Hi Kuba,
that's correct, the RDKit does not currently support COLLECTION blocks.
In this particular case, the COLLECTION block in question is connected to
extended stereochemistry. I hope that we'll have (at least some) support
for the in the RDKit in the next release.
Best,
-greg
On Mon, Jul 16, 2018 at 5:12 PM Kaminski Jakub (PSI) <jakub.kamin...@psi.ch>
wrote:
> Dear Community,
>
> I have SDF file with following block (pasting relevant fragment below):
>
> 0 0 0 0 0 0 0 V3000
> M V30 BEGIN CTAB
> M V30 COUNTS 8 6 0 0 0
> M V30 BEGIN ATOM
> M V30 1 Cl 0.0 0.0 0.0 0
> M V30 2 Cl 0.0 1.5025 0.0 0
> M V30 3 N -4.758 -0.5008 0.0 0
> M V30 4 C -3.5998 0.1565 0.0 0
> M V30 5 C -5.9162 0.1565 0.0 0
> M V30 6 C -3.5998 1.5025 0.0 0 CFG=2
> M V30 7 C -5.9162 1.5025 0.0 0
> M V30 8 N -2.6607 2.4416 0.0 0
> M V30 END ATOM
> M V30 BEGIN BOND
> M V30 1 1 3 4
> M V30 2 1 3 5
> M V30 3 1 4 6
> M V30 4 1 5 7
> M V30 5 1 6 8 CFG=3
> M V30 6 1 6 7
> M V30 END BOND
> M V30 BEGIN COLLECTION
> M V30 MDLV30/STERAC1 ATOMS=(1 6)
> M V30 END COLLECTION
> M V30 END CTAB
> M END
>
>
> I can read this information with RDKit using Chem.SDMolSupplier.
>
> When I write the same information to new file with SDWriter I have
> following message:
>
> "skipping block at line 97: BEGIN COLLECTION"
>
>
> and the block "M V30 BEGIN COLLECTION … M V30 END COLLECTION" is
> missing in the new file.
>
> Why is that? Is COLLECTION block not recognised/implemented in RDKit?
>
> I am using RDKit Version: 2017.09.3 on MacOS Sierra
>
> Thanks,
> Kuba
>
>
>
>
>
>
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