I think John has provided the solid argument for me to fix the reader so
that it accepts this construct by default. I certainly won't write "CL".
John, out of curiosity: how many of those applications would write "CL"
back out again to a molfile?
-greg
On Wed, Jan 20, 2016 at 10:43 AM, John M <[email protected]>
wrote:
> 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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