Create IUPAC-Name by Oracle package?

Hi,





is it possible to include JChem or required java-files in Oracle to create a IUPAC-Name by a given structure at oracle side? And what are the first steps to do it?








thanks in advanced!

Yes, it is possible in JChem Base, JChem Cartridge and in Instant JChem.





Required steps:





1. JChem Base


These steps can be done through JChem Manager, Instant JChem or API:


- Set up a JChem table with a calculated column "name()"


- Import structures into the JChem table, and the calculated columns will contain the corresponding IUPAC names.





See the JChem Administration Guide for using JChem Manager: http://www.chemaxon.com/jchem/doc/admin/


or the Developers Guide for the use of the API:


http://www.chemaxon.com/jchem/doc/guide/





2. Instant JChem GUI:


First connect to a remote Oracle database, then do the same as above.





Connect to remote(Oracle) databases:


http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/connections/adding_schema.html


Animation for creating Chemical Terms columns: http://www.chemaxon.com/anim/ijc/chemterms/chemterms.html





3. Oracle Cartridge:


3.1. You can do the same as above, and use jc_insert() cartridge function to insert into the JChem table.


http://www.chemaxon.com/jchem/doc/guide/cartridge/index.html#jctable





3.2. Non-JChem tables can be set up with similar pre-calculated columns, but in this case in JChem index ("autoCalcCt=..." parameter at index creation).


http://www.chemaxon.com/jchem/doc/guide/cartridge/index.html#index





3.3. Use the jc_molconvert operator or function with format name "name"


http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_molconvert





From your question, it seems that mostly one of the Cartridge options are relevant. Let us know if you need further information.





Best regards,


Szabolcs

Hi,





thanx for fast answering and step by step examples! But i assumed that is quite easier to implement without using GUI and Cartridges. Is it possible to only add an external java source an wrap these java functions in plsql-packages to get an iupac-name by given structure in sdf-format : for example? Because we have higher restricions on cusomers databases, so we prefer a simple solution for generating iupac-names. is there any way?





thanks in advanced!

Hi

Quote:

wrap these java functions in plsql-packages to get an iupac-name by given structure in sdf-format

Correct! You just need to load MarvinBeans.jar (or jchem.jar) into Oracle and write a PL/SQL wrapper around a thin Java wrapper around the MolConverter class (http://www.chemaxon.com/marvin/help/developer/beans/api/index.html). The Java wrapper would look something like this:

Code:

protected String molconvert(String structure, String[] options)             throws Exception {         ByteArrayOutputStream baos = new ByteArrayOutputStream();         ByteArrayInputStream bais =                 new ByteArrayInputStream(structure.getBytes());         String[] args = options;         MolConverter mc =                 MolConverter.createMolConverter(bais, baos, args, null, null);         try {             if (mc != null) {                 mc.convert();             }         } catch (java.lang.InternalError ie) {             if (ie.getMessage().indexOf("X11") != -1) {                 throw new RuntimeException("To enable image generation, set the system property 'java.awt.headless' to 'true'");             }         }         return new String(baos.toByteArray());     }

The PL/SQL wrapper is a standard/trivial wrapper around the above Java wrapper: http://download.oracle.com/docs/cd/B19306_01/java.102/b14187/chthree.htm#CACJJHGI





Note that current Marvin versions require Java 1.4+, so you need at least Oracle 10g for this to work.

hi,





code-sample looks great, thanx!





I created this compilable java-source

Code:

create or replace and compile java source named MolConvert as import java.io.ByteArrayOutputStream; import java.io.ByteArrayInputStream; import chemaxon.formats.MolConverter; public class MolConvertClass {   public static String molconvert(String structure, String[] options)             throws Exception {         ByteArrayOutputStream baos = new ByteArrayOutputStream();         ByteArrayInputStream bais = new ByteArrayInputStream(structure.getBytes());         String[] args = options;         MolConverter mc =                 MolConverter.createMolConverter(bais, baos, args, null, null);         try {             if (mc != null) {                 mc.convert();             }         } catch (java.lang.InternalError ie) {             if (ie.getMessage().indexOf("X11") != -1) {                 throw new RuntimeException("To enable image generation, set the system property 'java.awt.headless' to 'true'");             }         }         return new String(baos.toByteArray());     } }

a corresponding wrapper...

Code:

function convert(pSDF     varchar2,                    pOptions varchar2) return varchar2 as     language java name 'MolConvertClass.molconvert(java.lang.String, java.lang.String[])return java.lang.String';

and a calling function...

Code:

function GetIUPAC return varchar2 is     vSDF   varchar2(32000);     vIUPAC varchar2(500);    begin       select sdf       into vSDF       from molecule;       vIUPAC := convert(vSDF,???);       return(vIUPAC);     end;

There are several bugs already in there.. I gues the interfaces does not mach correctly and i'am unsure about the second parameter (options (args))!!





I hope you can help to make this code runable..





thanks in advanced!

If you're just after IUPAC names, then you can simply remove the second argument from both wrappers and create the MolConverter instance in the Java wrapper like this:

Code:

MolConverter mc =                 MolConverter.createMolConverter(bais, baos, new String[] {"name"}, null, null);

good morning,





thanks for the last code file.. looks now very good. but now i get an exception that i need a licens file to test it. i send a request to your technical support forum. hope, they can help





the aim is near! well done pkovacs!!





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Dear Andre,





You can ask for a free 30 days evaluaiton license for any of ChemAxon products.





Please send an email about your request to sales _at_ chemaxon.com. and we will get back to you.





BR,


Norci