Dear Hans, you might also consider uploading a short wiki entry with the SMARTS patterns.
Cheers & Thanks, Paul > > Hi Andrew, > > We are doing this with a set of Smarts-based replacements. I can > send you the Smarts but you will have to wait a couple of days as I > cannot access them right now. > > Bye for now, > Hans > > On 11 Oct 2012, at 08:52, Greg Landrum <greg.land...@gmail.com> wrote: > > > Andrew, > > > > On Tue, Oct 9, 2012 at 2:21 PM, Andrew Dalke > <da...@dalkescientific.com> wrote: > >> Is there anything in RDKit to neutralize charges, like what > >> Corina does with the 'neu' option? Quoting from the > >> Corina documentation: > >> > >> > >> • The new option -d neu neutralizes formal > >> charges at acids, alcoholates, and basic nitrogens > >> by adding or removing protons. Often it is useful > >> to have all molecules of a database in the same > >> protonation state. > >> > >> This feels like a set of simple structure transformations. > > > > Assuming that this really is just "remove Hs from positively charged > > atoms and remove Hs from negatively charged atoms until they're > > neutral" it should be relatively straightforward to do with a loop > > over atoms. There will be some book-keeping involved along the way to > > check for whether or not stereochemistry flags need to be removed or > > "specified implicit" Hs marked on the atoms, but that shouldn't be too > > bad. > > > > It would be a good cookbook recipe, but I'm unlikely to have the time > > to do it in the next few days. > > > > -greg This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
