structure search - Nitro groups

Hi,

Chemists using chemicalinventory has reported a problem with nitro-groups and the search results returned:

 

Nitrogroups (-NO2) can be written/drawn in to different ways that both are accepted/correct:

 

However, they are apparently registered as different groups since a search on our database with the two
“different” structures as substructures gives different results – but should be exacely the same:

Searching with the “neutral” version retrieves 30 compounds:

 

But when you run the search with the version below you get 341 hits:

 

Version information:

Marvin sketch: 5.4.0.1

JChem: 5.4.0.1015

Database MSSQL 2008 R2, IIS 7, .net application.

This is causing serious problems for the users when searching.

 

Best regards

Dann

Hi,

In order to recognize the two versions as same you have to define a custom standardization which contains a rule that brings them to the same format.

This standardization xml can be specified upon table creation.

http://www.chemaxon.com/jchem/doc/admin/#create

or

from API:

http://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/jchem/db/UpdateHandler.html#createStructureTable(chemaxon.util.ConnectionHandler,%20chemaxon.jchem.db.StructureTableOptions)

http://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/jchem/db/StructureTableOptions.html#standardizerConfig

about standardizer config:

http://www.chemaxon.com/jchem/doc/user/StandardizerConfiguration.html

example of nitro transformation:

http://www.chemaxon.com/jchem/doc/user/Standardizer_files/examples/Examples.html#12

for editing the standaridzation xml:

http://www.chemaxon.com/jchem/doc/user/Standardizer.html#applicationgui

 

Bye,

Robert

 

Hi Robert,

Thanks for taking the time with this issue.

just need to get this the correct way.(I am NOT a chemist so nitro group transformation/standardization leaves me in the dark :-))

Just wondering what the best way to approach this..

Will I have to change the strucutures in the db, or will a standardization xml perform the transformation when searching..? (leaving the db as is, just altering the search).

UPDATE:

I am creating a method that will read a structure from the DB apply standardization and return the structure..

This leaves me with a method like this:

private void ApplyStandardizer(Structure st) {

            Standardizer std = new Standardizer(new java.io.File(@"standardization.xml"));

            if (std != null) {
                std.setFinalClean();
                Molecule m = st.StructureMolecule;
                if (m != null) {

                    std.standardize(m);

                    // get applied task indexes
                    int[] inds = std.getAppliedTaskIndexes();

                    // get applied task IDs
                    String[] ids = std.getAppliedTaskIDs();

                    // store applied task indexes and IDs in molecule properties
                    String indsprop = "";
                    for (int i = 0; i < inds.Length; ++i) {
                        indsprop += inds + " ";
                    }
                    String idsprop = "";
                    for (int i = 0; i < ids.Length; ++i) {
                        idsprop += ids + " ";
                    }
                    m.setProperty("TASK_INDEXES", indsprop);
                    m.setProperty("TASK_IDS", idsprop);

                    MolHandler mol = new MolHandler(m);
                    
                    
                }
            }
        }

2 questions here:

A.: What does the following do??? and is it neccecary?

-------------------------------------------------

// get applied task indexes

                    int[] inds = std.getAppliedTaskIndexes();



                    // get applied task IDs

                    String[] ids = std.getAppliedTaskIDs();



                    // store applied task indexes and IDs in molecule properties

                    String indsprop = "";

                    for (int i = 0; i < inds.Length; ++i) {

                        indsprop += inds + " ";

                    }

                    String idsprop = "";

                    for (int i = 0; i < ids.Length; ++i) {

                        idsprop += ids + " ";

                    }

                    m.setProperty("TASK_INDEXES", indsprop);

                    m.setProperty("TASK_IDS", idsprop);

-------------------------------------------------

B: I Use a home grown Structure object that contains properties from the structure table. one of them being the cd_smiles that I use to create the molecule object.. but how do I go the other way..?

Molecule -> cd_smiles (string)??

Don't seem to find a method in the molhandler class for this.

Dann

Hi Dann,

Let me advise you two other ways to solve the problem:

If you have access  to JChemManager GUI than it gives a simple way to unify the different forms of nitro groups following these steps http://www.chemaxon.com/jchem/doc/admin/#table_settings: />1. Start JChemManager
2. Select Table Options from File menu
3. On Table Options dialog: Select the proper table from Database table list, select Custom standardization, click on Open Standardizer Editor
4. On Configure standardization dialog: Add Transform nitro, Aromatize, Remove explicit Hydrogens (the last two are the default values of standardization; please be careful because Aromatize has 3 options: default is general)
5.  Let the table be recalculated  after OK on Table Options dialog.
By default the 'Transform nitro' action changes nonionic nitro group into the ionic form but if you prefer the other direction it can be inverted within the Configure standardization dialog.


An other kind of solution is the application of recalculateTable method as described here:
http://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/jchem/db/UpdateHandler.html#recalculateTable%28chemaxon.util.ConnectionHandler,%20java.lang.String,%20boolean,%20java.lang.String,%20java.util.Map,%20java.lang.Boolean,%20chemaxon.jchem.file.ProgressWriter%29 />
Hope this helped

Best regards,
Krisztina

Hi Krisztina

 

Thanks for your reply, I will certainly investigate those options.

But as I see your solutions this is a task to be performed on the db as-is at the moment. Besides that I would like to ensure that future structure registrations and updates is also applied standardisation. That is the reason the the code I am writing.

Is the an example of fetching a structure from the db->performing standardisation->returning the strucuture to the db..?? (haven't been able to find one, only from a file)

BR

Dann

Hi Dann,

The execution of the custom standardization and recalculation on a table has three consequences:
- the structures being in the table at the moment will be standardized accordingly
- the structures being imported into the table in the future will be imported in the standardized form accordingly
- the query structures applied in future queries will be standardized accordingly

Find documentation here: http://www.chemaxon.com/jchem/doc/user/query_standard.html#standardizationDB />
Best regards
Krisztina

...aarrghh .. consequences..

I will have to consult the chemists having the actual issue. I can get jchemmanger to recalculate and add the new custom standardization file to the db..

Anyway thanks a lot

Dann