, INCHI_MODE *pbTautFlagsDone,
-                  struct tagInchiTime *ulMaxTime, char *pStrErrStruct);
+                  struct tagInchiTime *ulMaxTime, struct tagTautomerGroupsInfo *ti_out, char *pStrErrStruct);
 int FillOutInfAtom(inp_ATOM *norm_at, INF_ATOM_DATA *inf_norm_at_data, int init_num_at,
-                   int num_removed_H, int nNumRemovedProtons, NUM_H *nNumRemovedProtonsIsotopic, int bIsotopic,
+                   int num_removed_H, int bAdd_DT_to_num_H, int nNumRemovedProtons, NUM_H *nNumRemovedProtonsIsotopic, int bIsotopic,
                    INChI *pINChI, INChI_Aux *pINChI_Aux, int bAbcNumbers, INCHI_MODE nMode );
 int FillOutCompositeCanonInfAtom(COMP_ATOM_DATA *composite_norm_data, INF_ATOM_DATA *inf_norm_at_data,
                                  int bIsotopic, int bTautomeric,
                                  PINChI2 *pINChI2, PINChI_Aux2 *pINChI_Aux2, int bAbcNumbers, INCHI_MODE nMode);
 
+typedef enum tagInchiDiffBits {
+    IDIF_PROBLEM       = 0x00000001, /* severe: at least one InChI does not exist */
+    IDIF_NUM_AT        = 0x00000001, /* severe: different number of atoms in the skeleton */
+    IDIF_ATOMS         = 0x00000001, /* severe: diiferent types of skeleton atoms */
+    IDIF_NUM_EL        = 0x00000001, /* severe: formulas differ in another element */
+    IDIF_CON_LEN       = 0x00000001, /* severe: different connection table lengths */
+    IDIF_CON_TBL       = 0x00000001, /* severe: different connection tables */
+    IDIF_POSITION_H    = 0x00000002, /* difference in non-taut (Mobile-H) or all H (Fixed-H) location/number */
+    IDIF_MORE_FH       = 0x00000004, /* extra fixed H */
+    IDIF_LESS_FH       = 0x00000008, /* missing fixed H */
+    IDIF_MORE_H        = 0x00000010, /* formulas differ in number of H */
+    IDIF_LESS_H        = 0x00000020, /* formulas differ in number of H */
+    /*IDIF_TAUT_LEN      = 0x00000008,*/ /* different lengths of tautomer lists */
+    IDIF_NO_TAUT       = 0x00000040, /* restored structure has no taut groups while the original InChI has some */
+    IDIF_WRONG_TAUT    = 0x00000080, /* restored has tautomerism while the original does not have it */
+    IDIF_SINGLE_TG     = 0x00000100, /* restored has 1 taut. group while the original InChI has multiple tg */
+    IDIF_MULTIPLE_TG   = 0x00000200, /* restored has multiple tg while the original InChI has only one tg */
+    IDIF_NUM_TG        = 0x00000400, /* different number of tautomeric groups */
+    /*IDIF_LESS_TG_ENDP  = 0x00000200,*/ /* restores structure has less taut. endpoints */
+    /*IDIF_MORE_TG_ENDP  = 0x00000400,*/ /* restores structure has more taut. endpoints */
+    IDIF_EXTRA_TG_ENDP = 0x00000800, /* extra tautomeric endpoint(s) in restored structure */
+    IDIF_MISS_TG_ENDP  = 0x00001000, /* one or more tg endpoint is not in the restored structure */
+    IDIF_DIFF_TG_ENDP  = 0x00002000, /* lists of tg endpoints are different */
+    IDIF_TG            = 0x00004000, /* different tautomeric groups */
+    IDIF_NUM_ISO_AT    = 0x00008000, /* ?severe: restored struct. has different number of isotopic atoms */
+    IDIF_ISO_AT        = 0x00010000, /* ?severe: restored struct. has different locations/isotopes of isotopic atoms */
+    IDIF_CHARGE        = 0x00020000, /* restored structure has different charge */
+    IDIF_REM_PROT      = 0x00040000, /* proton(s) removed/added from the restored structure */
+    IDIF_REM_ISO_H     = 0x00080000, /* isotopic H removed */
+    IDIF_SC_INV        = 0x00100000, /* restores structure has different inversion stereocenter mark */
+    IDIF_SC_PARITY     = 0x00200000, /* restored structure has stereoatoms or allenes with different parity */
+    IDIF_SC_EXTRA_UNDF = 0x00400000, /* restored structure has extra undefined stereocenter(s) */
+    IDIF_SC_EXTRA      = 0x00800000, /* restored structure has extra stereocenter(s) */
+    IDIF_SC_MISS_UNDF  = 0x01000000,  /* restored structure has not some undefined stereocenter(s) */
+    IDIF_SC_MISS       = 0x02000000, /* restored structure has not some stereocenters that are not undefined */
+    IDIF_SB_PARITY     = 0x04000000, /* restored structure has stereobonds or cumulenes with different parity */
+    IDIF_SB_EXTRA_UNDF = 0x08000000, /* restored structure has extra undefined stereobond(s) */
+    IDIF_SB_EXTRA      = 0x10000000, /* restored structure has extra stereobond(s) */
+    IDIF_SB_MISS_UNDF  = 0x20000000, /* restored structure has not some undefined stereocenters */
+    IDIF_SB_MISS       = 0x40000000  /* restored structure has not some stereobonds that are not undefined */
+} IDIF;
+
+
+#define IDIFF_SB (IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF | IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS)
+#define IDIFF_SC (IDIF_SC_PARITY | IDIF_SC_EXTRA_UNDF | IDIF_SC_EXTRA | IDIF_SC_MISS_UNDF | IDIF_SC_MISS)
+
