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