On 2013-12-20 04:57, Greg Landrum wrote:
Hi Jan
On Thu, Dec 19, 2013 at 11:32 PM, Jan Holst Jensen
<j...@biochemfusion.com <mailto: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
Ah, OK. No worries; sounds like I am the only one who has run into it
this far. I'll just use a different output format for now.
Cheers
-- Jan
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