Hi Greg, Greg wrote: > yeah. Here's an even shorter illustration of correct behavior: > > In [11]: mol2 = Chem.MolFromSmiles(r'C\C=C\CB(O)O') > > In [12]: ps = rxn.RunReactants((mol1, mol2)) > > In [13]: Chem.MolToSmiles(ps[0][0], True) > Out[13]: 'C/C=C/Cc1ccccc1'
Yes, this was the first example that I went for as well - but then chemically I didn't like the idea of using allyl boronic acids in Suzuki reactions - because I couldn't recollect ever trying this, and if they did couple I would be worried about double-bond migrations; ironically making the question of stereochemistry rather mute! So my medchemist conscience won-out over clarity - and I concocted an example that I would happily test with 'wet' experiment! :-) >> Having got to the end of explaining that, I am thinking that the way I >> should handle this is to check for 'problem' reactants and pass to a more >> specific rSMARTS when required! > > I don't think that will help. Unfortunately the problem is in the way > stereochemical information is handled in the reaction code. My gut > feeling is that this is not going to be a quick one to fix, but I will > take a look. Thanks for looking into it! Kind regards James ______________________________________________________________________ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. ______________________________________________________________________ ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
