mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-06 22:39:55 +08:00
fix and test problems with reading aromatic Si from smiles
(github issue 5)
This commit is contained in:
Greg Landrum
@@ -1,6 +1,6 @@
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#line 2 "/Users/landrgr1/RDKit_trunk/Code/GraphMol/SmilesParse/lex.yysmiles.cpp"
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#line 2 "/scratch/RDKit_trunk/Code/GraphMol/SmilesParse/lex.yysmiles.cpp"
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#line 4 "/Users/landrgr1/RDKit_trunk/Code/GraphMol/SmilesParse/lex.yysmiles.cpp"
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#line 4 "/scratch/RDKit_trunk/Code/GraphMol/SmilesParse/lex.yysmiles.cpp"
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#define YY_INT_ALIGNED short int
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@@ -54,7 +54,6 @@ typedef int flex_int32_t;
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typedef unsigned char flex_uint8_t;
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typedef unsigned short int flex_uint16_t;
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typedef unsigned int flex_uint32_t;
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#endif /* ! C99 */
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/* Limits of integral types. */
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#ifndef INT8_MIN
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@@ -85,6 +84,8 @@ typedef unsigned int flex_uint32_t;
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#define UINT32_MAX (4294967295U)
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#endif
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#endif /* ! C99 */
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#endif /* ! FLEXINT_H */
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#ifdef __cplusplus
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@@ -158,7 +159,15 @@ typedef void* yyscan_t;
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/* Size of default input buffer. */
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#ifndef YY_BUF_SIZE
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#ifdef __ia64__
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/* On IA-64, the buffer size is 16k, not 8k.
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* Moreover, YY_BUF_SIZE is 2*YY_READ_BUF_SIZE in the general case.
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* Ditto for the __ia64__ case accordingly.
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*/
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#define YY_BUF_SIZE 32768
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#else
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#define YY_BUF_SIZE 16384
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#endif /* __ia64__ */
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#endif
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/* The state buf must be large enough to hold one state per character in the main buffer.
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@@ -170,11 +179,6 @@ typedef void* yyscan_t;
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typedef struct yy_buffer_state *YY_BUFFER_STATE;
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#endif
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#ifndef YY_TYPEDEF_YY_SIZE_T
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#define YY_TYPEDEF_YY_SIZE_T
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typedef size_t yy_size_t;
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#endif
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#define EOB_ACT_CONTINUE_SCAN 0
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#define EOB_ACT_END_OF_FILE 1
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#define EOB_ACT_LAST_MATCH 2
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@@ -197,6 +201,11 @@ typedef size_t yy_size_t;
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#define unput(c) yyunput( c, yyg->yytext_ptr , yyscanner )
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#ifndef YY_TYPEDEF_YY_SIZE_T
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#define YY_TYPEDEF_YY_SIZE_T
