Using ChemAxon's Instant JChem and JChem for office for desktop database management

1. Database Management on
Desktop with
JChem for Office &
Instant JChem
Surojit Sadhu

2. SECTION TITLE
Agenda
JChem for Office
– Overview key features
Instant JChem (IJC)
– What sets IJC apart from other DBMS
Coming Soon!!!
– Sneak preview of an upcoming feature in
JChem for Office

3. Live chemical structures throughout Microsoft Office
JCHEM FOR OFFICE

4. Structure representation
Chemical Search & Filtering
Naming and text conversion
Physico-chemical properties
Shareable files
R-group decomposition
SAR-matrix generation
Virtual library enumerationImport from files or databases
Reporting – MS Office Compatibility
JChem for Office Top 10
JChem for
Office

5. Bringing Chemistry Data into JChem for Office
• Create in Excel, Word or PowerPoint
• Import structures and associated data
from various file formats
• Relational database (JChem Tables)
• JChem Web Services
• Instant JChem, Plexus Suite
• Name and structure conversion
• Extract structures from documents

7. Search Panel
MarvinSketch
Detailed search options
Filtered compounds can be cloned or hidden
Hit treatment: hit substructure can be
- aligned according to the query (use query orientation)
- partial clean (clean up but restore match substructure
according to the query moiety)
Hit coloring can also be set up

8. Property Calculations/Predictions
• Structural Calculations:
– Charge, Conformer, Hückel,
Refractivity, Geometry, Hydrogen
Bond Donor/Acceptor (HBDA),
Structural Frameworks
calculations
• Protonation:
– pKa, Major Microspecies,
Isoelectric Point calculations
• Partitioning:
– logP, logD, HLB calculations
• Isomers:
– Tautomerization, Stereoisomers,
Resonance calculations
• Solubility Predictor
• NMR Predictor

9. Virtual Library Enumeration via Reactor
• Reaction-based library
enumeration
– Custom Excel functions
powered by Reactor
– Sequential mode
– Combinatorial mode
• Reactivity and selectivity
prediction via empirical smart
rules

10. SAR Table Creation
Click to launch
wizard

11. SAR Table Creation: R-group Decomposition
!

12. SAR Table Creation - Identify Gaps

13. Reporting and Presenting
JChem for Office

14. Let’s bring it all together
Akos prepares for group meeting…

15. JCHEM FOR OFFICE LITE

16. JChem for Office Lite
CDX
CDXML SKC
MRV
Copy-paste from
any major chemistry
editor
• Invisible, vendor-independent chemistry in Word, PowerPoint and Outlook (no
Excel component)
• JChem for Office without ribbon
• Faster load!
• Edit the Object with double click
>> Autodetection of the most appropriate editor
>> Preferred editor can be configured

17. Chemical data management from A to Z on desktop
INSTANT JCHEM

18. Instant JChem
A verstile data management framework for the chemist
Instant JChem
Create Explore
Share Analyse

19. Project
explorer
Query
builder
Standard
view

20. Manage Structural and Non-Structural Information

21. View & Manage Data - Grid View
● Spreadsheet-like layout;
● Manage column visibility;
● Conditional formatting for
faster overview;
● Customizing widgets

22. ● Custom layout for relational
data
● Various widgets for each value
type (single or multiple values,
tables, multi-tab widget…)
● Chart widgets (histogram,
scatter plot, radar chart,
boxplot)
View & Manage Data - Form View

23. Search & Explore
• Form-based search & Query
builder
• Chemical Terms filters
• Structure search
Substructure, Superstructure,
Full structure, Full fragment,
Duplicate, Similarity
• Complex queries
AND/OR logic
• Search domains
• Federated search

24. Analyse

25. Structures
Assay data
Project
data
Structures
Assay data
Project
data
DB tables IJC Entities
Structures
Assay data
Project
data
IJC Relationship
Structures
Assay data
Project
data
IJC Datatree
Grid view
Form view
DB backend IJC admin
End user view

26. Scripting
• Extend Instant JChem with complex operations not possible from the GUI
• Compound Registration
• ELN
• Inventory
• PDF Trawler: Trawls a directory for PDF files, extracts the molecules and inserts
them into a structure entity
• Connect to external database – e.g. for data migration
• Automate actions performed routinely
• Scripts can be run against a schema or a data tree
• Scripting language: groovy
• Script editor to edit and execute scripts
• Scripts can be run via Button widgets on forms

27. Instant JChem – MiniReg

28. Consistent chemistry
Standardizer Structure Checker
58 actions
available
65 checkers
available
(no fixer set)

29. Provides search for chemical structures
Displays rich content types (images, web pages and charts)
Highly extendable/customizable via scripting
Enables chemistry-aware interaction with your data
HOW is INSTANT JCHEM different
from a database manager?

30. JChem Table
Query JChem Table
Query JChem Table
Import structure files
directly
Import structure files
directly

31. Surojit Sadhu
Surojit@adventinformatics.com