On Sun, Dec 29, 2013 at 8:39 PM, Igor Filippov <igor.v.filip...@gmail.com>wrote:
> Greg,
>
> I just done it a quick try and it seems to be working fine for me!
>
Great.
> Is it allowed to mix V2000 and V3000 formats within the same SDF file?
>
According to the CTFile documentation:
"An SDfile (structure-data file) contains the structural information and
associated data items for one or more compounds, which can be V3000, V2000,
or a combination of both."
So it looks like it's no problem to mix formats in the same SDF. I have
certainly seen examples of this happening.
I have not yet (thanks for pointing it out) modified the SDWriter to add an
optional "forceV3000" argument, so with the RDKit you will end up with a
mixed SDF anytime you have a combination of molecules with more than 999
atoms/bonds and molecules with less than 999 atoms/bonds.
-greg
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