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typedef size_t yy_size_t;
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#endif
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#ifndef YY_STRUCT_YY_BUFFER_STATE
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#define YY_STRUCT_YY_BUFFER_STATE
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struct yy_buffer_state
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@@ -214,7 +223,7 @@ struct yy_buffer_state
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/* Number of characters read into yy_ch_buf, not including EOB
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* characters.
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*/
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yy_size_t yy_n_chars;
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int yy_n_chars;
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/* Whether we "own" the buffer - i.e., we know we created it,
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* and can realloc() it to grow it, and should free() it to
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@@ -293,7 +302,7 @@ static void yysmiles__init_buffer (YY_BUFFER_STATE b,FILE *file ,yyscan_t yyscan
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YY_BUFFER_STATE yysmiles__scan_buffer (char *base,yy_size_t size ,yyscan_t yyscanner );
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YY_BUFFER_STATE yysmiles__scan_string (yyconst char *yy_str ,yyscan_t yyscanner );
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YY_BUFFER_STATE yysmiles__scan_bytes (yyconst char *bytes,yy_size_t len ,yyscan_t yyscanner );
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YY_BUFFER_STATE yysmiles__scan_bytes (yyconst char *bytes,int len ,yyscan_t yyscanner );
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void *yysmiles_alloc (yy_size_t ,yyscan_t yyscanner );
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void *yysmiles_realloc (void *,yy_size_t ,yyscan_t yyscanner );
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@@ -349,8 +358,8 @@ static void yy_fatal_error (yyconst char msg[] ,yyscan_t yyscanner );
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*yy_cp = '\0'; \
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yyg->yy_c_buf_p = yy_cp;
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#define YY_NUM_RULES 137
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#define YY_END_OF_BUFFER 138
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#define YY_NUM_RULES 138
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#define YY_END_OF_BUFFER 139
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/* This struct is not used in this scanner,
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but its presence is necessary. */
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struct yy_trans_info
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@@ -358,15 +367,15 @@ struct yy_trans_info
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flex_int32_t yy_verify;
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flex_int32_t yy_nxt;
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};
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static yyconst flex_int16_t yy_accept[170] =
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static yyconst flex_int16_t yy_accept[171] =
|
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{ 0,
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0, 0, 0, 0, 138, 136, 135, 123, 132, 127,
|
||||
128, 119, 122, 121, 131, 126, 133, 134, 6, 100,
|
||||
101, 106, 110, 109, 102, 103, 104, 105, 129, 125,
|
||||
111, 112, 113, 114, 115, 116, 124, 120, 136, 100,
|
||||
101, 136, 136, 106, 136, 110, 109, 16, 136, 136,
|
||||
102, 103, 104, 136, 105, 136, 87, 20, 69, 136,
|
||||
35, 136, 130, 116, 136, 0, 0, 0, 0, 0,
|
||||
0, 0, 0, 0, 139, 137, 136, 124, 133, 128,
|
||||
129, 120, 123, 122, 132, 127, 134, 135, 6, 100,
|
||||
101, 106, 110, 109, 102, 103, 104, 105, 130, 126,
|
||||
111, 112, 113, 114, 115, 116, 125, 121, 137, 100,
|
||||
101, 137, 137, 106, 137, 110, 109, 16, 137, 137,
|
||||
102, 103, 104, 137, 105, 137, 87, 20, 69, 137,
|
||||
35, 137, 131, 116, 137, 0, 0, 0, 0, 0,
|
||||
0, 108, 107, 84, 43, 13, 90, 15, 30, 80,
