calculate Tinamoto coefficient for the base created in IJC

Hello!

Help me please to calculate the Tinamoto coefficient for the base created in the IJC.

in the support documentation I've read:: Dissimilarity function is available only in JChem.

I so understand that I have to upload my base into the sdf-file, and running a some script in the command line?

Thanks!

Igor.

Dear Igor,

Would you like to calculate similarities or dissimilarities?

 

Similarities can be easily calculated directly from InstantJChem, see grid view Query/Similarity search.

Optionally, for the comparision of two lists you may check the Menu Chemistry/Overlap analysis.

http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/tutorials/import/htmlFiles/import_sd_file.html

 

Dissimilarities can be calculated using the jcsearch utility.

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

Example:

jcsearch -t:i:0.7 -q "OC(=O)CCC(O)=O" -f sdf inputDB.sdf -o output.sdf

In this example the DB is exported into a SD file (inputDB.sdf).

The query structure is in SMILES.

In the output file you will find a column with the calculated dissimilarity values.

There are a couple of other options for the query structures (SMILES, file, etc).

The input file can be specified as a file (sdf, mrv, etc) or DB, please see the corresponding options in the jcsearch documentation.

jcsearch [options] DB:[table name]

 

Please let me know if you have any further questions.

Miklos

Hello 
Miklos!

Thanks for your answer!

 I don't understand clear how to calculate general Tanimoto  coef. for all my base.

in the support documentations is writed: "one or two molecules (if only one is specified then the other one is taken from the context)"  -  what is meant from context?

in my cases specified only one molecule, how I have to make this calculations...?

Thanks!

 

Dear Igor,

Here is an other solution with using the "Chemical Terms Field".

http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/editing_database/fields_chem_terms.html

You noted a special case for the usage of dissimilarity function:
http://www.chemaxon.com/marvin/help/chemicalterms/EvaluatorFunctions.html#dissimilarity_functions />"one or two molecules (if only one is
specified then the other one is taken from the context)"
In case of
InstantJChem, the contex means a set (or list) of molecules stored in a structure column.

Here is an example for the usage of Dissimilarity Chemical term in InstantJChem, which would calculate the dissimilariy of a molecule (chlorobenze) to all member of a structure list stored in an InstantJchem table.

dissimilarity("CF:Tanimoto", "ClC1=CC=CC=C1")

Please find also a screenshot attached.

Best Regards,

Miklos