Hi Noel,
I updated the fragmentation code.
My code is available at https://github.com/n-yoshikawa/contributed/blob/
master/c%2B%2B/fragments/obfragment.cpp
I enumerated ten most frequent fragments from our data by using this code.
The result was as follows:
SMILES percent
[C]1=CC=[C]C=C1 11.1425
[C]1=CC=CC=C1 7.94308
[C]1=CC=C[C]=C1 4.3803
[C]1=CC=[C][C]=C1 2.76544
[C]1=C[C]=[C]C=C1 2.74526
[CH]1[CH][CH][CH]O1 2.12959
[CH]1[CH][CH][CH]O[CH]1 1.87727
[C]1=CC=CC=[C]1 1.77634
[C]1=CC=C[C]=[C]1 1.31207
[C]1=C[C]=[C][C]=C1 1.18086
These fragments have some common parts.
I want to consolidate these into more common fragments.
As Geoff says:
> Most of these are benzene or other 6-membered aromatic rings.
> So 8 of them should consolidate to something like ｀c1ccccc1｀ and the
other two look like 5-membered and 6-membered sugars, which makes sense.
> I think the key problem is that the code is generating radicals (e.g.,
the [C] pieces.
> My suggestion would be to take these SMILES fragments, read them in again
and write out again.
> But I think Noel has a new way of generating canonical SMILES from
fragments. I’d suggest posting to the list and asking. Either way would
consolidate all these strings into c1ccccc1
Do you have any suggestion about generating canonical SMILES from fragments
or consolidating fragments?
Thanks,
Naruki
2018年5月17日(木) 20:45 Noel O'Boyle <baoille...@gmail.com>:
> It was on Github. Here you go: https://github.com/openbabel/
> openbabel/pull/1712
>
> Are you sure you don't just want the canonical labels? I'm happy to
> review...
>
> On 17 May 2018 at 11:47, Geoffrey Hutchison <geoff.hutchi...@gmail.com>
> wrote:
>
>> Hi Noel,
>>
>> I'm working with Naruki, the student with GSoC developing the
>> fragment-based coordinate generation.
>>
>> He's updating my old fragmentation code, which used the SMILES Atom Order
>> data to canonicalize fragments. I can't find your comments on this, and I
>> don't remember whether it was in the GitHub tracker or Open Babel
>> development list.
>>
>> Thanks,
>> -Geoff
>
>
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