J Chem For Excel: US UGM 2008


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JChem for Excel allows scientists to use JChem's features in the popular Office environment. It is implemented in .NET, so it also demonstrates the possibilities of integrating the Java based JChem, with .NET using open source technologies. The initial features are: Searching JChem databases, searching JChem Cartridge, R-group decomposition, calculation of molecular properties, SDF, XML import export.

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J Chem For Excel: US UGM 2008

  1. 1. JChem for Excel Tamas Peltz, Ferenc Csizmadia Solutions for Cheminformatics
  2. 2. Introduction • Microsoft Excel integrated solution for Marvin and JChem functionality • Use Excel’s powerful features: Functions, Sorting, Filtering, Charts… • Implemented in C# .NET, and Visual Studio • Proof that ChemAxon APIs can be used in a Java-less .NET environment • Easy to install and deploy • UNDER DEVELOPMENT
  3. 3. Features • Import from Databases using custom filters • Import from, and export to files. • Searching and R-Group Decomposition • Adding, editing structures • Chemical functions among Excel functions
  4. 4. Import from Database – Manage Connections • JChem Cartridge Databases – Structure search runs on the server • JChem Base Databases – Structure search runs locally – Databases supported • Oracle • Coming: MSSQL, Access, MySQL, ... • Connection settings are saved
  5. 5. Import from Database - Query • Common interface for client-side or server-side structure searching • Easy to use control for specifying search options • Chemical Terms filter expressions for queries • Optional substructure hit coloring and alignment • Additional SQL filters
  6. 6. Structure file import and export • Most file formats supported by Marvin could be exported and imported – MRV,SDF,RDF,SMILES , IUPAC name,… • Wizards guide you through the import and export processes
  7. 7. Import - Results SDF import results Database import results with hit coloring
  8. 8. R-group Decomposition • Run Decomposition on – JChem Database – Files – Excel Worksheet
  9. 9. Chemical Excel Functions • Chemical Terms functions and Marvin calculations are implemented as Excel functions: • Composition, Mass, MolFormula • AtomCount, BondCount, ChiralCenterCount,RingCount… • logP,logD, pKa, PSA, H-bond donor/acceptors • Bioavailability, GhoseFilter,LeadLikeness,Lipinski rule of 5… • SubstructureMatch, Dissimilarity • IUPAC Name • StructureImage(draws an image of a structure)
  10. 10. Chemical Excel Functions • Values are calculated from: • SMILES, SMARTS, IUPAC Name strings • Structure cells – structures resulting from imports, edit, or other functions • Marvin OLE Object (future) • Function results are automatically updated when structures edited or added
  11. 11. Chemical Excel functions – Demo Property calculations for Caffeine
  12. 12. Chemical Excel functions – Demo 2 MolFormula, Composition, IUPAC Name calculated from CD_STRUCTURE logD vs. pH calculated and displayed in a chart from a SMILES input
  13. 13. Reactor Excel Functions • JCReactGetProductImage(<GenericReaction>, <Reagent1>, <Reagent2>) • React the reagents based on the generic reaction, and put the image of the product in the cell • JCReactGetReactionImage(<GenericReaction>, <Reagent1>, <Reagent2>) • React the reagents based on the generic reaction, and put the image of the concrete reaction in the cell • JCReactGetProduct (<GenericReaction>, <Reagent1>, <Reagent2>, <Format>) • React the reagents based on the generic reaction, and put the string representation of the product in the cell(SMILES, IUPAC name) • JCReactGetReaction (<GenericReaction>, <Reagent1>, <Reagent2>, <Format>) • React the reagents based on the generic reaction, and put the string representation of the product in the cell(SMILES , IUPAC name)
  14. 14. Reactor Excel Functions - Demo =JCReactGetProductImage(<GenericReaction in A1>, <Reagents in A column>, <Reagents in Row1>)
  15. 15. Deployment • MSI Installer • No configuration needed • ~10MB File with JChem and Marvin API included • Automatic deployment and updates through Active Directory • ClickOnce (Planned Feature) • Update from Excel at startup or when needed
  16. 16. Find out more • Product descriptions & links www.chemaxon.com/products.html • Forum www.chemaxon.com/forum • Presentations and posters www.chemaxon.com/conf • Download www.chemaxon.com/download.html