Hi, there
Now, I'm using openbabel 2.4.1 to convert mol file with radicals to smiles.
Accordting to the openbabel document, I use the exmaple showed in this page
(http://openbabel.org/docs/2.3.0/Features/Radicals.html), but when I try to
convert the MOL file with explicit hydrogen to SMILES, it give me wrong
result.
The MOL file is as follows, which is named as test.mol :
openbabel command is "obabel -imol test.mol -ocan " , however, it returns the
SMILES as "CC"
ethyl radical
OpenBabel04010617172D
Has explicit hydrogen and implicit spin multiplicity
7 6 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0
1 2 1 0 0 0
1 3 1 0 0 0
1 4 1 0 0 0
1 5 1 0 0 0
2 6 1 0 0 0
2 7 1 0 0 0
M END
But ,if the mol file is this:
ethyl radical
OpenBabel04010617192D
Has explicit spin multiplicity and implicit hydrogen
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
1 2 1 0 0 0
M RAD 1 2 2
M END
openbabel 2.4.1 can give me correct SMILES code, C[CH2]
When I change openbabel to 2.3.1, both two MOL files can convert to correct
SMILES radicals.
So, Can you tell me if I make something wrong when using openbabel 2.4.1? How
can I get correct SMILES for radicals when I used the explicit hydrogen in MOL
files ?
Thanks in advance.
Yours,
Baohua Zhang
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