+#define IDIFF_CONSTIT (IDIF_POSITION_H | IDIF_MORE_FH | IDIF_LESS_FH | IDIF_MORE_H | IDIF_LESS_H |\
+                       IDIF_NO_TAUT | IDIF_WRONG_TAUT | IDIF_SINGLE_TG | IDIF_MULTIPLE_TG | \
+                       IDIF_NUM_TG | IDIF_EXTRA_TG_ENDP | IDIF_MISS_TG_ENDP | IDIF_TG | \
+                       IDIF_NUM_ISO_AT | IDIF_ISO_AT | IDIF_CHARGE | IDIF_REM_PROT | IDIF_REM_ISO_H |\
+                       IDIF_DIFF_TG_ENDP)
+#define IDIFF_STEREO  (IDIF_SC_INV | IDIF_SC_PARITY | IDIF_SC_EXTRA_UNDF | IDIF_SC_EXTRA | \
+                       IDIF_SC_MISS_UNDF | IDIF_SC_MISS | IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF |\
+                       IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS)
+
+
+/*************************************************************************************/
+#define ICR_MAX_ENDP_IN1_ONLY 32
+#define ICR_MAX_ENDP_IN2_ONLY 32
+#define ICR_MAX_DIFF_FIXED_H  32
+#define ICR_MAX_SB_IN1_ONLY   32
+#define ICR_MAX_SB_IN2_ONLY   32
+#define ICR_MAX_SC_IN1_ONLY   32
+#define ICR_MAX_SC_IN2_ONLY   32
+#define ICR_MAX_SB_UNDF       32
+#define ICR_MAX_SC_UNDF       32
+typedef struct tagInChICompareResults {
+
+    INCHI_MODE flags;
+
+    int tot_num_H1;
+    int tot_num_H2;
+    int num_taut_H1;
+    int num_taut_H2;
+    int num_taut_M1;
+    int num_taut_M2;
+    
+    /* 1 => InChI from reversed struct. 2 => input InChI */
+
+    AT_NUMB endp_in1_only[ICR_MAX_ENDP_IN1_ONLY]; /* endpoint canonical number = index+1 */
+    int     num_endp_in1_only;
+
+    AT_NUMB endp_in2_only[ICR_MAX_ENDP_IN2_ONLY]; /* endpoint canonical number = index+1 */
+    int     num_endp_in2_only;
+
+    AT_NUMB diff_pos_H_at[ICR_MAX_DIFF_FIXED_H];  /* non-tautomeric H */
+    S_CHAR  diff_pos_H_nH[ICR_MAX_DIFF_FIXED_H];
+    int     num_diff_pos_H;
+
+    AT_NUMB fixed_H_at1_more[ICR_MAX_DIFF_FIXED_H];  /* extra fixed_H */
+    S_CHAR  fixed_H_nH1_more[ICR_MAX_DIFF_FIXED_H];
+    int     num_fixed_H1_more;
+
+    AT_NUMB fixed_H_at2_more[ICR_MAX_DIFF_FIXED_H];  /* missed fixed_H */
+    S_CHAR  fixed_H_nH2_more[ICR_MAX_DIFF_FIXED_H];
+    int     num_fixed_H2_more;
+
+    AT_NUMB sc_in1_only[ICR_MAX_SC_IN1_ONLY];
+    int     num_sc_in1_only;
+    AT_NUMB sc_in2_only[ICR_MAX_SC_IN2_ONLY];
+    int     num_sc_in2_only;
+
+    AT_NUMB sb_in1_only[ICR_MAX_SB_IN1_ONLY];
+    int     num_sb_in1_only;
+    AT_NUMB sb_in2_only[ICR_MAX_SB_IN2_ONLY];
+    int     num_sb_in2_only;
+
+    AT_NUMB sb_undef_in1_only[ICR_MAX_SC_UNDF];
+    int     num_sb_undef_in1_only;
+    AT_NUMB sb_undef_in2_only[ICR_MAX_SC_UNDF];
+    int     num_sb_undef_in2_only;
+    
+    AT_NUMB sc_undef_in1_only[ICR_MAX_SB_UNDF];
+    int     num_sc_undef_in1_only;
+    AT_NUMB sc_undef_in2_only[ICR_MAX_SB_UNDF];
+    int     num_sc_undef_in2_only;
+
+} ICR;
+
+
+INCHI_MODE CompareReversedINChI2( INChI *i1 /* InChI from reversed struct */, INChI *i2 /* input InChI */, INChI_Aux *a1, INChI_Aux *a2, ICR *picr, int *err );
+int CompareIcr( ICR *picr1, ICR *picr2, INCHI_MODE *pin1, INCHI_MODE *pin2, INCHI_MODE mask );
+
+int CompareReversedINChI( INChI *i1, INChI *i2, INChI_Aux *a1, INChI_Aux *a2 );
+const char *CompareReversedInchiMsg( int code );
+
 #define EQL_EXISTS   1
 #define EQL_SP3      2
 #define EQL_SP3_INV  4
@@ -122,6 +253,7 @@ int INChI_SegmentAction( char cDifSegs );
 #define FLAG_SORT_PRINT_NO_NFIX_H_REC  8 /* no fixed H non-isotopic in the reconnected InChI layer */
 #define FLAG_SORT_PRINT_NO_IFIX_H_BAS 16 /* no fixed H isotopic in the main InChI layer */
 #define FLAG_SORT_PRINT_NO_IFIX_H_REC 32 /* no fixed H isotopic in the the reconnected InChI layer */
+#define FLAG_SORT_PRINT_ReChI_PREFIX  64 /* Output ReChI instead of InChI */
 
 int OutputINChI1( char *pStr, int nStrLen, INCHI_SORT *pINChISortTautAndNonTaut[][TAUT_NUM], int iINChI,
                 ORIG_STRUCT *pOrigStruct,
@@ -153,20 +285,27 @@ int OutputINChIXmlStructEndTag( INCHI_FILE *output_file, char *pStr, int nStrLen
 
 int GetInpStructErrorType(INPUT_PARMS *ip, int err, char *pStrErrStruct, int num_inp_atoms );
 int ProcessStructError( INCHI_FILE *output_file, INCHI_FILE *log_file, /*int err,*/ char *pStrErrStruct, int nErrorType,
-                         int *bXmlStructStarted, int num_inp, INPUT_PARMS *ip, char *pStr, int nStrLen );
+                         int *bXmlStructStarted, long num_inp, INPUT_PARMS *ip, char *pStr, int nStrLen );
 
 int bNumHeterAtomHasIsotopicH( inp_ATOM *atom, int num_atoms );
 
 int WriteToSDfile( const INP_ATOM_DATA *inp_at_data, INCHI_FILE* fcb, const char* name, const char* comment,
                    const char *szLabel, const char *szValue );
 int WriteOrigAtomDataToSDfile( const ORIG_ATOM_DATA *inp_at_data, INCHI_FILE* fcb, const char* name, const char* comment,
-                   int bChiral, const char *szLabel, const char *szValue);
+                   int bChiral, int bAtomsDT, const char *szLabel, const char *szValue);
