Look up reaction transforms

User 8710c16ea0

20-05-2010 08:59:06

I have previously used Daylight but am now changing to use Chemaxon and since i am new to chemaxon i was hoping someone could explain how i would look up the reaction transforms of a smiles string. Previously i have used the daylight transformation function however chemaxon does not seem to have an equivalent?


 


Thanks a lot for any help

ChemAxon d76e6e95eb

20-05-2010 12:31:36

Please help me to understand clearly the functionality you are looking for. Would you like to search in a database of reaction SMILES with queries like reaction SMARTS, or you would like to enumerate a library using SMIRKS as generic reaction scheme? Or something else?

ChemAxon a3d59b832c

20-05-2010 13:07:08

Or perhaps you are looking for jc_react or jc_standardize to perform custom transformations on molecules?


See the Cartridge API for more details: http://www.chemaxon.com/jchem/doc/dev/cartridge/cartapi.html


 


Best regards,


Szabolcs

User 8710c16ea0

20-05-2010 13:12:51

I would like to enumerate a library using SMIRKS as generic reaction scheme i think.


I currently have a library of SMIRKS. The user will enter a SMILES string. I then want to compare each of the SMIRKS to the SMILES string that has been entered to see if any of these SMIRKS apply as a reaction transformation to the specific SMILES string.


Hope this is clearer!

ChemAxon d76e6e95eb

20-05-2010 13:19:18

Yes, thank you. The link sent by Szabolcs is relevant. We do support virtual reactions specified in SMIRKS operating on SMILES. We provide various interfaces for these transforms, jc_react is a JChem Cartridge function, but the same can be achived with the Reactor Wizard using files, an Instant JChem module operating on local databases, JChem for Excel (if you prefer a spreadsheet environment), Web Services (for scripting languages, Java and .NET API and command line tools.

User 8710c16ea0

20-05-2010 13:24:34

ok so i can call this jc_react function from the .NET environment? and is there an example somewhere of it being used so that i can follow it?


Thanks for all the help guys

ChemAxon d76e6e95eb

20-05-2010 13:41:44

Yes, jc_react can be called as an Oracle SQL function from .NET environment. Pease see some example SQL statements at the end of the jc_react section here.


Additionally, apart from the Java API  of Reactor we provide the jchem toolkit in native .NET format, so you can directly call the functions of the Reactor class from .NET. Examples can be found in the links. If you think, that a web discussion would be useful in the first steps, I can contact you via mail.

User 8710c16ea0

21-05-2010 08:09:35

ok yes that looks perfect for what i'm looking for...just 1 hopefully last question...what database does this sql statement require and how do i get access to it?


Thankyou for all your help

ChemAxon d76e6e95eb

21-05-2010 09:06:06

Cartidge is an Oracle technology, so it requires an Oracle database. Please see the requirements here.


If you prefer other databases like SQL Server, MySQL, PostgreSQL, DB/2, etc. you might select JChem Base, JChem.NET or JChem Web Service.

User 8710c16ea0

02-06-2010 13:54:29

just got one last question...i have a database sorted and connect to it but how exactly do i get the product back after using the jc_transform method...heres what i have so far...


 


string connectionstring = "blah blah blah";

                using (OracleConnection connection = new OracleConnection(connectionstring))
                {
                    
                    
                    OracleCommand oc = new OracleCommand("SELECT jc_transform('smirks string','smiles string' from dual;", connection);
                   
                    connection.Open();


                    OracleDataReader dr = oc.ExecuteReader();


                    dr.Read();

                    if (dr.GetString(0).ToString().Length > 0)
                    {
                        listBox1.Items.Add(GetString(0));
                    }

                    connection.Close();
                }

ChemAxon aa7c50abf8

03-06-2010 08:54:42

heres what i have so far...

This looks very promising. You can find the description of the jc_transform operator here: https://www.chemaxon.com/jchem/doc/dev/cartridge/cartapi.html#jc_transform