|
||||
74, 51, 9, 78, 92, 17, 44, 53, 93, 91,
|
||||
23, 21, 50, 26, 61, 63, 94, 58, 24, 95,
|
||||
@@ -377,7 +386,7 @@ static yyconst flex_int16_t yy_accept[170] =
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56, 79, 54, 73, 89, 83, 33, 70, 99, 41,
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||||
81, 40, 47, 18, 31, 14, 57, 46, 34, 68,
|
||||
60, 39, 48, 85, 19, 76, 64, 49, 65, 27,
|
||||
36, 117, 118, 2, 4, 5, 3, 1, 0
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||||
36, 118, 117, 119, 2, 4, 5, 3, 1, 0
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||||
} ;
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static yyconst flex_int32_t yy_ec[256] =
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@@ -423,15 +432,15 @@ static yyconst flex_int32_t yy_meta[66] =
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1, 1, 1, 1, 1
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} ;
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static yyconst flex_int16_t yy_base[170] =
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static yyconst flex_int16_t yy_base[171] =
|
||||
{ 0,
|
||||
0, 0, 51, 0, 158, 237, 237, 237, 237, 237,
|
||||
237, 237, 237, 237, 237, 237, 237, 237, 80, 96,
|
||||
97, 237, 237, 237, 237, 237, 237, 237, 237, 237,
|
||||
0, 0, 51, 0, 161, 237, 237, 237, 237, 237,
|
||||
237, 237, 237, 237, 237, 237, 237, 237, 80, 98,
|
||||
101, 237, 237, 237, 237, 237, 237, 237, 237, 237,
|
||||
237, 237, 237, 237, 237, 237, 237, 237, 69, 51,
|
||||
88, 77, 46, 79, 54, 68, 85, 80, 102, 102,
|
||||
118, 73, 124, 143, 152, 168, 237, 237, 237, 78,
|
||||
77, 97, 237, 73, 72, 201, 81, 70, 70, 61,
|
||||
88, 88, 46, 79, 54, 68, 85, 81, 102, 102,
|
||||
118, 79, 124, 143, 152, 168, 237, 237, 237, 85,
|
||||
76, 97, 237, 74, 72, 201, 81, 70, 70, 61,
|
||||
43, 237, 237, 237, 237, 237, 237, 237, 237, 237,
|
||||
237, 237, 237, 237, 237, 237, 237, 237, 237, 237,
|
||||
237, 237, 237, 237, 237, 237, 237, 237, 237, 237,
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||||
@@ -442,29 +451,29 @@ static yyconst flex_int16_t yy_base[170] =
|
||||
237, 237, 237, 237, 237, 237, 237, 237, 237, 237,
|
||||
237, 237, 237, 237, 237, 237, 237, 237, 237, 237,
|
||||
237, 237, 237, 237, 237, 237, 237, 237, 237, 237,
|
||||
237, 237, 237, 237, 237, 237, 237, 237, 237
|
||||
237, 237, 237, 237, 237, 237, 237, 237, 237, 237
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||||
} ;
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static yyconst flex_int16_t yy_def[170] =
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static yyconst flex_int16_t yy_def[171] =
|
||||
{ 0,
|
||||
169, 1, 1, 3, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
170, 1, 1, 3, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 0
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 0
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||||
} ;
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static yyconst flex_int16_t yy_nxt[303] =
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@@ -475,34 +484,34 @@ static yyconst flex_int16_t yy_nxt[303] =
|
||||
27, 6, 6, 28, 6, 6, 6, 6, 6, 6,
|
||||
6, 29, 30, 6, 6, 31, 32, 6, 6, 6,
|
||||
6, 6, 6, 6, 6, 6, 33, 34, 35, 6,
|
||||
36, 6, 6, 6, 37, 38, 168, 39, 40, 41,
|
||||
36, 6, 6, 6, 37, 38, 169, 39, 40, 41,
|
||||
42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
|
||||
52, 53, 66, 54, 55, 56, 57, 58, 59, 60,
|
||||
61, 62, 167, 166, 63, 82, 67, 68, 102, 83,
|
||||
61, 62, 168, 167, 63, 82, 67, 68, 102, 83,
|
||||
|
||||
165, 103, 104, 84, 85, 96, 97, 164, 98, 69,
|
||||
166, 103, 104, 84, 85, 96, 97, 165, 98, 69,
|
||||
72, 64, 65, 70, 71, 74, 105, 106, 107, 75,
|
||||
163, 162, 159, 76, 77, 108, 158, 99, 78, 79,
|
||||
80, 81, 86, 127, 100, 87, 88, 89, 101, 111,
|
||||
95, 109, 73, 90, 110, 91, 112, 92, 93, 116,
|
||||
94, 73, 117, 160, 113, 72, 161, 169, 118, 119,
|
||||
169, 114, 120, 121, 115, 122, 123, 169, 128, 129,
|
||||
124, 130, 169, 169, 169, 125, 126, 169, 169, 131,
|
||||
169, 132, 169, 133, 169, 134, 135, 136, 137, 169,
|
||||
169, 138, 139, 169, 140, 169, 169, 143, 144, 141,
|
||||
164, 159, 162, 76, 77, 108, 163, 99, 78, 79,
|
||||
80, 81, 86, 158, 100, 87, 88, 89, 101, 127,
|
||||