+int bIsMetalSalt( inp_ATOM *at, int i );
 
 
-extern char gsMissing[];
-extern char gsEmpty[];
-extern char gsSpace[];
-extern char gsEqual[];
+extern const char gsMissing[];
+extern const char gsEmpty[];
+extern const char gsSpace[];
+extern const char gsEqual[];
+/*
+#define gsMissing  "is missing"
+#define gsEmpty    ""
+#define gsSpace    " "
+#define gsEqual    "="
+*/
 /* format string for SDF_LBL_VAL(L,V): %s%s%s%s (four strings) */
 /*#define SDF_LBL_VAL(L,V)  ((L)&&(L)[0])?gsSpace:gsEmpty, ((L)&&(L)[0])?L:gsEmpty, ((L)&&(L)[0])? (((V)&&(V)[0])?gsEqual:gsSpace):gsEmpty, ((L)&&(L)[0])?((V)&&(V)[0]?V:gsMissing):gsEmpty*/
 #define SDF_LBL_VAL(L,V)  ((L)&&(L)[0])?gsSpace:gsEmpty, ((L)&&(L)[0])?L:gsEmpty, ((L)&&(L)[0])? (((V)&&(V)[0])?gsEqual:gsSpace):gsEmpty, ((V)&&(V)[0])?V:((L)&&(L)[0])?gsMissing:gsEmpty

data/ext/src/util.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
  */
 
@@ -34,6 +34,7 @@ typedef struct tagElData {
      int     nNormAtMass;  /* Atomic mass of the most abundant isotope */
      double  dAtMass;      /* exact mw of the most abundant isotope */
      int     nType;        /* METAL or METAL2 */
+     int     nElNegPauling10; /* Pauling electronegativity x 10; 0 => unknown */
      int     bDoNotAddH;   /* InChI does not add imlicit H to atoms that have bDoNotAddH != 0 */
      S_CHAR  cValence[NUM_ATOM_CHARGES][MAX_NUM_VALENCES];
 } ELDATA;
@@ -41,115 +42,115 @@ typedef struct tagElData {
 /* 2004=05-10: Added valences {1,3,5,7,} for As(2-) */
 
 const ELDATA ElData[] = {
-/*       avg  norm                        No  -------- Valence(s) of an ion or neutral atom -------------*/
-/*        mw  mass  exact mw     type     H   -2          -1          0           +1         +2          */
-{ "H",    1,   1,   1.007825035,     0 ,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "D",    2,   2,   2.014101778,     0 ,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "T",    3,   3,   3.016049268,     0 ,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "He",   4,   4,   4.002600000,     0 ,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
-{ "Li",   7,   7,   7.016000000, METAL ,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "Be",   9,   9,   9.012180000, METAL ,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
-{ "B",   11,  11,  11.009300000,     0 ,  0, {{3,},       {4,},       {3,},       {2,},       {1,}       }},
-{ "C",   12,  12,  12.000000000,     0 ,  0, {{2,},       {3,},       {4,},       {3,},       {2,}       }},
-{ "N",   14,  14,  14.003074000,     0 ,  0, {{1,},       {2,},       {3,5},      {4,},       {3,}       }},
-{ "O",   16,  16,  15.994914630,     0 ,  0, {{0,},       {1,},       {2,},       {3,5,},     {4,}       }},
-{ "F",   19,  19,  18.998403220,     0 ,  0, {{0,},       {0,},       {1,},       {2,},       {3,5}      }},
-{ "Ne",  20,  20,  19.992440000,     0 ,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
-{ "Na",  23,  23,  22.989770000, METAL ,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "Mg",  24,  24,  23.985000000, METAL ,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
-{ "Al",  27,  27,  26.981540000, METAL ,  0, {{3,5,},     {4,},       {3,},       {2,},       {1,}       }},
-{ "Si",  28,  28,  27.976927100,     0 ,  0, {{2,},       {3,5},      {4,},       {3,},       {2,}       }},
-{ "P",   31,  31,  30.973762000,     0 ,  0, {{1,3,5,7,}, {2,4,6,},   {3,5,},     {4,},       {3,}       }},
-{ "S",   32,  32,  31.972070700,     0 ,  0, {{0,},       {1,3,5,7,}, {2,4,6},    {3,5,},     {4,}       }},
-{ "Cl",  35,  35,  34.968852730,     0 ,  0, {{0,},       {0,},       {1,3,5,7},  {2,4,6},    {3,5,}     }},
-{ "Ar",  40,  40,  39.962400000,     0 ,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
-{ "K",   39,  39,  38.963700000, METAL ,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "Ca",  40,  40,  39.962600000, METAL ,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
-{ "Sc",  45,  45,  44.955910000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Ti",  48,  48,  47.947950000, METAL ,  1, {{0,},       {0,},       {3,4},      {0,},       {0,}       }},
-{ "V",   51,  51,  50.943960000, METAL ,  1, {{0,},       {0,},       {2,3,4,5,}, {0,},       {0,}       }},
-{ "Cr",  52,  52,  51.940500000, METAL ,  1, {{0,},       {0,},       {2,3,6,},   {0,},       {0,}       }},
-{ "Mn",  55,  55,  54.938050000, METAL2,  1, {{0,},       {0,},       {2,3,4,6,}, {0,},       {0,}       }},
-{ "Fe",  56,  56,  55.934900000, METAL2,  1, {{0,},       {0,},       {2,3,4,6,}, {0,},       {0,}       }},
-{ "Co",  59,  59,  58.933200000, METAL2,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
-{ "Ni",  59,  58,  57.935300000, METAL2,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
-{ "Cu",  64,  63,  62.929600000, METAL ,  1, {{0,},       {0,},       {1,2,},     {0,},       {0,}       }},
