The problem is that there is no "correct" answer to your question. The
specifications for the MOL format doesn't include a clear definition of the
assumed valence of each atomic element. So when you specify 5 hydrogens in
the file instead of six, but no "M RAD" line, does it mean it's a radical?
Or does it mean that you just specified 5 hydrogens for some other reason?
The MOL specification is ambiguous.

That is why the "M RAD" line is necessary when specifying radicals.
Consider this example: You draw a molecule with one stereo center, and in
order to get the stereochemistry right, your MOL file contains one H atom.
Does that mean that all of the other carbon atoms in your molecule are
radicals? No, of course not.  Specifying one H atom in a MOL file
*does not* mean
that you have specified *all* hydrogens.

The OpenBabel 2.4.1 interpretation of your MOL file is more correct than
the 2.3.1 interpretation. Use "M RAD" if you are specifying radicals.

By contrast, the SMILES specification is very clear about valence
assumptions and the meaning of hydrogen atoms. If you want to specify a
radical, you have to put the hydrogen inside the carbon atom's brackets,
e.g. "C[CH2]". When you put a hydrogen as a separate atom, e.g.
"CC([H])[H]", it is not a radical, and the canonical SMILES is "CC". When
Weininger wrote the original SMILES specification, he recognized this
deficiency in the MOL specification and wanted to make sure SMILES didn't
have this ambiguity.

Best,
Craig


On Wed, Apr 25, 2018 at 8:52 PM, dfjk-123 <dfjk-...@163.com> wrote:

> 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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>


-- 
---------------------------------
Craig A. James
Chief Technology Officer
eMolecules, Inc.
---------------------------------
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