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 > > ------------------------------------------------------------------------------ > 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 ------------------------------------------------------------------------------ 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
