Molformula dot disconnected ?

Hi.


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Hi.


How do I set so that molformulas are stored (and returned from jc_formula)


so they get dot-disconnected between fragments ?





ex: select jc_formula('Cl.c1ccccc1') from dual;


C6H7Cl





I would like to have that returned C6H7.Cl





Regards,


/Mikael

Hi.


Is it possible to get the cd_formula with dot separated fragments ?





It is very urgent because our registration system is dependent on the dot separated molformula.





/Mikael

Hi Mikael,





We are just discussing what would be the best approach. We will get back soon.





Just a few questions in the meantime:





1. I suppose the correct formula would be to your example "C6H6.ClH" Is that right?





2. How should the fragments be ordered?





(Ordering by simply atom index would give "ClH.C6H6" but that would not be canonical enough and you just referred to the other order.)





Best regards,


Szabolcs

Hi.


1: Yes that is right.


2: Order by weight, heaviest first.





/Mikael

Hi Mikael,





We will add a new function to Chemical Terms for dot-connected formula, so you will be able to use it through jc_evaluate. We will be able to implement it in a relatively short time, so this will be included in one of the coming minor releases.





Do you know any other rule we have to be aware of when generating this formula? And how standard is this? (I mean what systems is this formula used in?)





Best regards,


Szabolcs

Hi.


The following applies to the formula.


Identify the "active" fragment and put that first, then take the rest and sort them by weight


putting the largest first (after the active).





Almost every chemical system uses this syntax (MDL, Tripos, Accelrys, ACD/Labs etc)





/Micke

The components will be sorted by carbon-content then by atom count. I hope that this will provide the expected result.

This feature has been implemented and will be included in the next JChem release. It will be available via the jc_evaluate_x operator and the jcf_evaluate_x function.





Example:

Code:

select jc_evaluate_x('CCO.CO', 'chemTerms:dotDisconnectedFormula()') from dual     ==> C2H6O.CH4O

Hi.


When is this going to be released ?





Also: Will this be applied to the default cd_molformula column ?





/Mikael

Quote:

When is this going to be released ?

This code will be present in the next release of Marvin, and in the next JChem that is built on this Marvin version.


We do not have a specific date set, but it may take month.





We can build you a test release if needed, but it may not be as stable as an official version - you decide if you take the risk of using it in a live system.

Quote:

Also: Will this be applied to the default cd_molformula column ?

No, we do not plan such a change.





Best regards,





Szilard

Do you think it will be released this month ?


If not, I'll have to write my own procedure to calculate the


molformula correctly.


/Mikael

Quote:

Do you think it will be released this month ?

We will try to come out with something next week.





Best regards,





Szilard