111, 109, 73, 90, 110, 91, 112, 92, 93, 116,
|
||||
94, 95, 117, 160, 113, 73, 161, 72, 118, 119,
|
||||
170, 114, 120, 121, 115, 122, 123, 170, 128, 129,
|
||||
124, 130, 170, 170, 170, 125, 126, 170, 170, 131,
|
||||
170, 132, 170, 133, 170, 134, 135, 136, 137, 170,
|
||||
170, 138, 139, 170, 140, 170, 170, 143, 144, 141,
|
||||
|
||||
145, 169, 169, 66, 146, 142, 169, 147, 148, 169,
|
||||
169, 149, 150, 151, 152, 169, 153, 67, 68, 154,
|
||||
155, 169, 156, 157, 169, 169, 169, 169, 169, 169,
|
||||
69, 169, 169, 169, 70, 71, 5, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
145, 170, 170, 66, 146, 142, 170, 147, 148, 170,
|
||||
170, 149, 150, 151, 152, 170, 153, 67, 68, 154,
|
||||
155, 170, 156, 157, 170, 170, 170, 170, 170, 170,
|
||||
69, 170, 170, 170, 70, 71, 5, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
|
||||
169, 169
|
||||
170, 170
|
||||
} ;
|
||||
|
||||
static yyconst flex_int16_t yy_chk[303] =
|
||||
@@ -520,11 +529,11 @@ static yyconst flex_int16_t yy_chk[303] =
|
||||
|
||||
68, 45, 45, 40, 40, 43, 43, 67, 43, 19,
|
||||
40, 3, 3, 19, 19, 39, 46, 46, 46, 39,
|
||||
65, 64, 61, 39, 39, 46, 60, 44, 39, 39,
|
||||
39, 39, 41, 52, 44, 41, 41, 41, 44, 48,
|
||||
42, 47, 41, 41, 47, 41, 49, 41, 41, 50,
|
||||
41, 21, 50, 62, 49, 20, 62, 5, 50, 50,
|
||||
0, 49, 51, 51, 49, 51, 51, 0, 53, 53,
|
||||
65, 61, 64, 39, 39, 46, 64, 44, 39, 39,
|
||||
39, 39, 41, 60, 44, 41, 41, 41, 44, 52,
|
||||
48, 47, 41, 41, 47, 41, 49, 41, 41, 50,
|
||||
41, 42, 50, 62, 49, 21, 62, 20, 50, 50,
|
||||
5, 49, 51, 51, 49, 51, 51, 0, 53, 53,
|
||||
51, 53, 0, 0, 0, 51, 51, 0, 0, 53,
|
||||
0, 53, 0, 53, 0, 53, 53, 54, 54, 0,
|
||||
0, 54, 54, 0, 54, 0, 0, 55, 55, 54,
|
||||
@@ -532,15 +541,15 @@ static yyconst flex_int16_t yy_chk[303] =
|
||||
55, 0, 0, 66, 55, 54, 0, 55, 55, 0,
|
||||
0, 55, 56, 56, 56, 0, 56, 66, 66, 56,
|
||||
56, 0, 56, 56, 0, 0, 0, 0, 0, 0,
|
||||
66, 0, 0, 0, 66, 66, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
169, 169, 169, 169, 169, 169, 169, 169, 169, 169,
|
||||
66, 0, 0, 0, 66, 66, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
170, 170, 170, 170, 170, 170, 170, 170, 170, 170,
|
||||
|
||||
169, 169
|
||||
170, 170
|
||||
} ;
|
||||
|
||||
/* The intent behind this definition is that it'll catch
|
||||
@@ -553,7 +562,7 @@ static yyconst flex_int16_t yy_chk[303] =
|
||||
#line 1 "smiles.ll"
|
||||
#line 6 "smiles.ll"
|
||||
|
||||
// $Id: smiles.ll 2064 2012-05-18 05:56:45Z glandrum $
|
||||
// $Id: smiles.ll 2241 2012-10-12 08:58:38Z glandrum $
|
||||
//
|
||||
// Copyright (C) 2001-2010 Randal Henne, Greg Landrum and Rational Discovery LLC
|
||||
//
|
||||
@@ -590,7 +599,7 @@ void smiles_lexer_error(const char *msg) {
|
||||
}
|
||||
|
||||
|
||||
#line 594 "/Users/landrgr1/RDKit_trunk/Code/GraphMol/SmilesParse/lex.yysmiles.cpp"
|
||||
#line 603 "/scratch/RDKit_trunk/Code/GraphMol/SmilesParse/lex.yysmiles.cpp"
|
||||
|
||||
#define INITIAL 0
|
||||
#define IN_ATOM_STATE 1
|
||||
@@ -620,8 +629,8 @@ struct yyguts_t
|
||||
size_t yy_buffer_stack_max; /**< capacity of stack. */
|
||||
YY_BUFFER_STATE * yy_buffer_stack; /**< Stack as an array. */
|
||||
char yy_hold_char;
|
||||
yy_size_t yy_n_chars;
|
||||
yy_size_t yyleng_r;
|
||||
int yy_n_chars;
|
||||
int yyleng_r;
|
||||
char *yy_c_buf_p;
|
||||
int yy_init;
|
||||
int yy_start;
|
||||
@@ -674,7 +683,7 @@ FILE *yysmiles_get_out (yyscan_t yyscanner );
|
||||
|
||||
void yysmiles_set_out (FILE * out_str ,yyscan_t yyscanner );
|
||||
|
||||
yy_size_t yysmiles_get_leng (yyscan_t yyscanner );
|
||||
int yysmiles_get_leng (yyscan_t yyscanner );
|
||||
|
||||
char *yysmiles_get_text (yyscan_t yyscanner );
|
||||
|
||||
@@ -720,7 +729,12 @@ static int input (yyscan_t yyscanner );
|
||||
|
||||
/* Amount of stuff to slurp up with each read. */
|
||||
#ifndef YY_READ_BUF_SIZE
|
||||
#ifdef __ia64__
|
||||
/* On IA-64, the buffer size is 16k, not 8k */
|
||||
#define YY_READ_BUF_SIZE 16384
|
||||
#else
|
||||
#define YY_READ_BUF_SIZE 8192
|
||||
#endif /* __ia64__ */
|
||||
#endif
|
||||
|
||||
/* Copy whatever the last rule matched to the standard output. */
|
||||
@@ -728,7 +742,7 @@ static int input (yyscan_t yyscanner );
|
||||
/* This used to be an fputs(), but since the string might contain NUL's,
|
||||
* we now use fwrite().
