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dalke  committed 75fae23

Cleaned up some of the SMILES (my validation wasn't as strict
as I thought it was)

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  • Parent commits 307fce8

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File patterns.dat

 [BH]N[BH] 6,7,14,272,275,299
 
 # there's an aromatic boron in CID 10899214
-[b]1ccccc1 AAADcYJgAAAAAAAAAAAAAAAAAAAAAAAAAAAkAAAAAAAAAAABgAAgGAAAAAAACACAEAAwAIAAAACAACBCAAACAAAgAAAIiAAAAIgIICKAERCAIAAggAAIiAYAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==
+#[b]1ccccc1 #AAADcYJgAAAAAAAAAAAAAAAAAAAAAAAAAAAkAAAAAAAAAAABgAAgGAAAAAAACACAEAAwAIAAAACAACBCAAACAAAgAAAIiAAAAIgIICKAERCAIAAggAAIiAYAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==
 
 
 # Carbon
 
 c1cc1=O 9,18,115,116,255,283,284,286,332,341,344,352,355,370,371,381,382,384
 c1nc1=O 9,14,18,115,117,118,255,256,283-286,344,345,351,352,358,365,370,372,373,376,381,387,390,396,403
-c1c[as]1=O 9,18,65,115,118,255,256,283,284,295,344,370
+
+# CACTVS supports aromatic arsenic. So does OEChem.
+# But OEChem' aromaticity perception algorithms will remove aromaticity
+# XXX FIXME to allow (require?) users to set the aromaticity model
+# c1c[as]1=O 9,18,65,115,118,255,256,283,284,295,344,370
 
 C1CC1 0,9,115,119,283,284,332,344
 C1C=C1 0,9,115,119,283,284,332,344,416,434,441,446,516
 
 c1cc1=O.c1cc1=O 0,9-10,18-19,115,116,122-123,255,283,284,286,332,341,344,352,355,370,371,381,382,384,420
 c1nc1=O.c1nc1=O 9-10,14-15,18-19,115,117,118,122,124-125,255,256,283-286,344,345,351,352,358,365,370,372,373,376,381,387,390,396,403,420
-c1c[as]1=O.c1c[as]1=O 0,9-10,18-19,65,115,122,125,118,255,256,283,284,295,344,370,420
+## XXX FIXME: I repercieve input aromaticity, which turns the [as] into [As]
+#c1c[as]1=O.c1c[as]1=O 0,9-10,18-19,65,115,122,125,118,255,256,283,284,295,344,370,420
 
 
 [C]1[C][C]1[C][C][C]1[C][C]1 9-11,115,119,122,126,284,332-333,582,679,688,696,697,708,709
 [Al][H] 318 X
 [Al]Cl 319 X
 [SiH] 320 X 
-[Si]-H 320 X 
+[Si]-[H] 320 X 
 [Si]-[Si] 321 X 
 [Si]#[Si] 321 X 
 [Si][Cl] 322 X
 C(C)(C)(=N)C 336 X
 
 C(C)(C)(C)(O) 337 X
-C(C)(C)(H)(N) 338 X
+C(C)(C)([H])(N) 338 X
 
 C(C)(C)([H])(O) 339 X
 C(C)(C)(O) 339 X
 
 ## Section 5
 
+# There should be nothing in this set which triggers any of these bits
+[Cl].[C].[O].[S].[P].[N] X 115-881
+
 CC X 416,417
 C=C 416 417
 C#C 417 416