-{ "Zn",  65,  64,  63.929147000, METAL ,  1, {{0,},       {0,},       {2,},       {0,},       {0,}       }},
-{ "Ga",  70,  69,  68.925600000, METAL ,  0, {{3,5,},     {4,},       {3,},       {0,},       {1,}       }},
-{ "Ge",  73,  74,  73.921177400,     0 ,  0, {{2,4,6,},   {3,5,},     {4,},       {3,},       {0,}       }},
-{ "As",  75,  75,  74.921594200,     0 ,  0, {{1,3,5,7,}, {2,4,6,},   {3,5,},     {4,},       {3,}       }},
-{ "Se",  79,  80,  79.916519600,     0 ,  0, {{0,},       {1,3,5,7,}, {2,4,6,},   {3,5,},     {4,}       }},
-{ "Br",  80,  79,  78.918336100,     0 ,  0, {{0,},       {0,},       {1,3,5,7,}, {2,4,6,},   {3,5,}     }},
-{ "Kr",  84,  84,  83.911500000,     0 ,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
-{ "Rb",  85,  85,  84.911800000, METAL ,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "Sr",  88,  88,  87.905600000, METAL ,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
-{ "Y",   89,  89,  88.905860000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Zr",  91,  90,  89.904700000, METAL ,  1, {{0,},       {0,},       {4,},       {0,},       {0,}       }},
-{ "Nb",  93,  93,  92.906400000, METAL ,  1, {{0,},       {0,},       {3,5,},     {0,},       {0,}       }},
-{ "Mo",  96,  98,  97.905400000, METAL ,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
-{ "Tc",  98,  98,  97.907200000, METAL ,  1, {{0,},       {0,},       {7,},       {0,},       {0,}       }},
-{ "Ru", 101, 102, 101.904300000, METAL ,  1, {{0,},       {0,},       {2,3,4,6,}, {0,},       {0,}       }},
-{ "Rh", 103, 103, 102.905500000, METAL ,  1, {{0,},       {0,},       {2,3,4,},   {0,},       {0,}       }},
-{ "Pd", 106, 106, 105.903500000, METAL ,  1, {{0,},       {0,},       {2,4,},     {0,},       {0,}       }},
-{ "Ag", 108, 107, 106.905100000, METAL ,  1, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "Cd", 112, 114, 113.903400000, METAL ,  1, {{0,},       {0,},       {2,},       {0,},       {0,}       }},
-{ "In", 115, 115, 114.903900000, METAL ,  0, {{3,5,},     {2,4,},     {3,},       {0,},       {1,}       }},
-{ "Sn", 119, 120, 119.902200000, METAL2,  0, {{2,4,6,},   {3,5},      {2,4,},     {3,},       {0,}       }},
-{ "Sb", 122, 121, 120.903800000, METAL,   0, {{1,3,5,7,}, {2,4,6,},   {3,5,},     {2,4,},     {3,}       }},
-{ "Te", 128, 130, 129.906200000,     0 ,  0, {{0,},       {1,3,5,7,}, {2,4,6,},   {3,5,},     {2,4,}     }},
-{ "I",  127, 127, 126.904500000,     0 ,  0, {{0,},       {0,},       {1,3,5,7,}, {2,4,6},    {3,5,}     }},
-{ "Xe", 131, 132, 131.904100000,     0 ,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
-{ "Cs", 133, 133, 132.905430000, METAL ,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "Ba", 137, 138, 137.905200000, METAL ,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
-{ "La", 139, 139, 138.906360000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Ce", 140, 140, 139.905400000, METAL2,  1, {{0,},       {0,},       {3,4,},     {0,},       {0,}       }},
-{ "Pr", 141, 141, 140.907660000, METAL2,  1, {{0,},       {0,},       {3,4,},     {0,},       {0,}       }},
-{ "Nd", 144, 142, 141.907719000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Pm", 145, 145, 144.912800000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Sm", 150, 152, 151.919700000, METAL2,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
-{ "Eu", 152, 153, 152.921200000, METAL2,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
-{ "Gd", 157, 158, 157.924099000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Tb", 159, 159, 158.925350000, METAL2,  1, {{0,},       {0,},       {3,4,},     {0,},       {0,}       }},
-{ "Dy", 163, 164, 163.929200000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }}, /*  mw rounding uncertain */
-{ "Ho", 165, 165, 164.930300000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Er", 167, 166, 165.930300000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Tm", 169, 169, 168.934230000, METAL2,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
-{ "Yb", 173, 174, 173.938900000, METAL2,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
-{ "Lu", 175, 175, 174.940800000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Hf", 178, 180, 179.946600000, METAL ,  1, {{0,},       {0,},       {4,},       {0,},       {0,}       }},
-{ "Ta", 181, 181, 180.948010000, METAL ,  1, {{0,},       {0,},       {5,},       {0,},       {0,}       }},
-{ "W",  184, 184, 183.951000000, METAL2,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
-{ "Re", 186, 187, 186.955800000, METAL2,  1, {{0,},       {0,},       {2,4,6,7,}, {0,},       {0,}       }},
-{ "Os", 190, 192, 191.961500000, METAL2,  1, {{0,},       {0,},       {2,3,4,6,}, {0,},       {0,}       }},
-{ "Ir", 192, 193, 192.962900000, METAL2,  1, {{0,},       {0,},       {2,3,4,6,}, {0,},       {0,}       }},
