Re: [Rdkit-discuss] Fragmentation
Greg, You probably doing some fixes for nitro groups, etc. somewhere (probably in MolFromSmiles). I think this can be useful to identify exceptions. Can you please point me where this staff is? Regards, Evgueni 2009/8/10 Greg Landrum > On Mon, Aug 10, 2009 at 12:43 PM, Evgueni Kolossov > wrote: > > One more question about salts stripping - is there way to suppress > charges? > > Let's say you will remove [Na+] but the negative charge will be on anion. > > How we can remove it? The same if you say removing [Cl-] and there will > be > > for example (R)3-NH+ we need to remove H+ from it. > > Any thought about this? > > You could loop through the molecule and set the formal charges to > zero. You'll have to be figure out some way to solve the problems this > will cause with nitro groups (and related substructures) though. > > -greg > -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Fragmentation
Evgueni, take a look at the function RDKit/Code/GraphMol/MolOps.cpp:cleanUp() -greg On Tue, Aug 11, 2009 at 11:28 AM, Evgueni Kolossov wrote: > Greg, > > You probably doing some fixes for nitro groups, etc. somewhere (probably in > MolFromSmiles). I think this can be useful to identify exceptions. Can you > please point me where this staff is? > > Regards, > Evgueni >
