openmolecules.org

 
Home » DataWarrior » Bug Reports » Stereo issue? (Conversion from Smiles to MOL: missing stereo center)
Stereo issue? [message #65] Mon, 01 June 2015 01:49 Go to next message
bruno.b is currently offline  bruno.b
Messages: 13
Registered: October 2014
Location: Germaniy
Junior Member
Hi Thomas,

I wrote a small Java program that uses the open source Datawarrior library. This program converts the smiles of the drug benazepril into a MOL file. I used the smiles from Pubchem. The generated MOL has only one stereo center instead of two. I have attached the MOL output and the java code to this post.

I am not sure that the Java program I wrote is correct.

Thank you for providing the library,


Bruno

Report message to a moderator

Re: Stereo issue? [message #66 is a reply to message #65] Thu, 18 June 2015 20:50 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 736
Registered: June 2014
Senior Member
Hi Bruno,

I am sorry for answering so late. My intention is to answer within 24 hours after being aware of a question. If you don't get a quick answer, you may assume, that I simply didn't see your question (as in this case). Then please send me an e-mail...

I checked your source code, which seem perfectly correct. With the current SmilesParser it also works fine. The problem is
that Smiles were not used at Actelion and therefore I didn't notice that the stereo recognition was not working well.
Recently, we published a paper and a website with structure search on all Wikipedia structures. Since this requires parsing
the Smiles strings from the Wikipedia database, I enhanced the SmilesParser and fixed lots of stereochemistry related and other
issues. You can find the up-to-date version on GitHub in the OpenChemLib project. It will also arrive as part of the
source code of the upcoming new DataWarrior release in hopefully early June.

Thomas

Report message to a moderator

Re: Stereo issue? [message #116 is a reply to message #66] Thu, 05 November 2015 10:23 Go to previous messageGo to next message
bruno.b is currently offline  bruno.b
Messages: 13
Registered: October 2014
Location: Germaniy
Junior Member
It is indeed improved.


I tested further the SMILES to structure generator, Here is a SMILES that does not give good 2D coordinates: c1ccc(C23C(N(c4ccc(cc4)C)C(C2C2c4c(C3c3c2cccc3)cccc4)=O)=O)c c1


This is not an easy case.


Best regards,

Bruno

Report message to a moderator

Re: Stereo issue? [message #119 is a reply to message #116] Tue, 10 November 2015 15:54 Go to previous message
thomas is currently offline  thomas
Messages: 736
Registered: June 2014
Senior Member
This is indeed a little tricky. But it is a problem of the CoordinateInventor and not of the SmilesParser.
Generating coordinates is a never ending story. Paul Labute has once written a nice paper about it...

Best wishes,

Thomas

Report message to a moderator

Previous Topic: copy/paste from ChemBioDraw 14 to latest DW causes crash
Next Topic: Macros
Goto Forum:
  

[ Syndicate this forum (XML) ] [ RSS ] [ PDF ]

Current Time: Fri Oct 31 09:59:32 CET 2025

Total time taken to generate the page: 0.54986 seconds
openmolecules.org