how to get the IUPAC name for the reactants and products

User 18396094a5

03-12-2008 09:40:04

Hi,





How to get the IUPAC names, molecular formular, MW. for the reactants and product in a reaction from a database? What license is required to perform such function? Besides, I would like to use jsp or PHP to write the script for this.





Thank you very much!


Best regards,


Xu

ChemAxon e274e1bada

04-12-2008 12:16:49

Hi,





I moved this topic to the appropriate forum.





You can use the dataFieldNames, dataFieldValues parameters of getHitsAs Molecules method in JChemSearch. You have to use a Chemical Terms column for retrieve IUPAC name. See: GetHitsAsMolecules


http://www.chemaxon.com/chemterms.html,


http://www.chemaxon.com/jchem/doc/admin/index.html


You don't need extra license for this features.





If you were using JSP you would access this API directly. We have an open source JSP example, which is part of the JChem package, feel free to change and use this. You can check the online version of that: http://www.chemaxon.com/jchem/examples/db_search/index.jsp





If you were using PHP and Oracle, I would recommend JChem Cartridge, which can be used from any environment accessing oracle SQL. User's guide: http://www.chemaxon.com/jchem/doc/guide/cartridge/index.html


This product requires a JChem Cartridge license.








Regards, Edvard

ChemAxon 9c0afc9aaf

04-12-2008 20:44:09

Hi,





You need "IUPAC Naming Plugin" license to be able to calculate the IUPAC name.





If IUPAC name calculation is applied to a reaction you will get the names of all the fragments as a list, but from that list it's not clear which fragment was a reactant or product.





Also mass and formula are not applicable (not meaningful) to reactions, only to the individual molecules.





So you might want to generate the values individually for these structures, this might require some programming.





You can crtate a molecule from a string (mol, SDF, SMILES, etc) with MolImporter.


In case of reaction the returned object is an RxnMolecule. It has methdos like getReactantCount, getProductCount, getReactant(index) so you can get everything piece by piece.





To generate a name from a Molecule, you can simply use Molecule.toFormat("name").





http://www.chemaxon.com/jchem/doc/api/chemaxon/formats/MolImporter.html


http://www.chemaxon.com/jchem/doc/api/chemaxon/struc/RxnMolecule.html


http://www.chemaxon.com/jchem/doc/api/chemaxon/struc/Molecule.html#toFormat(java.lang.String)





If not a problem for other reasons, I definitely recommend JSP instead of PHP. From JSP you can conveniently access any part of our Java API, and the direct Java integration is also the most efficient.





Best regards,





Szilard