|
||||
*/
|
||||
#define ECHO fwrite( yytext, yyleng, 1, yyout )
|
||||
#define ECHO do { if (fwrite( yytext, yyleng, 1, yyout )) {} } while (0)
|
||||
#endif
|
||||
|
||||
/* Gets input and stuffs it into "buf". number of characters read, or YY_NULL,
|
||||
@@ -739,7 +753,7 @@ static int input (yyscan_t yyscanner );
|
||||
if ( YY_CURRENT_BUFFER_LVALUE->yy_is_interactive ) \
|
||||
{ \
|
||||
int c = '*'; \
|
||||
yy_size_t n; \
|
||||
size_t n; \
|
||||
for ( n = 0; n < max_size && \
|
||||
(c = getc( yyin )) != EOF && c != '\n'; ++n ) \
|
||||
buf[n] = (char) c; \
|
||||
@@ -827,7 +841,7 @@ YY_DECL
|
||||
#line 46 "smiles.ll"
|
||||
|
||||
|
||||
#line 831 "/Users/landrgr1/RDKit_trunk/Code/GraphMol/SmilesParse/lex.yysmiles.cpp"
|
||||
#line 845 "/scratch/RDKit_trunk/Code/GraphMol/SmilesParse/lex.yysmiles.cpp"
|
||||
|
||||
yylval = yylval_param;
|
||||
|
||||
@@ -882,7 +896,7 @@ yy_match:
|
||||
while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state )
|
||||
{
|
||||
yy_current_state = (int) yy_def[yy_current_state];
|
||||
if ( yy_current_state >= 170 )
|
||||
if ( yy_current_state >= 171 )
|
||||
yy_c = yy_meta[(unsigned int) yy_c];
|
||||
}
|
||||
yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c];
|
||||
@@ -1229,7 +1243,7 @@ YY_RULE_SETUP
|
||||
case 117:
|
||||
YY_RULE_SETUP
|
||||
#line 192 "smiles.ll"
|
||||
{ yylval->atom = new Atom( 34 );
|
||||
{ yylval->atom = new Atom( 14 );
|
||||
yylval->atom->setIsAromatic(true);
|
||||
return AROMATIC_ATOM_TOKEN;
|
||||
}
|
||||
@@ -1237,14 +1251,22 @@ YY_RULE_SETUP
|
||||
case 118:
|
||||
YY_RULE_SETUP
|
||||
#line 196 "smiles.ll"
|
||||
{ yylval->atom = new Atom( 52 );
|
||||
{ yylval->atom = new Atom( 34 );
|
||||
yylval->atom->setIsAromatic(true);
|
||||
return AROMATIC_ATOM_TOKEN;
|
||||
}
|
||||
YY_BREAK
|
||||
case 119:
|
||||
YY_RULE_SETUP
|
||||
#line 201 "smiles.ll"
|
||||
#line 200 "smiles.ll"
|
||||
{ yylval->atom = new Atom( 52 );
|
||||
yylval->atom->setIsAromatic(true);
|
||||
return AROMATIC_ATOM_TOKEN;
|
||||
}
|
||||
YY_BREAK
|
||||
case 120:
|
||||
YY_RULE_SETUP
|
||||
#line 205 "smiles.ll"
|
||||
{ yylval->atom = new Atom( 0 );
|
||||
yylval->atom->setProp("dummyLabel",
|
||||
std::string("*"));
|
||||
@@ -1253,24 +1275,24 @@ YY_RULE_SETUP
|
||||
return ORGANIC_ATOM_TOKEN;
|
||||
}
|
||||
YY_BREAK
|
||||
case 120:
|
||||
YY_RULE_SETUP
|
||||
#line 209 "smiles.ll"
|
||||
{ return COLON_TOKEN; }
|
||||
YY_BREAK
|
||||
case 121:
|
||||
YY_RULE_SETUP
|
||||
#line 211 "smiles.ll"
|
||||
{ return MINUS_TOKEN; }
|
||||
#line 213 "smiles.ll"
|
||||
{ return COLON_TOKEN; }
|
||||
YY_BREAK
|
||||
case 122:
|
||||
YY_RULE_SETUP
|
||||
#line 213 "smiles.ll"
|
||||
{ return PLUS_TOKEN; }
|
||||
#line 215 "smiles.ll"
|
||||
{ return MINUS_TOKEN; }
|
||||
YY_BREAK
|
||||
case 123:
|
||||
YY_RULE_SETUP
|
||||
#line 215 "smiles.ll"
|
||||
#line 217 "smiles.ll"
|
||||
{ return PLUS_TOKEN; }
|
||||
YY_BREAK
|
||||
case 124:
|
||||
YY_RULE_SETUP
|
||||
#line 219 "smiles.ll"
|
||||
{ yylval->bond = new Bond();
|
||||
Bond::BondType bt=Bond::UNSPECIFIED;
|
||||
switch(yytext[0]){
|
||||
@@ -1290,89 +1312,89 @@ YY_RULE_SETUP
