Re: [Rdkit-discuss] Fragmentation

[Evgueni Kolossov]

Hi Greg,

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?

Regards,
Evgueni

2009/7/20 Greg Landrum 

> Hi Evgueni
>
> On Mon, Jul 20, 2009 at 7:05 PM, Evgueni Kolossov
> wrote
> >
> > Another related question: is there any way to strip salts or I need to
> > implement it myself?
>
> There is a deleteSubstructs() function in ChemTransforms that does the
> work, but it needs to be fed with a set of substructure definitions
> for the salts. There isn't currently such a thing distributed with the
> RDKit.
>
> -greg
>



-- 
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel.   +44(0)1628 627168
Mob. +44(0)7812070446

Re: [Rdkit-discuss] Fragmentation

[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