Huh, that looks correct! That is SO much cleaner than what I was trying to
write...Thanks, I'll give it a shot!
Cheers,
John
***********************************
John Bruning, Post-Doctoral Scholar
Stanford University, Glenn Lab
CCSR Building, #3110
***********************************
________________________________
From: Benjamin Bucior <bbuc...@u.northwestern.edu>
Sent: Tuesday, July 3, 2018 3:32:33 PM
To: John Michael Bruning
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] Creating a Symmetric Disulfide Containing SMILES
string
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<mailto: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
***********************************
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