|
||||
yylval->bond->setBondType(bt);
|
||||
return BOND_TOKEN; }
|
||||
YY_BREAK
|
||||
case 124:
|
||||
YY_RULE_SETUP
|
||||
#line 234 "smiles.ll"
|
||||
{ yylval->bond = new QueryBond();
|
||||
yylval->bond->setQuery(makeBondNullQuery());
|
||||
return BOND_TOKEN; }
|
||||
YY_BREAK
|
||||
case 125:
|
||||
YY_RULE_SETUP
|
||||
#line 238 "smiles.ll"
|
||||
{ yylval->bond = new Bond(Bond::SINGLE);
|
||||
yylval->bond->setBondDir(Bond::ENDDOWNRIGHT);
|
||||
{ yylval->bond = new QueryBond();
|
||||
yylval->bond->setQuery(makeBondNullQuery());
|
||||
return BOND_TOKEN; }
|
||||
YY_BREAK
|
||||
case 126:
|
||||
YY_RULE_SETUP
|
||||
#line 242 "smiles.ll"
|
||||
{ yylval->bond = new Bond(Bond::SINGLE);
|
||||
yylval->bond->setBondDir(Bond::ENDUPRIGHT);
|
||||
yylval->bond->setBondDir(Bond::ENDDOWNRIGHT);
|
||||
return BOND_TOKEN; }
|
||||
YY_BREAK
|
||||
case 127:
|
||||
YY_RULE_SETUP
|
||||
#line 246 "smiles.ll"
|
||||
{ return GROUP_OPEN_TOKEN; }
|
||||
{ yylval->bond = new Bond(Bond::SINGLE);
|
||||
yylval->bond->setBondDir(Bond::ENDUPRIGHT);
|
||||
return BOND_TOKEN; }
|
||||
YY_BREAK
|
||||
case 128:
|
||||
YY_RULE_SETUP
|
||||
#line 247 "smiles.ll"
|
||||
{ return GROUP_CLOSE_TOKEN; }
|
||||
#line 250 "smiles.ll"
|
||||
{ return GROUP_OPEN_TOKEN; }
|
||||
YY_BREAK
|
||||
case 129:
|
||||
YY_RULE_SETUP
|
||||
#line 250 "smiles.ll"
|
||||
{ BEGIN IN_ATOM_STATE; return ATOM_OPEN_TOKEN; }
|
||||
#line 251 "smiles.ll"
|
||||
{ return GROUP_CLOSE_TOKEN; }
|
||||
YY_BREAK
|
||||
case 130:
|
||||
YY_RULE_SETUP
|
||||
#line 251 "smiles.ll"
|
||||
{ BEGIN INITIAL; return ATOM_CLOSE_TOKEN; }
|
||||
#line 254 "smiles.ll"
|
||||
{ BEGIN IN_ATOM_STATE; return ATOM_OPEN_TOKEN; }
|
||||
YY_BREAK
|
||||
case 131:
|
||||
YY_RULE_SETUP
|
||||
#line 253 "smiles.ll"
|
||||
{ return SEPARATOR_TOKEN; }
|
||||
#line 255 "smiles.ll"
|
||||
{ BEGIN INITIAL; return ATOM_CLOSE_TOKEN; }
|
||||
YY_BREAK
|
||||
case 132:
|
||||
YY_RULE_SETUP
|
||||
#line 255 "smiles.ll"
|
||||
{ return PERCENT_TOKEN; }
|
||||
#line 257 "smiles.ll"
|
||||
{ return SEPARATOR_TOKEN; }
|
||||
YY_BREAK
|
||||
case 133:
|
||||
YY_RULE_SETUP
|
||||
#line 257 "smiles.ll"
|
||||
{ yylval->ival = 0; return ZERO_TOKEN; }
|
||||
#line 259 "smiles.ll"
|
||||
{ return PERCENT_TOKEN; }
|
||||
YY_BREAK
|
||||
case 134:
|
||||
YY_RULE_SETUP
|
||||
#line 258 "smiles.ll"
|
||||
{ yylval->ival = atoi( yytext ); return NONZERO_DIGIT_TOKEN; }
|
||||
#line 261 "smiles.ll"
|
||||
{ yylval->ival = 0; return ZERO_TOKEN; }
|
||||
YY_BREAK
|
||||
case 135:
|
||||
/* rule 135 can match eol */
|
||||
YY_RULE_SETUP
|
||||
#line 262 "smiles.ll"
|
||||
{ yylval->ival = atoi( yytext ); return NONZERO_DIGIT_TOKEN; }
|
||||
YY_BREAK
|
||||
case 136:
|
||||
/* rule 136 can match eol */
|
||||
YY_RULE_SETUP
|
||||
#line 266 "smiles.ll"
|
||||
return 0;
|
||||
YY_BREAK
|
||||
case YY_STATE_EOF(INITIAL):
|
||||
case YY_STATE_EOF(IN_ATOM_STATE):
|
||||
#line 264 "smiles.ll"
|
||||
#line 268 "smiles.ll"
|
||||
{ return EOS_TOKEN; }
|
||||
YY_BREAK
|
||||
case 136:
|
||||
YY_RULE_SETUP
|
||||
#line 265 "smiles.ll"
|
||||
return yytext[0];
|
||||
YY_BREAK
