Hi,
I have this MDL file (I removed the header):
12 11 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 9 1 0 0 0 0
3 8 1 0 0 0 0
3 4 1 0 0 0 0
4 11 1 0 0 0 0
4 10 1 0 0 0 0
4 5 1 0 0 0 0
5 12 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
M END
It should correspond to this molecule: O1OCCC1O (in SMILES format). I
verified the MDL file manually. However, when I convert the file to a SMILES
string with openbabel, I get this: O1OCCC1O.[H], which is almost correct,
but for some reason it decides to add on a random hydrogen. I am treating
the hydrogens explicitly in the MDL file, because I have to keep track of
their exact indices, so I cannot remove them from the file. The script I am
using is
import pybel
mol = pybel.readfile('mdl', 'mol.mdl').next()
print mol.write(format='smi')
What am I missing?
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