-{ "Pt", 195, 195, 194.964800000, METAL2,  1, {{0,},       {0,},       {2,4,},     {0,},       {0,}       }},
-{ "Au", 197, 197, 196.966560000, METAL ,  1, {{0,},       {0,},       {1,3,},     {0,},       {0,}       }},
-{ "Hg", 201, 202, 201.970617000, METAL2,  1, {{0,},       {0,},       {1,2,},     {0,},       {0,}       }},
-{ "Tl", 204, 205, 204.974400000, METAL2,  0, {{3,5,},     {2,4,},     {1,3,},     {0,},       {0,}       }},
-{ "Pb", 207, 208, 207.976627000, METAL2,  0, {{2,4,6,},   {3,5},      {2,4,},     {3,},       {0,}       }},
-{ "Bi", 209, 209, 208.980390000, METAL ,  0, {{1,3,5,7,}, {2,4,6,},   {3,5,},     {2,4,},     {3,}       }},
-{ "Po", 209, 209, 208.982400000, METAL2,  0, {{0,},       {1,3,5,7,}, {2,4,6,},   {3,5,},     {2,4,}     }},
-{ "At", 210, 210, 209.987100000,     0 ,  0, {{0,},       {0,},       {1,3,5,7,}, {2,4,6},    {3,5,}     }},
-{ "Rn", 222, 222, 222.017500000,     0 ,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
-{ "Fr", 223, 223, 223.019700000, METAL ,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "Ra", 226, 226, 226.025410000, METAL ,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
-{ "Ac", 227, 227, 227.027750000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Th", 232, 232, 232.038050000, METAL2,  1, {{0,},       {0,},       {3,4,},     {0,},       {0,}       }},
-{ "Pa", 231, 231, 231.035880000, METAL2,  1, {{0,},       {0,},       {3,4,5,},   {0,},       {0,}       }},
-{ "U",  238, 238, 238.050790000, METAL2,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
-{ "Np", 237, 237, 237.048170000, METAL2,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
-{ "Pu", 244, 244, 244.064200000, METAL2,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
-{ "Am", 243, 243, 243.061370000, METAL2,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
-{ "Cm", 247, 247, 247.070300000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Bk", 247, 247, 247.070300000, METAL ,  1, {{0,},       {0,},       {3,4,},     {0,},       {0,}       }},
-{ "Cf", 251, 251, 251.079600000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Es", 252, 252, 252.082800000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Fm", 257, 257, 257.095100000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "Md", 258, 258, 258.098600000, METAL ,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
-{ "No", 259, 259, 259.100900000, METAL ,  1, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "Lr", 260, 260, 260.105400000, METAL ,  1, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "Rf", 261, 261, 261.108700000, METAL ,  1, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
-{ "",     0,   0,   0.000000000,     0 ,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
+/*       avg  norm                      El    No  -------- Valence(s) of an ion or neutral atom -------------*/
+/*        mw  mass  exact mw     type   neg   H   -2          -1          0           +1         +2          */
+{ "H",    1,   1,   1.007825035,     0 , 21,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "D",    2,   2,   2.014101778,     0 , 21,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "T",    3,   3,   3.016049268,     0 , 21,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "He",   4,   4,   4.002600000,     0 ,  0,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
+{ "Li",   7,   7,   7.016000000, METAL , 10,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "Be",   9,   9,   9.012180000, METAL , 15,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
+{ "B",   11,  11,  11.009300000,     0 , 20,  0, {{3,},       {4,},       {3,},       {2,},       {1,}       }},
+{ "C",   12,  12,  12.000000000,     0 , 25,  0, {{2,},       {3,},       {4,},       {3,},       {2,}       }},
+{ "N",   14,  14,  14.003074000,     0 , 30,  0, {{1,},       {2,},       {3,5},      {4,},       {3,}       }},
+{ "O",   16,  16,  15.994914630,     0 , 35,  0, {{0,},       {1,},       {2,},       {3,5,},     {4,}       }},
+{ "F",   19,  19,  18.998403220,     0 , 40,  0, {{0,},       {0,},       {1,},       {2,},       {3,5}      }},
+{ "Ne",  20,  20,  19.992440000,     0 ,  0,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
+{ "Na",  23,  23,  22.989770000, METAL ,  9,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "Mg",  24,  24,  23.985000000, METAL , 12,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
+{ "Al",  27,  27,  26.981540000, METAL , 15,  0, {{3,5,},     {4,},       {3,},       {2,},       {1,}       }},
+{ "Si",  28,  28,  27.976927100,     0 , 18,  0, {{2,},       {3,5},      {4,},       {3,},       {2,}       }},
+{ "P",   31,  31,  30.973762000,     0 , 21,  0, {{1,3,5,7,}, {2,4,6,},   {3,5,},     {4,},       {3,}       }},
+{ "S",   32,  32,  31.972070700,     0 , 25,  0, {{0,},       {1,3,5,7,}, {2,4,6},    {3,5,},     {4,}       }},
+{ "Cl",  35,  35,  34.968852730,     0 , 30,  0, {{0,},       {0,},       {1,3,5,7},  {2,4,6},    {3,5,}     }},