|
||||
case 137:
|
||||
YY_RULE_SETUP
|
||||
#line 267 "smiles.ll"
|
||||
#line 269 "smiles.ll"
|
||||
return yytext[0];
|
||||
YY_BREAK
|
||||
case 138:
|
||||
YY_RULE_SETUP
|
||||
#line 271 "smiles.ll"
|
||||
ECHO;
|
||||
YY_BREAK
|
||||
#line 1376 "/Users/landrgr1/RDKit_trunk/Code/GraphMol/SmilesParse/lex.yysmiles.cpp"
|
||||
#line 1398 "/scratch/RDKit_trunk/Code/GraphMol/SmilesParse/lex.yysmiles.cpp"
|
||||
|
||||
case YY_END_OF_BUFFER:
|
||||
{
|
||||
@@ -1557,7 +1579,7 @@ static int yy_get_next_buffer (yyscan_t yyscanner)
|
||||
|
||||
else
|
||||
{
|
||||
yy_size_t num_to_read =
|
||||
int num_to_read =
|
||||
YY_CURRENT_BUFFER_LVALUE->yy_buf_size - number_to_move - 1;
|
||||
|
||||
while ( num_to_read <= 0 )
|
||||
@@ -1571,7 +1593,7 @@ static int yy_get_next_buffer (yyscan_t yyscanner)
|
||||
|
||||
if ( b->yy_is_our_buffer )
|
||||
{
|
||||
yy_size_t new_size = b->yy_buf_size * 2;
|
||||
int new_size = b->yy_buf_size * 2;
|
||||
|
||||
if ( new_size <= 0 )
|
||||
b->yy_buf_size += b->yy_buf_size / 8;
|
||||
@@ -1602,7 +1624,7 @@ static int yy_get_next_buffer (yyscan_t yyscanner)
|
||||
|
||||
/* Read in more data. */
|
||||
YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]),
|
||||
yyg->yy_n_chars, num_to_read );
|
||||
yyg->yy_n_chars, (size_t) num_to_read );
|
||||
|
||||
YY_CURRENT_BUFFER_LVALUE->yy_n_chars = yyg->yy_n_chars;
|
||||
}
|
||||
@@ -1664,7 +1686,7 @@ static int yy_get_next_buffer (yyscan_t yyscanner)
|
||||
while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state )
|
||||
{
|
||||
yy_current_state = (int) yy_def[yy_current_state];
|
||||
if ( yy_current_state >= 170 )
|
||||
if ( yy_current_state >= 171 )
|
||||
yy_c = yy_meta[(unsigned int) yy_c];
|
||||
}
|
||||
yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c];
|
||||
@@ -1693,11 +1715,11 @@ static int yy_get_next_buffer (yyscan_t yyscanner)
|
||||
while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state )
|
||||
{
|
||||
yy_current_state = (int) yy_def[yy_current_state];
|
||||
if ( yy_current_state >= 170 )
|
||||
if ( yy_current_state >= 171 )
|
||||
yy_c = yy_meta[(unsigned int) yy_c];
|
||||
}
|
||||
yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c];
|
||||
yy_is_jam = (yy_current_state == 169);
|
||||
yy_is_jam = (yy_current_state == 170);
|
||||
|
||||
return yy_is_jam ? 0 : yy_current_state;
|
||||
}
|
||||
@@ -1715,7 +1737,7 @@ static int yy_get_next_buffer (yyscan_t yyscanner)
|
||||
if ( yy_cp < YY_CURRENT_BUFFER_LVALUE->yy_ch_buf + 2 )
|
||||
{ /* need to shift things up to make room */
|
||||
/* +2 for EOB chars. */
|
||||
register yy_size_t number_to_move = yyg->yy_n_chars + 2;
|
||||
register int number_to_move = yyg->yy_n_chars + 2;
|
||||
register char *dest = &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[
|
||||
YY_CURRENT_BUFFER_LVALUE->yy_buf_size + 2];
|
||||
register char *source =
|
||||
@@ -1765,7 +1787,7 @@ static int yy_get_next_buffer (yyscan_t yyscanner)
|
||||
|
||||
else
|
||||
{ /* need more input */
|
||||
yy_size_t offset = yyg->yy_c_buf_p - yyg->yytext_ptr;
|
||||
int offset = yyg->yy_c_buf_p - yyg->yytext_ptr;
|
||||
