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 ------------------------------------------------------------------------------ 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
