JChem for Excel is a Microsoft Excel add-in that integrates ChemAxon's JChem and Marvin technologies. It allows users to import and analyze chemical structure data within Excel. Key features include importing structures from databases and files, running structure searches and decomposition, and utilizing chemical properties and calculations as Excel functions. The add-in is implemented in .NET and can be easily installed and deployed within organizations.

1. JChem for Excel
Tamas Peltz, Ferenc Csizmadia
Solutions for Cheminformatics

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. 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. 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. 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. 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. Import - Results
SDF import results
Database import results
with hit coloring

8. R-group Decomposition
• Run Decomposition on
– JChem Database
– Files
– Excel Worksheet

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. 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. Chemical Excel functions – Demo
Property calculations for
Caffeine

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. 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. Reactor Excel Functions - Demo
=JCReactGetProductImage(<GenericReaction in A1>,
<Reagents in A column>, <Reagents in Row1>)

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. 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