On Thu, Nov 9, 2017 at 6:32 AM, Brian Cole wrote:
> Hi Cheminformaticians,
>
> This is an extreme subtlety in the interpretation of SMILES atom
> stereochemistry and I think a bug in RDKit. Specifically, I think the
> following SMILES should be the same molecule:
>
> >>>
Chenyang,
I haven't looked at your smarts strings yet, but I do have this list of
SMARTS strings for the joback method I compiled myself (for use here:
https://www.wolframalpha.com/input/?i=2,3-methano-5,6-dichloroindene=3
).
Perhaps this can be of use. If you spot any mistakes, please let me
The Daylight website is a very good resource for SMILES, SMARTS, and
SMIRKS.
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
JW
___
JW Feng, Ph.D.
Denali Therapeutics Inc.
151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080 | (650)
270-0628
On Wed, Nov
Dear Andy,
Thank you for a quick and thorough email. I find it very instructional,
although I need to read it a couple times more to digest it.
Cheers,
Chenyang
On Wed, Nov 8, 2017 at 2:27 PM, Andrew Dalke
wrote:
> On Nov 8, 2017, at 21:00, Chenyang Shi
On Nov 8, 2017, at 21:00, Chenyang Shi wrote:
> =C= : [CH0;A;X2;!R](=[$(*)])=[$(*)]
The recursive SMARTS notation, which is the term inside of the [$(...)], finds
a match for the entire pattern and returns the first atom in that pattern.
> For example, if I search "C=C=O"
Dear RDKitters,
I have a question regarding SMARTS codes for three simple functional
groups, these are =C=, #CH and #C-. I am new to SMARTS/SMILES. I indeed
tried to guess their codes. Here are my guesses:
=C= : [CH0;A;X2;!R](=[$(*)])=[$(*)]
#CH : [CH1;A;X2;!R]#[$(*)]
#C- :
Brian, Greg, and David,
Thank you for your suggestions. I will try to respond to your questions
and comments:
I am trying to reproduce results from a literature paper that used
non-PYTHON and non-RDkit
code to identify certain patterns in molecules as part of a group contribution
Peter,
Thank you for your suggestions and accompanying code.
I have modified your code slightly and have created 3 tuples
for testing. Your code works for tuples, match1 and match2, but
does not work for match3. The code should return a 2 for match3,
because there are 2 sets of 3
There is mention of RPM distributions of RDKit
(https://copr.fedorainfracloud.org/coprs/giallu/rdkit/).
But on trying these:
1. the distro is based on the 2017_03_1 release
2. it fails due to missing libinchi.so.1 dependency.
This is presumably no longer being maintained?
Anything that can be
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