John,
Is this the SMILES you're trying to generate from the first thiol?
S(CCC(=O)NC1CCN(CC1)Cc1ccccc1)SCCC(=O)NC1CCN(CC1)Cc1ccccc1
Assuming so, my favorite shortcut is by using a dot-disconnected SMILES
<http://opensmiles.org/opensmiles#_other_uses_of_ring_numbers_and_dot_bond>.
Attaching the number 91 to your first sulfur as an example,
obabel -:"S%91CCC(=O)NC1CCN(CC1)Cc2ccccc2.S%91CCC(=O)NC1CCN(CC1)Cc2ccccc2"
-osmi
Cheers,
Ben
On Tue, Jul 3, 2018 at 6:20 PM John Michael Bruning <brun...@stanford.edu>
wrote:
> Apologies if this is off-topic, but this seems like a good community to
> ask:
>
>
> I have ~ 2000 thiol containing molecules (as SMILES) that I would like to
> generate the symmetric, disulfide containing SMILES for. For example, the
> starting molecules look like:
>
>
>
>
> *SCCC(=O)NC1CCN(CC1)Cc2ccccc2 SCCC(=O)NCc1c(cccc1)Sc(c2CO)cccc2
> SCCC(=O)N(CC1)Cc(c1c23)[nH]c2cccc3 *
>
> I was wondering if anyone had any clever ideas to do this in batch -- I am
> trying to write something in bash but it's looking pretty kludgy...
>
>
> Cheers,
>
> John
>
>
> ***********************************
>
> John Bruning, Post-Doctoral Scholar
>
> Stanford University, Glenn Lab
>
> CCSR Building, #3110
>
> ***********************************
>
>
>
> ------------------------------------------------------------------------------
> 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
