Hi Jan
On Thu, Dec 19, 2013 at 11:32 PM, Jan Holst Jensen
<j...@biochemfusion.com>wrote:
>
> The first lines of C:/temp/big.mol are:
>
> HERCEPTIN FAB (ANTIBODY) - LIGHT CHAIN
> RDKit 3D
>
> 78908023 0 0 0 0 0 0 0 0999 V2000
> 34.5390 88.7520 88.2980 N 0 0 0 0 0 0 0 0 0 0 0 0
> 34.7910 87.4610 89.0350 C 0 0 2 0 0 0 0 0 0 0 0 0
> 35.9070 86.7790 88.2540 C 0 0 0 0 0 0 0 0 0 0 0 0
>
>
> which is unreadable since there are 7890 atoms and 8023 bonds and V2000
> format supports max. 999 atoms/bonds. I would have expected RDKit to switch
> to V3000 format automatically (?). I don't see any parameter in
> MolToMolBlock() that can force V3000 output ?
>
That's a perfectly reasonable expectation, but, unfortunately, the RDKit
has a "small" hole in the functionality it provides: there is no V3000 mol
block writer. I just added the feature request in github and will try to
get it in for the next release.
Sorry for the inconvenience.
-greg
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