counting alkynes and alkynyl anions - ChemAxon Forum Archive

User 870ab5b546

28-02-2011 02:40:53

Hi,

I'm looking for a SMARTS string that MolMatcher will match the same number of times to both alkynes and alkynyl anions when exact charge matching is turned on. (It's on by default, and I don't want to turn it off just for this one case.)

So far I've come up with [$(C#C),$(C#[CX1-])], but the problem with this string is that MolMatcher finds two matches in neutral alkynes and only one in charged alkynes.

I thought maybe C#[$(C),$([CX1-])] or C#[$([CX1-]),$(C)] would work, but MolMatcher does not find it in the alkynyl anion.

Any ideas?

-- Bob

ChemAxon 8407015329

01-03-2011 09:08:49

Hi Bob,

It seems that MolMatcher does not check for charge in the recursive part of the SMARTS query, and therefor it does not find the hit in this case. We have recorded the issue and will investigate it further.

Meanwhile we created a query which will behave as desired in this case (see attachment).

Best regards,

Vencel

User 870ab5b546

01-03-2011 14:22:07

Thanks. It works if I use the MRV format. If I convert it into cxsmarts format, it becomes

C#[$([#6]),$([#6-])] |$;_R1$|

Then, when I paste or import this expression into Marvin, then look at the source, it becomes,

C#[$([#1,*])] |$;_R1$|

and it no longer matches to both alkynes and alkynyl anions. ???

ChemAxon a3d59b832c

01-03-2011 14:32:49

Yes, we know about this. Unfortunately, cxsmarts currently loses the R-group definitions.

We will enhance it to be able to store and keep that information as well.

The workaround is to keep using the mrv for these queries.

I am sorry for the inconvenience.

User 870ab5b546

03-05-2011 13:57:59

Has this problem been solved in JChem 5.5? If not, when is it scheduled to be fixed?

ChemAxon 25dcd765a3

05-05-2011 08:37:53

It will be surely fixed in 5.6 (coming out at the end of the summer) but hopefully in 5.5.1 fix release. I cannot promise the fix for 5.5.1 surely, but we do our best.

(5.5.1 has commit deadline at 31 May, than comes the testing period so I expect you can have it in mid June).