+{ "Ar",  40,  40,  39.962400000,     0 ,  0,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
+{ "K",   39,  39,  38.963700000, METAL ,  8,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "Ca",  40,  40,  39.962600000, METAL , 10,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
+{ "Sc",  45,  45,  44.955910000, METAL , 13,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Ti",  48,  48,  47.947950000, METAL , 15,  1, {{0,},       {0,},       {3,4},      {0,},       {0,}       }},
+{ "V",   51,  51,  50.943960000, METAL , 16,  1, {{0,},       {0,},       {2,3,4,5,}, {0,},       {0,}       }},
+{ "Cr",  52,  52,  51.940500000, METAL , 16,  1, {{0,},       {0,},       {2,3,6,},   {0,},       {0,}       }},
+{ "Mn",  55,  55,  54.938050000, METAL2, 15,  1, {{0,},       {0,},       {2,3,4,6,}, {0,},       {0,}       }},
+{ "Fe",  56,  56,  55.934900000, METAL2, 18,  1, {{0,},       {0,},       {2,3,4,6,}, {0,},       {0,}       }},
+{ "Co",  59,  59,  58.933200000, METAL2, 18,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
+{ "Ni",  59,  58,  57.935300000, METAL2, 18,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
+{ "Cu",  64,  63,  62.929600000, METAL , 19,  1, {{0,},       {0,},       {1,2,},     {0,},       {0,}       }},
+{ "Zn",  65,  64,  63.929147000, METAL , 16,  1, {{0,},       {0,},       {2,},       {0,},       {0,}       }},
+{ "Ga",  70,  69,  68.925600000, METAL , 18,  0, {{3,5,},     {4,},       {3,},       {0,},       {1,}       }},
+{ "Ge",  73,  74,  73.921177400,     0 , 18,  0, {{2,4,6,},   {3,5,},     {4,},       {3,},       {0,}       }},
+{ "As",  75,  75,  74.921594200,     0 , 20,  0, {{1,3,5,7,}, {2,4,6,},   {3,5,},     {4,},       {3,}       }},
+{ "Se",  79,  80,  79.916519600,     0 , 24,  0, {{0,},       {1,3,5,7,}, {2,4,6,},   {3,5,},     {4,}       }},
+{ "Br",  80,  79,  78.918336100,     0 , 28,  0, {{0,},       {0,},       {1,3,5,7,}, {2,4,6,},   {3,5,}     }},
+{ "Kr",  84,  84,  83.911500000,     0 ,  0,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
+{ "Rb",  85,  85,  84.911800000, METAL ,  8,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "Sr",  88,  88,  87.905600000, METAL , 10,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
+{ "Y",   89,  89,  88.905860000, METAL , 12,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Zr",  91,  90,  89.904700000, METAL , 14,  1, {{0,},       {0,},       {4,},       {0,},       {0,}       }},
+{ "Nb",  93,  93,  92.906400000, METAL , 16,  1, {{0,},       {0,},       {3,5,},     {0,},       {0,}       }},
+{ "Mo",  96,  98,  97.905400000, METAL , 18,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
+{ "Tc",  98,  98,  97.907200000, METAL , 19,  1, {{0,},       {0,},       {7,},       {0,},       {0,}       }},
+{ "Ru", 101, 102, 101.904300000, METAL , 22,  1, {{0,},       {0,},       {2,3,4,6,}, {0,},       {0,}       }},
+{ "Rh", 103, 103, 102.905500000, METAL , 22,  1, {{0,},       {0,},       {2,3,4,},   {0,},       {0,}       }},
+{ "Pd", 106, 106, 105.903500000, METAL , 22,  1, {{0,},       {0,},       {2,4,},     {0,},       {0,}       }},
+{ "Ag", 108, 107, 106.905100000, METAL , 19,  1, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "Cd", 112, 114, 113.903400000, METAL , 17,  1, {{0,},       {0,},       {2,},       {0,},       {0,}       }},
+{ "In", 115, 115, 114.903900000, METAL , 17,  0, {{3,5,},     {2,4,},     {3,},       {0,},       {1,}       }},
+{ "Sn", 119, 120, 119.902200000, METAL2, 18,  0, {{2,4,6,},   {3,5},      {2,4,},     {3,},       {0,}       }},
+{ "Sb", 122, 121, 120.903800000, METAL,  19,  0, {{1,3,5,7,}, {2,4,6,},   {3,5,},     {2,4,},     {3,}       }},
+{ "Te", 128, 130, 129.906200000,     0 , 21,  0, {{0,},       {1,3,5,7,}, {2,4,6,},   {3,5,},     {2,4,}     }},
+{ "I",  127, 127, 126.904500000,     0 , 25,  0, {{0,},       {0,},       {1,3,5,7,}, {2,4,6},    {3,5,}     }},
+{ "Xe", 131, 132, 131.904100000,     0 ,  0,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
+{ "Cs", 133, 133, 132.905430000, METAL ,  7,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "Ba", 137, 138, 137.905200000, METAL ,  9,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
+{ "La", 139, 139, 138.906360000, METAL , 11,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Ce", 140, 140, 139.905400000, METAL2,  0,  1, {{0,},       {0,},       {3,4,},     {0,},       {0,}       }},
+{ "Pr", 141, 141, 140.907660000, METAL2,  0,  1, {{0,},       {0,},       {3,4,},     {0,},       {0,}       }},
+{ "Nd", 144, 142, 141.907719000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Pm", 145, 145, 144.912800000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Sm", 150, 152, 151.919700000, METAL2,  0,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
+{ "Eu", 152, 153, 152.921200000, METAL2,  0,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
