JChem for Excel
Tamas Peltz, Ferenc Csizmadia
Solutions for Cheminformatics
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
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
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
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
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
Import - Results
SDF import resultsDatabase import results with hit coloring
R-group Decomposition
• Run Decomposition on– JChem Database– Files– Excel Worksheet
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)
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
Chemical Excel functions – Demo
Property calculations for Caffeine
Chemical Excel functions – Demo 2
logD vs. pH calculated and displayed
in a chart from a SMILES input
MolFormula,
Composition, IUPAC
Name calculated from
CD_STRUCTURE
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)
Reactor Excel Functions - Demo
=JCReactGetProductImage(<GenericReaction in A1>, <Reagents in A column>, <Reagents in Row1>)
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
Find out more
• Product descriptions & linkswww.chemaxon.com/products.html
• Forumwww.chemaxon.com/forum
• Presentations and posterswww.chemaxon.com/conf
• Downloadwww.chemaxon.com/download.html
