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
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