There is a more recent build of the docs at
https://open-babel.readthedocs.io/en/latest/, but it really should be
available on our main website.
On 27 April 2018 at 01:49, dfjk-123 <dfjk-...@163.com> wrote:
> Thanks for your reply.
> When I read openbabel document, I just find the 2.3.1 version. (
> http://openbabel.org/docs/current/ )
> So, where can I get the document of 2.4.1?
>
> Best,
> Baohua
>
> At 2018-04-26 22:16:44, "Craig James" <cja...@emolecules.com> wrote:
>
> 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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