a question

Hi

I would like to calculate solubility in Chemaxon according to GSE equation: logS=0.5-0.01(Tm-25)-logP, where Tm is a melting point. I have made a column in my database where I have written Tm values for my compounds (field type -> text). How the equation should be written then to calculate solubility using logP calculated by chemaxon and written by me Tm values ???

logS=0.5-0.01*("Tm"-25)-logP() ???

Thanks

Currently the options are a bit limited. The only real option is to add a column to the database that does the calculation using a trigger, having already added melting point and logP columns (logP can be calcuated using a chemical terms columnn but I think you will need to provide the melting point values, as you have described). A tutorial on adding columns using triggers can be found here:
http://www.chemaxon.com/instantjchem/ijc_latest/docs/admin/tips/triggers/index.html />If you need help with this then please get in touch.

We do plan to allow calculations like this to be done directly in IJC in the furture, but for now the trigger column is the best approach.

Tim

Hi Tim,

Does JChem calculate solubility automatically? I do not see a solubility coefficient (e.g. logS) mentioned in the calculated properties.

Thanks

Hi Renju,

as far as I know JChem does not include automatical solubility calculations. There are various Calculator Plugins ( http://www.chemaxon.com/products/calculator-plugins/ ) which can be included in Instant JChem. But in terms of solubility they include only logP and logD coefficient calculations. Final solubility estimation might be done by using equation mentioned above and by utilizing Calculated Fields: http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/editing_database/fields_calc.html .

Hope it helps.

Filip

We (ChemAxon) started the development of a solubility predictor, but it will not be completed in the near future.

Hi,

Since I find the Calculated Fields somewaht limiting (not sortable or queryable) I have reached the point where I feel the need to use database triggers. My experience with this however is zill. I have read the documentation on this and have a general feeling for how it works. I wondered if you could provide me with an example Derby trigger that populates a structure table B whenever a structures is added to structure table A.

Thanks,

Evert

Hi Evert,

You may have a look at http://www.chemaxon.com/instantjchem/ijc_latest/docs/admin/tips/triggers/Derby.html  />and also to Apache Derby documentation at http://db.apache.org/derby/docs/10.1/ref/rrefsqlj43125.html.

Filip 

Hi Filip,

I already had read the indicated IJC documentation. However, when it comes to triggering replication of structures from one table to another, there are presumably multiple database fields that have to be inserted (cd_structure, cd_hash) etc.). Therefore it would be great if you could provide me with an example of such a trigger, if this is at all possible.

Thanks,

Evert

Hi Evert,

yes this is possible, if both tables have the same table structure.For Derby DB, it may look like this:

create trigger copy after update on NCI_DRUGS
REFERENCING NEW AS newrow FOR EACH ROW MODE DB2SQL
INSERT INTO NCI_DRUGS_COPY select * from NCI_DRUGS where CD_ID = newrow.CD_ID; 

However I found one major limitation, when I simply recreate the second table directly in DB. In IJC the table is promoted as Standard table and not as JChem structure table. This may by workarounded if the second table is created directly in IJC.

Hope it helps.

Filip

Hi,

Thanks for this. In your example would I need to create the trigger at the level of the NCI_DRUGS table or directly under the top-level database connection (I am working in the Services window) ?

Evert

You should create the trigger at the level of NCI_DRUGS table. At least this worked for me :) Otherwise you may need to reference the table like APP.NCI_DRUGS.

fz.

Hi,

Sorry to bother you again but I can't get it to work. I have created two empty Structure entities, one called MOLECULES and one called SUMMARY, and want to trigger copying of structures from MOLECULES to SUMMARY upoon insertion of a new row in MOLECULES. In the Services window I executed the following command on the MOLECULES table:

create trigger copy_structure after update on MOLECULES
REFERENCING NEW AS newrow FOR EACH ROW MODE DB2SQL
INSERT INTO SUMMARY select * from MOLECULES where CD_ID = newrow.CD_ID;

After discconecting and reconnecting in the Project window, I add a molecule to the MOLECULES entity, but nothing is added to the SUMMARY.

What am I missing?

Hi, I would say that you have to change line:

create trigger copy_structure after update on MOLECULES

to

create trigger copy_structure AFTER INSERT on MOLECULES

The former one copies row after its update (change) wherease AFTER INSERT triggers an action after new row is insterted to the table.

Filip

Thanks Filip,

Now it works, but only once. The second molecule I add to the MOLECULES entity is not added to the SUMMARY entity...

Btw, is there a way to list defined triggers in the Services window? Probably requires som SQL I presume...

Evert

Evert,

I have no problem with the trigger, it copies every added molecule to the "other" table.

As for the list of defined trigers:
1. Go to SYS schema.
2. View content of SYSTRIGGERS

Your welcome! 

Filip