Dear Greg,
On 2013-05-01 09:58, Greg Landrum wrote:
> Dear Jan,
>
> On Mon, Apr 29, 2013 at 8:03 AM, Jan Holst Jensen <j...@biochemfusion.com>
> wrote:
>> Hi RDKitters,
>>
>> I wonder why the InChI strings generated by RDKit differ from the ones
>> generated by the standard IUPAC inchi-1 executable.
> At least some were due to an RDKit bug that has been fixed for a while
> (it's in the 2013.03 release). The fix isn't reflected in the knime
> nodes because we haven't done an update of the knime binaries in a
> while; that's coming in the next day or so.
Ah - sounds wonderful. Thanks.
Out of sheer laziness my Python-enabled RDKit builds have been without
InChI support so I couldn't compare with the KNIME nodes - just assumed
that they behaved identically. Well... as they say "Assumption is the
mother of all sc***-ups" :-).
> OK, now those InChI samples look like they are heavy on fringe cases and
> perhaps thus likely to really stress toolkits.
> These are the best kind. :-)
Indeed :-).
>> So I took something more peaceful and ran a peptide from PubChem through
>> (pubchem_71296070.mol - attached).
>>
>>
> In [4]: Chem.MolToInchi(Chem.MolFromMolFile('pubchem_71296070.mol'))
> Out[4]:
> 'InChI=1S/C33H55N9O10/c1-18(43)26(37)31(49)40-23(16-20-10-4-3-5-11-20)30(48)39-21(12-6-8-14-34)28(46)38-22(13-7-9-15-35)29(47)42-27(19(2)44)32(50)41-24(33(51)52)17-25(36)45/h3-5,10-11,18-19,21-24,26-27,43-44H,6-9,12-17,34-35,37H2,1-2H3,(H2,36,45)(H,38,46)(H,39,48)(H,40,49)(H,41,50)(H,42,47)(H,51,52)/t18-,19-,21+,22+,23+,24+,26+,27+/m1/s1'
>
> also looks fine.
Yep. Everything should be in order then.
Cheers
-- Jan
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