Correct message thread this time:
The joys of the molfile - was curious whether it was accepted/correctly
> interpreted:
>
> ISIS Draw 2.5 Yes (arguably the arbitrator of the format)
> ChemDraw 15 Yes
> ChemDoodle No (accepted but only as a text label 'CL' no conversion)
> MarvinSketch Yes
> CDK Yes
> OEChem Yes
> Open Babel Yes
> Indigo Yes
J
On 20 January 2016 at 05:26, Greg Landrum <[email protected]> wrote:
> Paul,
>
> On Tue, Jan 19, 2016 at 7:59 PM, Paul Emsley <[email protected]>
> wrote:
>
>>
>> Thanks for that.
>>
>> Why do I ask? Because the sdf files [1] distributed by the wwPDB, such
>> as this one:
>>
>> http://www.rcsb.org/pdb/files/ligand/CQ8_ideal.sdf
>>
>> from this page:
>>
>> http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CQ8
>>
>> are upper-cased. I didn't know whether that was right or not (and, as
>> you imply, RDKit will not parse it). I'll get in touch with them and see
>> if they can get it changed.
>>
>
> It's an important data source, so it would be great if they were supplying
> data that's correctly formatted (assuming, of course, that my reading of
> that "spec" is correct). In the meantime, it would be pretty easy to modify
> the RDKit to handle these cases correctly when the "strictParsing" option
> is set to false. I'll add a github issue for this and get it in there.
>
>
>> [1] I thought that they were molfiles when I wrote the mail - and I
>> suppose the same thinking applies.
>>
>
> Yeah, the format of the CTAB piece is identical for mol files and SDFs.
>
> -greg
>
>
>
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