+{ "Gd", 157, 158, 157.924099000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Tb", 159, 159, 158.925350000, METAL2,  0,  1, {{0,},       {0,},       {3,4,},     {0,},       {0,}       }},
+{ "Dy", 163, 164, 163.929200000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }}, /*  mw rounding uncertain */
+{ "Ho", 165, 165, 164.930300000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Er", 167, 166, 165.930300000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Tm", 169, 169, 168.934230000, METAL2,  0,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
+{ "Yb", 173, 174, 173.938900000, METAL2,  0,  1, {{0,},       {0,},       {2,3,},     {0,},       {0,}       }},
+{ "Lu", 175, 175, 174.940800000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Hf", 178, 180, 179.946600000, METAL , 13,  1, {{0,},       {0,},       {4,},       {0,},       {0,}       }},
+{ "Ta", 181, 181, 180.948010000, METAL , 15,  1, {{0,},       {0,},       {5,},       {0,},       {0,}       }},
+{ "W",  184, 184, 183.951000000, METAL2, 17,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
+{ "Re", 186, 187, 186.955800000, METAL2, 19,  1, {{0,},       {0,},       {2,4,6,7,}, {0,},       {0,}       }},
+{ "Os", 190, 192, 191.961500000, METAL2, 22,  1, {{0,},       {0,},       {2,3,4,6,}, {0,},       {0,}       }},
+{ "Ir", 192, 193, 192.962900000, METAL2, 22,  1, {{0,},       {0,},       {2,3,4,6,}, {0,},       {0,}       }},
+{ "Pt", 195, 195, 194.964800000, METAL2, 22,  1, {{0,},       {0,},       {2,4,},     {0,},       {0,}       }},
+{ "Au", 197, 197, 196.966560000, METAL , 24,  1, {{0,},       {0,},       {1,3,},     {0,},       {0,}       }},
+{ "Hg", 201, 202, 201.970617000, METAL2, 19,  1, {{0,},       {0,},       {1,2,},     {0,},       {0,}       }},
+{ "Tl", 204, 205, 204.974400000, METAL2, 18,  0, {{3,5,},     {2,4,},     {1,3,},     {0,},       {0,}       }},
+{ "Pb", 207, 208, 207.976627000, METAL2, 18,  0, {{2,4,6,},   {3,5},      {2,4,},     {3,},       {0,}       }},
+{ "Bi", 209, 209, 208.980390000, METAL , 19,  0, {{1,3,5,7,}, {2,4,6,},   {3,5,},     {2,4,},     {3,}       }},
+{ "Po", 209, 209, 208.982400000, METAL2, 20,  0, {{0,},       {1,3,5,7,}, {2,4,6,},   {3,5,},     {2,4,}     }},
+{ "At", 210, 210, 209.987100000,     0 , 22,  0, {{0,},       {0,},       {1,3,5,7,}, {2,4,6},    {3,5,}     }},
+{ "Rn", 222, 222, 222.017500000,     0 ,  0,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
+{ "Fr", 223, 223, 223.019700000, METAL ,  0,  0, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "Ra", 226, 226, 226.025410000, METAL ,  0,  0, {{0,},       {0,},       {2,},       {1,},       {0,}       }},
+{ "Ac", 227, 227, 227.027750000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Th", 232, 232, 232.038050000, METAL2,  0,  1, {{0,},       {0,},       {3,4,},     {0,},       {0,}       }},
+{ "Pa", 231, 231, 231.035880000, METAL2,  0,  1, {{0,},       {0,},       {3,4,5,},   {0,},       {0,}       }},
+{ "U",  238, 238, 238.050790000, METAL2,  0,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
+{ "Np", 237, 237, 237.048170000, METAL2,  0,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
+{ "Pu", 244, 244, 244.064200000, METAL2,  0,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
+{ "Am", 243, 243, 243.061370000, METAL2,  0,  1, {{0,},       {0,},       {3,4,5,6,}, {0,},       {0,}       }},
+{ "Cm", 247, 247, 247.070300000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Bk", 247, 247, 247.070300000, METAL ,  0,  1, {{0,},       {0,},       {3,4,},     {0,},       {0,}       }},
+{ "Cf", 251, 251, 251.079600000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Es", 252, 252, 252.082800000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Fm", 257, 257, 257.095100000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "Md", 258, 258, 258.098600000, METAL ,  0,  1, {{0,},       {0,},       {3,},       {0,},       {0,}       }},
+{ "No", 259, 259, 259.100900000, METAL ,  0,  1, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "Lr", 260, 260, 260.105400000, METAL ,  0,  1, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "Rf", 261, 261, 261.108700000, METAL ,  0,  1, {{0,},       {0,},       {1,},       {0,},       {0,}       }},
+{ "",     0,   0,   0.000000000,     0 ,  0,  0, {{0,},       {0,},       {0,},       {0,},       {0,}       }},
 
 };
  /*
@@ -247,18 +248,28 @@ int get_unusual_el_valence( int nPeriodicNum, int charge, int radical, int bonds
 /***********************************************************************************
  *  output valence needed to unumbiguosly reconstruct number of H
  ***********************************************************************************/
-int needed_unusual_el_valence( int nPeriodicNum, int charge, int radical, int bonds_valence, int num_H, int num_bonds )
