Instant JChem

create, explore and share chemical data

Instant JChem is a desktop application designed for the chemist. With Instant JChem you can create, explore and share chemical and non-chemical data in local and remote databases without additional administration. Instant JChem has a wide and growing range of functionality including customisable database views, integration of library enumeration and dynamic population of columns with singular and combined molecular property and descriptor predictions.

Product Type:application
Interfaces:GUI ( Desktop )API ( Java )

Ease of database management on your desktop

Easy local and remote database management

In Instant JChem local and remote databases can easily be created and administered by end users. Using either a local database engine or a remote enterprise database (Oracle & MySQL) millions of structures can be explored and managed.

Easy Local and Remote Database

Instant JChem allows you to open and manage several databases simultaneously. In addition to simple chemical structures you can also store non-chemical data, reactions or even Markush structures in a database. Handling relational data is supported, making Instant JChem a great tool for managing and reporting your assay and chemical data.

Flexible import and export to databases

Structure and non-structure data fields can be imported into and exported from databases using the wizard. Fields to be imported can also be selected and mapped. Apart from the standard chemical file formats (SDF, RDF, SMILES, SMARTS, CDX, SKC, InChI, etc.) Instant JChem also supports Markush DARC file format.

Instant JChem as a viewer

Even without a license Instant JChem can be used to visualize data in Instant JChem projects and provides full structure search and form design capabilities, but is limited to handling data sets that are already present within the Instant JChem local database. This provides a great way to distribute data to your colleagues.

Even more flexibility in data sharing is available through our new Plexus Suite, which allows making your chemical database content available in a browser environment. Plexus Suite offers full access to your database managed with Instant JChem, including form views, predicted and calculated values, lists and search features in secure fashion.

Visualization of database content

Customised grid view for database content visualisation

The grid view provides a simple means to view tabular data (or spreadsheet like). When you import data, a corresponding grid view is automatically generated for you. The grid view offers a representation of the data in the table, enabling you to both view and edit the data. Because the view is synchronized with the database table, any edits you make will cause the database table to automatically update.

ˇ Customized Grid View

Customised form view for database content visualisation

The form view allows the creation of more complex reports from relational data tables. The form builder allows multiple reports to be easily designed and laid out. You can add display widgets to the form, and bind them to particular field(s). Each widget can be re-sized and re-positioned, allowing your fine grain control of the design. Relational data can be displayed, with the contents of the widgets updating reflect the current content and selection. Forms can also be shared and copied. Furthermore, with the help of the Button Widget one can perform custom made actions, defined by the user in a Groovy script.

Fast and powerful structure searches on your desktop

Structure searches

You can search for structures by a query structure and specified search options. Similarity, substructure, full fragment, fragment, superstructure and duplicate searches are directly available in Instant JChem. It is possible to apply further structure filtering sequentially to narrow the hit list. Structure searches can be combined with other data field searches via ChemAxon’s Chemical Terms language. An overlap analysis function lets users compare the entire contents of two database tables using any of the structure search operators. Federated searches enables users to perform structure searches on several data tables simultaneously.

List and query management

Instant JChem contains powerful list and query management features, allowing queries and hit lists to be saved and re-used at a later time. Lists can be combined using logical (AND, OR, NOT…) operators, and lists for different fields can be managed and inter-converted.

List and Query Management


Standardizer is a structure canonicalization tool for converting molecules from different sources into standard representational forms and could be considered as allowing building of chemical business rules. Standardizer can automate the identification of mesomers, tautomers, stereoisomers and counter-ion removal. Aromatization or cleaning can also be automatically applied. Using the Standardizer wizard within Instant JChem helps users to store the structures in a canonicalized form that is essential for accurate structure searches.


Facilitating Medicinal Chemistry on your desktop

Synthetically feasible virtual library generation

Instant JChem uses ChemAxon’s Reactor, a synthesis engine for virtual library generation. The reaction can be chosen from ChemAxon’s ‘smart’ reaction library, or entered by the user. The reactants are sourced from IJC database table(s), and products are written into a new database table. Reagents can be arranged in a sequential or combinatorial mode. Products or the whole reaction can be generated.

ChemAxon’s empirical smart rules are available in Instant JChem, predicting the reactivity and selectivity and can be specified by the user through a generic reaction. For more about generating generic reaction see Reactor rules.

ChemAxon’s enumeration technology allows applying empirical ‘smart’ rules in Instant JChem, predicting the reactivity and selectivity. Reactivity rules are Boolean expressions describing natural conditions – these conditions should be satisfied, otherwise the reaction does not take place. Selectivity rules are real-valued chemical expressions that order products according to their occurrence. Through applying and tuning these rules the user can define libraries that are synthetically feasible.


