Hi Huw,
When you represent a carborane as SMILES you are saying that all of the
bonds are single bonds. This isn't an accurate description of the bonding
in the species.
The RDKit sees B atoms with >3 single bonds and C atoms with >4 single
bonds; both of those are non-physical valences, so the molecules fail
sanitization.
You could theoretically turn off the strict valence checking:
In [11]: m =
Chem.MolFromSmiles("[B]1234[B]567[B]118[B]229[B]33%10[B]454[B]656[B]711[B]822[C]933[B]%1045[C]6123",sanitize=False)
In [12]: m.UpdatePropertyCache(strict=False)
But then you're going to end up with a molecule that is not really useable
for much (the ring finding code doesn't currently work well for molecules
with lots of fused rings that have atoms with connectivity>4).
I'm afraid the RDKit is not currently a particularly good choice for
working with carboranes.
-greg
On Tue, Nov 5, 2013 at 8:35 PM, Huw Jones <[email protected]> wrote:
> Hi,
>
> Somewhat of a corner case I know but thought it might be worth just
> mentioning.
>
> This class of compounds:
>
> http://www.molport.com/buy-chemicals/molecular-formula/C2B10
>
> I’m assuming that the SMILES are valid so:
>
> Python 2.7.5 (default, Jul 30 2013, 12:06:31)
> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from rdkit import Chem
> >>> m =
> Chem.MolFromSmiles("[B]1234[B]567[B]118[B]229[B]33%10[B]454[B]656[B]711[B]822[C]933[B]%1045[C]6123")
> [19:33:19] Explicit valence for atom # 0 B, 5, is greater than permitted
>
> I have rdkit-2013.03.2 installed currently.
>
> Kind regards
>
>
> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models.
> Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and
> register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
