Hello,
Awhile back I had noticed that rdkit has issues with boron containing
compounds. One is below, and I admit it is a strange one. I read in an sdf
file and write it out after calculating a formal charge on the molecule.
It seems to be read into rdkit ok but writing errored out with "ValueError:
could not find number of expected rings."
I think it odd that the compound can be read in, but not written out. Should I
just ignore this molecule?
Brian
OpenBabel08161816583D
12 30 0 0 0 0 0 0 0 0999 V2000
0.7000 -4.9240 -0.0370 B 0 0 0 0 0 0 0 0 0 0 0 0
1.5320 -2.2270 -0.0390 B 0 0 0 0 0 0 0 0 0 0 0 0
0.0470 -3.3430 -0.0100 B 0 0 0 0 0 0 0 0 0 0 0 0
3.9570 -0.6710 -0.0740 B 0 0 0 0 0 0 0 0 0 0 0 0
-1.3100 0.9460 0.0290 B 0 0 0 0 0 0 0 0 0 0 0 0
-0.7380 -1.0010 0.0270 B 0 0 0 0 0 0 0 0 0 0 0 0
3.8030 -1.9300 -0.2150 B 0 0 0 0 0 0 0 0 0 0 0 0
2.0560 0.0860 -0.0260 B 0 0 0 0 0 0 0 0 0 0 0 0
-0.7320 -1.1240 -0.0280 B 0 0 0 0 0 0 0 0 0 0 0 0
-1.8540 -2.5110 -0.1560 B 0 0 0 0 0 0 0 0 0 0 0 0
0.8030 1.3740 0.1040 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2660 -0.0510 -0.0220 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
1 6 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 7 1 0 0 0 0
2 8 1 0 0 0 0
3 6 1 0 0 0 0
3 7 1 0 0 0 0
3 10 1 0 0 0 0
4 5 1 0 0 0 0
4 8 1 0 0 0 0
4 9 1 0 0 0 0
5 6 1 0 0 0 0
5 9 1 0 0 0 0
5 12 1 0 0 0 0
6 10 1 0 0 0 0
6 12 1 0 0 0 0
7 8 1 0 0 0 0
7 10 1 0 0 0 0
7 11 1 0 0 0 0
8 9 1 0 0 0 0
8 11 1 0 0 0 0
9 11 1 0 0 0 0
9 12 1 0 0 0 0
10 11 1 0 0 0 0
10 12 1 0 0 0 0
11 12 1 0 0 0 0
M END
$$$$
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