I am reading in a .sdf file and experiencing issues with molecules that have wildcard atoms. The first example ended up placing double bonds in the molecule. The second example one double bond position is moved. The information below is the before and after import. Is there a way to ensure the .sdf file is read exactly as produced?
Below is what I imported 24 26 0 0 0 0 999 V2000 9.9500 6.4289 0.0000 C 0 0 9.1250 6.4289 0.0000 N 0 0 8.7125 5.7145 0.0000 C 0 0 9.1250 5.0000 0.0000 C 0 0 9.9500 5.0000 0.0000 C 0 0 10.3625 5.7145 0.0000 C 0 0 10.3625 7.1434 0.0000 O 0 0 7.8875 5.7145 0.0000 N 0 0 7.4750 6.4289 0.0000 C 0 0 6.6500 6.4289 0.0000 C 0 0 6.2375 5.7145 0.0000 N 0 0 6.6500 5.0000 0.0000 C 0 0 7.4750 5.0000 0.0000 C 0 0 5.4125 5.7145 0.0000 C 0 0 5.0000 5.0000 0.0000 C 0 0 8.7125 7.1434 0.0000 C 0 0 9.1250 7.8579 0.0000 C 0 0 8.7125 8.5724 0.0000 O 0 0 9.7084 8.4413 0.0000 N 0 0 10.5053 8.2277 0.0000 A 0 0 11.0886 8.8111 0.0000 A 0 0 10.8751 9.6080 0.0000 A 0 0 10.0782 9.8215 0.0000 A 0 0 9.4948 9.2382 0.0000 A 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 1 1 0 1 7 2 0 3 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 8 1 0 11 14 1 0 14 15 1 0 2 16 1 0 16 17 1 0 17 18 2 0 17 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 19 1 0 M END This is what was produced upon import 24 26 0 0 0 0 0 0 0 0999 V2000 9.9500 6.4289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1250 6.4289 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 8.7125 5.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1250 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.9500 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3625 5.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3625 7.1434 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.8875 5.7145 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 7.4750 6.4289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6500 6.4289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2375 5.7145 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.6500 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4750 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4125 5.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0000 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7125 7.1434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1250 7.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7125 8.5724 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7084 8.4413 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 10.5053 8.2277 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 11.0886 8.8111 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 10.8751 9.6080 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 10.0782 9.8215 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 9.4948 9.2382 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 1 1 0 1 7 2 0 3 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 8 1 0 11 14 1 0 14 15 1 0 2 16 1 0 16 17 1 0 17 18 2 0 17 19 1 0 19 20 1 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 19 1 0 M END This is the second molecule. 20 22 0 0 0 0 999 V2000 10.9421 6.4289 0.0000 C 0 0 10.1170 6.4289 0.0000 N 0 0 9.7045 5.7145 0.0000 C 0 0 10.1170 5.0000 0.0000 C 0 0 10.9421 5.0000 0.0000 C 0 0 11.3546 5.7145 0.0000 C 0 0 11.3546 7.1434 0.0000 O 0 0 8.8795 5.7145 0.0000 N 0 0 8.4670 6.4289 0.0000 C 0 0 7.6420 6.4289 0.0000 C 0 0 7.2295 5.7145 0.0000 N 0 0 7.6420 5.0000 0.0000 C 0 0 8.4670 5.0000 0.0000 C 0 0 6.4045 5.7145 0.0000 C 0 0 5.9920 5.0000 0.0000 O 0 0 5.9920 6.4290 0.0000 C 0 0 6.3276 7.1827 0.0000 A 0 0 5.7145 7.7347 0.0000 A 0 0 5.0000 7.3222 0.0000 A 0 0 5.1715 6.5152 0.0000 A 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 1 1 0 1 7 2 0 3 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 8 1 0 11 14 1 0 14 15 2 0 14 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 19 20 1 0 20 16 1 0 M END Second molecule after reading in. 20 22 0 0 0 0 0 0 0 0999 V2000 10.9421 6.4289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1170 6.4289 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 9.7045 5.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1170 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.9421 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.3546 5.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.3546 7.1434 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.8795 5.7145 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 8.4670 6.4289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6420 6.4289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2295 5.7145 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 7.6420 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4670 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4045 5.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9920 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9920 6.4290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3276 7.1827 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 5.7145 7.7347 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 5.0000 7.3222 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 5.1715 6.5152 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 1 1 0 1 7 2 0 3 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 8 1 0 11 14 1 0 14 15 2 0 14 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 16 2 0 M END _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss