In relation to the original question, I've just checked, and the current
behaviour of Open Babel is in keeping with the current behaviour of BIOVIA
Draw, the inheritors of the MOL file format.
Regards,
- Noel
On 29 April 2018 at 08:06, Noel O'Boyle <baoille...@gmail.com> wrote:
> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>>
>>
>>
>> --
>> ---------------------------------
>> Craig A. James
>> Chief Technology Officer
>> eMolecules, Inc.
>> ---------------------------------
>>
>>
>>
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
