Re: [Rdkit-discuss] RDKit appears to be parsing SMILES stereochemistry differently

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: > > >>>

Re: [Rdkit-discuss] SMARTS for Joback and Reid method

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

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 121, Issue 15

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

Re: [Rdkit-discuss] SMARTS for =C=, #CH, #C-

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

Re: [Rdkit-discuss] SMARTS for =C=, #CH, #C-

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"

[Rdkit-discuss] SMARTS for =C=, #CH, #C-

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- :

Re: [Rdkit-discuss] Python code to merge tuples from a SMARTS match

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

Re: [Rdkit-discuss] Python code to merge tuples from a SMARTS match

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

[Rdkit-discuss] RPM distros

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