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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