+int needed_unusual_el_valence( int nPeriodicNum, int charge, int radical, int bonds_valence,
+                               int actual_bonds_valence, int num_H, int num_bonds )
 {
     int i, num_found, num_found_known, chem_valence, rad_adj, known_chem_valence, exact_found;
+    int num_H_expected;
+    char szElement[4];
     /*
     if ( !num_bonds && !num_H )
         return 0;
     */
+    if ( num_bonds && !GetElementFormulaFromAtNum(nPeriodicNum, szElement ) ) {
+        num_H_expected = get_num_H( szElement, 0, NULL, charge, radical, actual_bonds_valence, 0,0,0,0 );
+    } else {
+        num_H_expected = num_H;
+    }
+
     chem_valence = bonds_valence + num_H;
     if ( charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE ||
          !get_el_valence( nPeriodicNum, charge, 0 ) || 
-         do_not_add_H( nPeriodicNum ) ) {
-        if ( !num_H )
+         do_not_add_H( nPeriodicNum ) || bonds_valence != actual_bonds_valence ||
+         num_H_expected != num_H ) {
+        if ( !num_H && !num_H_expected && bonds_valence == actual_bonds_valence )
             return 0; /* no H */
         return chem_valence; /* needs to add H-atoms */
     }
@@ -515,8 +526,11 @@ int get_num_H (const char* elname, int inp_num_H, S_CHAR inp_num_iso_H[],
             */
             num_H = inchi_max( 0, val - chem_bonds_valence );
         }
-        for ( i = 0, num_iso_H = 0; i < NUM_H_ISOTOPES; i ++ ) {
-            num_iso_H += inp_num_iso_H[i];
+        num_iso_H = 0;
+        if ( inp_num_iso_H ) {
+            for ( i = 0; i < NUM_H_ISOTOPES; i ++ ) {
+                num_iso_H += inp_num_iso_H[i];
+            }
         }
         /*  should not happen because atom here is not aliased */
         if ( num_iso_H ) {
@@ -634,7 +648,7 @@ char *fgetsTab( char *szLine, int len, FILE *f );
 /*******************************************************************/
 char *fgetsTab( char *szLine, int len, FILE *f )
 {
-    int  length=0, c;
+    int  length=0, c=0;
     len --;
     while ( length < len && EOF != (c = fgetc( f )) ) {
         if ( c == '\t' )
@@ -718,6 +732,31 @@ int my_fgets( char *szLine, int len, FILE *f, int *bTooLongLine )
     } while ( !length );
     return length;
 }
+#if ( FIX_READ_LONG_LINE_BUG == 1 )
+/********************************************************************/
+int my_fgetsUpToLfOrTab( char *szLine, int len, FILE *f )
+{
+    int  length;
+    char *p;
+    char szSkip[256];
+    int  bTooLongLine = 0;
+    do {
+        p = fgetsTab( szLine, len, f );
+        if ( !p ) {
+            return -1; /* end of file or cannot read */
+        }
+        bTooLongLine = ( (int)strlen(szLine) == len-1 && szLine[len-2] != '\n' );
+        LtrimRtrim( szLine, &length );
+    } while ( !length );
+    if ( bTooLongLine ) {
+        while ( p = fgetsTab( szSkip, sizeof(szSkip)-1, f ) ) {
+            if ( strchr( szSkip, '\n' ) )
+                break;
+        }
+    }
+    return length;
+}
+#else
 /********************************************************************/
 int my_fgetsUpToLfOrTab( char *szLine, int len, FILE *f )
 {
@@ -746,6 +785,7 @@ int my_fgetsUpToLfOrTab( char *szLine, int len, FILE *f )
     }
     return length;
 }
+#endif
 /******************************************************************/
 /* read not more than line_len bytes from an lf-terminated line   */
 /* if input line is too long quietly ignore the rest of the line  */
@@ -829,6 +869,24 @@ AT_NUMB *is_in_the_list( AT_NUMB *pathAtom, AT_NUMB nNextAtom, int nPathLen )
         ;
     return nPathLen? pathAtom : NULL;
 }
+/******************************************************************************************************/
+int nBondsValToMetal( inp_ATOM* at, int iat )
+{
+    int i, neigh, bond_type, nVal2Metal = 0;
+    inp_ATOM* a  = at + iat;
+    for ( i = 0; i < a->valence; i ++ ) {
+        neigh = a->neighbor[i];
+        if ( is_el_a_metal( at[(int)a->neighbor[i]].el_number ) ) {
+            bond_type = a->bond_type[i];
+            if ( bond_type <= BOND_TYPE_TRIPLE ) {
+                nVal2Metal += bond_type;
+            } else {
+                return -1;  /* bond to metal order is not well defined */
+            }
+        }
+    }
+    return nVal2Metal;
+}
 /************************************************************************/
 int num_of_H( inp_ATOM *at, int iat )
 {
@@ -1070,7 +1128,7 @@ int MakeRemovedProtonsString( int nNumRemovedProtons, NUM_H *nNumExchgIsotopicH,
 /*************************************************************************/
 #define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) )
 
-#if ( !defined(_MSC_VER) || defined(__STDC__) && __STDC__ == 1 )
+#if ( defined(ADD_NON_ANSI_FUNCTIONS) || defined(__STDC__) && __STDC__ == 1 )
 /* support (VC++ Language extensions) = OFF && defined(INCHI_ANSI_ONLY) */
 int memicmp ( const void * p1, const void * p2, size_t length )
 {