Re: [Open Babel] Openbabel 2.4.1 reading MOL file with radicals failed

[Noel O'Boyle]

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  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"  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  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
>> 0.0.0. C   0  0  0  0  0
>> 0.0.0. C   0  0  0  0  0
>> 0.0.0. H   0  0  0  0  0
>> 0.0.0. H   0  0  0  0  0
>> 0.0.0. H   0  0  0  0  0
>> 0.0.0. H   0  0  0  0  0
>> 0.0.0. 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
>> 0.0.0. C   0  0  0  0  0
>> 0.0.0. 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

Re: [Open Babel] Openbabel 2.4.1 reading MOL file with radicals failed

[Noel O'Boyle]

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  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  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"  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  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
>>> 0.0.0. C   0  0  0  0  0
>>> 0.0.0. C   0  0  0  0  0
>>> 0.0.0. H   0  0  0  0  0
>>> 0.0.0. H   0  0  0  0  0
>>> 0.0.0. H   0  0  0  0  0
>>> 0.0.0. H   0  0  0  0  0
>>> 0.0.0. 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
>>> 0.0.0. C   0  0  0  0  0
>>> 0.0.0. 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.
>> 

Re: [Open Babel] Openbabel 2.4.1 reading MOL file with radicals failed

[dfjk-123]

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"  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  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
0.0.0. C   0  0  0  0  0
0.0.0. C   0  0  0  0  0
0.0.0. H   0  0  0  0  0
0.0.0. H   0  0  0  0  0
0.0.0. H   0  0  0  0  0
0.0.0. H   0  0  0  0  0
0.0.0. 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
0.0.0. C   0  0  0  0  0
0.0.0. 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

Re: [Open Babel] Openbabel 2.4.1 reading MOL file with radicals failed

[Craig James]

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  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
> 0.0.0. C   0  0  0  0  0
> 0.0.0. C   0  0  0  0  0
> 0.0.0. H   0  0  0  0  0
> 0.0.0. H   0  0  0  0  0
> 0.0.0. H   0  0  0  0  0
> 0.0.0. H   0  0  0  0  0
> 0.0.0. 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
> 0.0.0. C   0  0  0  0  0
> 0.0.0. 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