Competitor analysis is one of the major steps during drug discovery. Researchers can investigate a smaller set of patent IUPAC names which can be imported directly and will automatically be converted into structures, then further characterized. IUPAC names can also be generated for existing data sets which can be used in the patent application.

Fast 2D/3D cleaning

Often imported chemical structures do not look correct. Users can clean structures easily either in 2D or 3D using the built-in Standardizer module. The calculation generates acceptable 3D structures and conformers of a given molecule. The 3D structure (conformation) strongly affects the properties and the reactions of molecules, so a medicinal chemist can have a first quick estimation in Instant JChem about the 3D representation which often has an intuitive value during research.

Physical-chemical property and molecular descriptor calculations

A key feature Instant JChem is the degree of integration of our structure based calculations (Calculator Plugins). Directly from Instant JChem users can populate columns with physicochemical properties, molecular descriptors and topology analysis results. Various indices used in drug discovery are also implemented such as Lipinski drug-likeness. Chemical Terms, a language for combining and extending Calculator Plugins is also natively integrated, letting users easily set up complex structure based arguments to populate cells. Another benefit of the deep integration is that adding new rows or editing structures automatically updated dependent columns.

Physical-chemical Property

Data Visualization and Analysis

Instant JChem supports advanced graphical visualization of database content using various chart formats. The charts are fully synchronized with the query and selection features, allowing interactive browsing and visualization of data.

Visualize your data

Instant JChem offers rich data visualization functionality to create histograms, scatter plots and radar charts. In addition to that, box charts can be applied for statistical analysis of the data. These widgets can be used in the form designer to plot data points in an interactive way facilitating visual analysis of chemical structures and related data sets. Any selection in the visualization widgets are shared and synchronized with other widgets in the form view, allowing direct identification of chemical structures associated with the data.

Instant JChem viz

Wide selection of widgets and formatting options

Tabbed pane widgets allow users increase complexity of a form when there are different fields, e.g. Molecular properties and Assay data, belonging to a chemical structure and creating separate boxes would be confusing.

Multi-field sheet widget further offers way to create a two column table with the first column being the field names and the second being the value for the field for the current row. This provides a more compact way to display data than the current range of widgets allow, and allow fields to be grouped together into sets. The TreeTable widget allows hierarchical grouping of the database content based on user-selected data categories.

Chemical structures can also be visualized in a dense matrix representation similarly to the current table widget, but with one structure per cell rather than one per row. An additional data field can also be displayed so that you can display the compound ID alongside each structure.

Instant JChem viz

Users have the ability to format data and colour the background of cells in tables or widgets in form based on criteria specified by the user using the conditional formation improvement.

Instant JChem viz

Integration with Spotfire

Powerful data visualization and statistical analysis

The integration of Instant JChem with TIBCO’s Spotfire Professional results in a powerful solution allowing researchers to speed up the analysis of large chemical libraries. A smooth two-way communication is set up between the two clients by Instant JChem’s personal server, which provides an active interface via Open Data protocol language.

This interactive communication makes sharing structural and non-structural information with Spotfire seamless, also allowing users to work with relational data models. Once loaded into Spotfire, the data can be processed with its powerful analytical and visualization methods producing results for high quality reports, or results that instantly can be seen back in IJC, and used there for further processing.

Spotfire integration in Instant JChem

A pivot entity as visualisation tool

A pivot table is a data sumarization tool which is a usual part of data visualization packages, as it can display various data sorted into different ‘categories’. Therefore, in IJC version, we introduced a new Entity type, enabling the users to create a virtual data view, which can pivot data from the original entity.


Its usage is covered by the Instant JChem VIZ license. The pivotted data can be visualised by various types of widgets, but the most suitable is a Grid View, or a Table Widget. For more detailed information on how the Pivot entity is created and its possibilities, including basic aggregation functions, see the documentation For a more detailed tutorial, please see here.

Articles in the library

ChemAxon US User Meeting, San Francisco, April 10-11, 2017

Apr 10, 2017 - Report
  Introduction US ChemAxon users gathered at the Sheraton Fisherman’s Wharf, San Francisco for the annual meeting. A hands-on workshop and biomolecule forum took place in the mor…

AMRI Leverages Instant JChem for Compound Libraries

Sep 15, 2016 - Presentation
AMRI recently launched a Compound Library Consortium (CLC), to deliver 70,000 compounds within 2.5 years for three different partners. AMRI selected Instant JChem (IJC) from ChemAxon to …

Plexus Suite and Instant JChem

Apr 11, 2017 - Presentation
Instant JChem is a desktop application designed for researchers and can be considered as a predecessor of the emerging Plexus Suite. Instant JChem allows you to create, explore, and share…

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