On 11 April 2017 at 04:37, Robert Hanson <hans...@stolaf.edu> wrote:
> 2) What did you get for the other test case, that one checks you have the
>> ordering ranking for atomic masses.
>>
>>> CC[C@@](CO)([H])[14CH2]C
>>
>>
> R.
>
There you go, that should also be S, ordering is: *CO, *[14CH2]C, *CC, *[H]
https://nextmovesoftware.com/blog/2015/01/21/r-or-s-lets-vote/.
Q: Is there software that does a nice job with producing digraphs from
> SMILES?
I think I added a utility in Centres, however I've barely looked at the
code in 5 years - but am planning to brush it off and clean up now though.
BTW if you look closely, Centres is abstract and wraps around existing
toolkits - I only wrapped it around CDK though in theory you could do the
same with JMol.
Q: These all implement Rule 1b and the rest of the rules? Have they been
> validated in some systematic, common way, so we know they don't have any
> bugs?
>
I don't think so. IIRC 1b was introduced to fix this case:
O[C@H](C(CCC1CC1)(CCC1CC1)CCC1CC1)C12CCC(CC1)CC2.
If you use that molecule you can tell whether it does/doesn't implement
that rule. Without rule 1b it should not be possible to label it. In
centres you can change the rules of the ranking: CDKPerceptor.java
<https://github.com/johnmay/centres/blob/develop/cdk/src/main/java/uk/ac/ebi/centres/cdk/CDKPerceptor.java#L77-L108>
.
Q: Doesn't this argue against the "Why bother doing this -- it's been done
> seven times already" argument? Which one is IUPAC-2013-standard?
>
It wasn't me who said that, I'd only say don't do it because the
implementation will drive you mad :-). The "blessed" version would allow
everyone to confirm against it, as your original question asks - you want
to test yours it would be much simpler just to point to a complete one
leave it there. However from my previous testing I don't know if a complete
one exists anywhere (maybe the LHASA one:
http://pubs.acs.org/doi/abs/10.1021/ci00019a004 but of course this maybe
doesn't exist anymore, will ask them).
I guess this would matter if you had 1,000,000 compounds to check; the
> 100-line algorithm (Rules 1 and 2) I wrote seems quite straightforward and
> suitable for my purposes. Hard to believe any molecule of interest would
> push the limits for such.
CHEBI:51439, whether that's of interest or not is of course subjective
John
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