On Mon, Nov 25, 2013 at 5:10 AM, Greg Landrum <greg.land...@gmail.com>wrote:
>
>
>> Another problem is that I cannot read pdbs containing metals (e.g. 1vj5)
>>
>>
>>
>> Is there any workaround for that problem? I hope you can help me…
>>
>
> That bug is reproducible on linux as well. The normal solution to this
> would be to skip the sanitization step that causes the error, but
> unfortunately it seems that also causes the PDB parser to fail. I'll take a
> look at fixing it.
>
I've now fixed the problem with not being able to skip sanitization, but I
am still stuck on this particular protein.
1VJ5 has a Mg atom (#4333) with CONECT records to six other atoms. This
leads to a valence on Mg that is higher than the RDKit normally accepts.
How should this type of situation be handled by the PDB parser?
The irony of a PDB file wth *too many* CONECT records is killing me. :-)
-greg
------------------------------------------------------------------------------
Shape the Mobile Experience: Free Subscription
Software experts and developers: Be at the forefront of tech innovation.
Intel(R) Software Adrenaline delivers strategic insight and game-changing
conversations that shape the rapidly evolving mobile landscape. Sign up now.
http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
