Thanks Greg, maybe it would be worth to add this info to the documentation.
On Wed, Jan 29, 2014 at 5:12 AM, Greg Landrum <[email protected]> wrote: > Looks like you guys have this one answered, but just for the sake of > completeness here's a bit of explanation. > > the cleanUp() function currently makes the following modifications: > 1) neutral 5 coordinate N with a double bond to O is converted to the > charge-separated form. This cleans up nitro groups and N oxides. Examples: > N(=O)=O -> -[N+](-[O-)=O and C1=CC=CN(=O)=C1 -> C1=CC=C[N+]([O-])=C1 > 2) neutral 5 coordinate N with a triple bond to an N to the charge-separated > form, example: -N=N#N -> -N=[N+]=[N-] > 3) perchlorate to the charge-separated form: Cl(=O)(=O)(=O)[O-] -> > [Cl+3]([O-])([O-])([O-])[O-] > > The theme is to convert certain unambiguous "hypervalent" representations > into something where a Lewis dot structure can be drawn. > > -greg > > > > On Tue, Jan 28, 2014 at 4:41 PM, Michał Nowotka <[email protected]> wrote: >> >> Yes Mikołaj, thank you very much for your very helpful advice of >> reading the code. Excellent pointers! >> >> Cheers, >> >> Michał >> >> On Tue, Jan 28, 2014 at 3:20 PM, Mikolaj Kowalik <[email protected]> wrote: >> > On Tue, 28 Jan 2014 12:22:34 +0000 >> > Michał Nowotka <[email protected]> wrote: >> > >> >> According to the documentation >> >> >> >> (http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#Cleanup): >> >> >> >> "cleans up certain common bad functionalities in the molecule" >> >> >> >> What are those 'certain common bad functionalities' that are being >> >> cleaned >> >> up? >> > >> > Until Greg comes up with a more apt answer, I think you can find some >> > pointers by looking through comments of in >> > $RDBASE/Code/GraphMol/MolOps.cpp. >> > >> > Functions cleanUp() and nitrogenCleanUp() are defined at the beginning >> > of the >> > source file. >> > >> > Best, >> > >> > -- >> > Mikołaj Kowalik >> > >> > >> > ------------------------------------------------------------------------------ >> > WatchGuard Dimension instantly turns raw network data into actionable >> > security intelligence. It gives you real-time visual feedback on key >> > security issues and trends. Skip the complicated setup - simply import >> > a virtual appliance and go from zero to informed in seconds. >> > >> > http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk >> > _______________________________________________ >> > Rdkit-discuss mailing list >> > [email protected] >> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> ------------------------------------------------------------------------------ >> WatchGuard Dimension instantly turns raw network data into actionable >> security intelligence. It gives you real-time visual feedback on key >> security issues and trends. Skip the complicated setup - simply import >> a virtual appliance and go from zero to informed in seconds. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > ------------------------------------------------------------------------------ > WatchGuard Dimension instantly turns raw network data into actionable > security intelligence. It gives you real-time visual feedback on key > security issues and trends. Skip the complicated setup - simply import > a virtual appliance and go from zero to informed in seconds. > http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ------------------------------------------------------------------------------ WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