++yyg->yy_c_buf_p;
|
||||
|
||||
switch ( yy_get_next_buffer( yyscanner ) )
|
||||
@@ -1789,7 +1811,7 @@ static int yy_get_next_buffer (yyscan_t yyscanner)
|
||||
case EOB_ACT_END_OF_FILE:
|
||||
{
|
||||
if ( yysmiles_wrap(yyscanner ) )
|
||||
return 0;
|
||||
return EOF;
|
||||
|
||||
if ( ! yyg->yy_did_buffer_switch_on_eof )
|
||||
YY_NEW_FILE;
|
||||
@@ -2049,7 +2071,7 @@ void yysmiles_pop_buffer_state (yyscan_t yyscanner)
|
||||
*/
|
||||
static void yysmiles_ensure_buffer_stack (yyscan_t yyscanner)
|
||||
{
|
||||
yy_size_t num_to_alloc;
|
||||
int num_to_alloc;
|
||||
struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
|
||||
|
||||
if (!yyg->yy_buffer_stack) {
|
||||
@@ -2142,16 +2164,17 @@ YY_BUFFER_STATE yysmiles__scan_string (yyconst char * yystr , yyscan_t yyscanner
|
||||
|
||||
/** Setup the input buffer state to scan the given bytes. The next call to yysmiles_lex() will
|
||||
* scan from a @e copy of @a bytes.
|
||||
* @param bytes the byte buffer to scan
|
||||
* @param len the number of bytes in the buffer pointed to by @a bytes.
|
||||
* @param yybytes the byte buffer to scan
|
||||
* @param _yybytes_len the number of bytes in the buffer pointed to by @a bytes.
|
||||
* @param yyscanner The scanner object.
|
||||
* @return the newly allocated buffer state object.
|
||||
*/
|
||||
YY_BUFFER_STATE yysmiles__scan_bytes (yyconst char * yybytes, yy_size_t _yybytes_len , yyscan_t yyscanner)
|
||||
YY_BUFFER_STATE yysmiles__scan_bytes (yyconst char * yybytes, int _yybytes_len , yyscan_t yyscanner)
|
||||
{
|
||||
YY_BUFFER_STATE b;
|
||||
char *buf;
|
||||
yy_size_t n, i;
|
||||
yy_size_t n;
|
||||
int i;
|
||||
|
||||
/* Get memory for full buffer, including space for trailing EOB's. */
|
||||
n = _yybytes_len + 2;
|
||||
@@ -2261,7 +2284,7 @@ FILE *yysmiles_get_out (yyscan_t yyscanner)
|
||||
/** Get the length of the current token.
|
||||
* @param yyscanner The scanner object.
|
||||
*/
|
||||
yy_size_t yysmiles_get_leng (yyscan_t yyscanner)
|
||||
int yysmiles_get_leng (yyscan_t yyscanner)
|
||||
{
|
||||
struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
|
||||
return yyleng;
|
||||
@@ -2536,7 +2559,7 @@ void yysmiles_free (void * ptr , yyscan_t yyscanner)
|
||||
|
||||
#define YYTABLES_NAME "yytables"
|
||||
|
||||
#line 267 "smiles.ll"
|
||||
#line 271 "smiles.ll"
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -189,6 +189,10 @@ s { yylval->atom = new Atom( 16 );
|
||||
return AROMATIC_ATOM_TOKEN;
|
||||
}
|
||||
|
||||
<IN_ATOM_STATE>si { yylval->atom = new Atom( 14 );
|
||||
yylval->atom->setIsAromatic(true);
|
||||
return AROMATIC_ATOM_TOKEN;
|
||||
}
|
||||
<IN_ATOM_STATE>se { yylval->atom = new Atom( 34 );
|
||||
yylval->atom->setIsAromatic(true);
|
||||
return AROMATIC_ATOM_TOKEN;
|
||||
|
||||
@@ -97,7 +97,8 @@ void testPass(){
|
||||
"b1ccccc1",
|
||||
"C[Rf]C", // issue 3535668
|
||||
"[C:1]",
|
||||
"[C:0]", // issue 3525776
|
||||
"[C:0]", // issue 3525776
|
||||
"[si]1cccc[si]1", // aromatic Si (github issue 5)
|
||||
"EOS"};
|
||||
while( smis[i] != "EOS" ){
|
||||
string smi = smis[i];
|
||||
|
||||
Reference in New Issue
Block a user