Cheminformatics updates

New features available in ‘Similarity search’ and ‘Diversity search’ functions:

  • Similarity metric and fingerprint are shown in the right top corner of the main screen. By clicking on the link property panel is opened.
  • Changing molecule size is available on a property panel
  • Selection of search column is available on a property panel


Molecule queries

Out-of-the-box, you can paste SMILES, MOLBLOCK, and InChi keys into the input field, and the sketcher
automatically translates it to a structure. In addition to that, you can make sketcher understand
other structure notations (such as from your company’s internal database of structures) by registering
a function annotated in a special way. The following example provides support for Chembl. The important
tags are:

  • --meta.role: converter: indicates that such a function serves as a value converter
  • --meta.inputRegexp: (CHEMBL[0-9]+): RegExp that is evaluated to check if this function
    is applicable to the user input. The captured group (in this case the whole input) is then
    passed to this function as a parameter.
  • --output: string smiles { semType: Molecule }: should return string with the semType Molecule
--name: chemblIdToSmiles
--meta.role: converter
--meta.inputRegexp: (CHEMBL[0-9]+)
--connection: Chembl
--input: string id = CHEMBL1185
--output: string smiles { semType: Molecule }
select canonical_smiles from compound_structures s
join molecule_dictionary d on s.molregno = d.molregno
where d.chembl_id = @id

This is how it looks in action:


A molecule query does not have to be a database query, any function
will do. For instance, InChi query is implemented as a Python script.

Support for .mol files added in Chem v0.52

New sketcher features:

Favorite and recent structures

Access the recently sketched structures from the ☰ -> Recent menu.

☰ -> Favorites contains your favorite structures. To add current molecule
to the favorites, click on ☰ -> Favorites -> Add to Favorites.

Elemental analysis is now available in Chem. Its main purpose is to show atom counts.

With this newly implemented tool you can:

  • get columns with atom counts (same order as in the periodic table);
  • get a radar chart for every single molecule which makes it possible to compare each molecule with the whole dataset.

In order to use the new feature, select Chem | Elemental analysis from the main menu.

Radar chart can be visualized in 2 ways:

  1. A new column with radar charts is added.

  1. Radar chart appears in a new window. It changes automatically when you click on the new row.


Now you can easily add calculated properties right from the “Properties” panel:

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New functionality is available in Similarity/Diversity search.
Information from any column of initial dataset can now be added to molecules panes. To to that go to context panel and select columns from Molecule Properties field. You can add as many columns as you need.
Please note that color coding applied to initial dataframe is saved in molecule panes. Color coding can be applied to background or text.

This new feature significantly simplifies visual data analysis. All required information becomes available at once in molecule panes. You do not need to scroll initial grid to exact column and cell to get the data.


You can now copy a molecule in several different formats, including Smiles, Molfile V2000, Molfile V3000, and Smarts.

To do so simply right-click on the cell and select Current value -> Copy as <format>.


Dimensionality reduction algorithms can now be customized to suit specific needs. This technique is particularly useful in Chemical space and Activity cliffs functions when visualizing high-dimensional molecule data on a 2D scatter plot. To achieve this, UMAP and t-SNE are two available options.

To customize parameters, simply click on the Settings icon near the algorithm selection field, which will expand the list of parameters. Each algorithm has its own set of adjustable parameters, accompanied by a tooltip providing more detailed information.

By utilizing these customizable settings, data exploration becomes more precise by tailoring the settings according to the specifics of the data.


Scaffold Tree is a tool for the generation and analysis of molecular scaffold networks and trees that is now available in Chem. This tool has the capability to process large sets of input molecules and provides users with the ability to perform hierarchy generation either automatically or manually.

To access Scaffold Tree, simply open a dataset with molecules and then select Chem | Analyze Structure | Scaffold Tree from the top menu. Once you’ve opened the tool, you can start generating your Scaffold Tree. The initial tree is automatically generated, but you also have the option to sketch the tree manually or modify the automatically generated one.

In addition, with this tool you can:

  • filter the molecules exclusively in your dataset by a particular scaffold;
  • highlight rows matching a particular scaffold;
  • save Scaffold Tree as a part of the layout, or as part of the dashboard;
  • load a previously saved tree.


Overall, Scaffold Tree is an incredibly powerful tool for anyone working in the fields of chemistry and biology. Its user-friendly interface and advanced capabilities make it a valuable addition to any researcher’s toolkit.

For further information, please follow the link.


We are excited to announce the initial release of the ADMETox plugin that predicts ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties for chemical structures.

The binary files of all the models have been obtained from the publicly accessible ADMETlab repository and are open-source.

With ADMETox, you can easily:

  • obtain predictions for either a single structure and for the entire column;
  • get a well-designed and easily navigable forms for every structure in your dataset;
  • get a deeper understanding of what each of values mean with the help of our tooltips and color coding tools.

To evaluate predictions for a single molecule, click on it and expand the ADME/Tox pane in the Context Panel.


To calculate properties for the entire column, go to the top menu and select Chem | ADME/Tox | Calculations. The corresponding predictions will be added to the table as numerical columns, so you can visualize or filter them using the built-in tools.


To see detailed information on a structure in a well-formed and color-coded form, select Chem | ADME/Tox | Add form… from the top menu. The form gets updated as you move between rows.


With ADMETox, we believe that evaluating molecule properties has never been easier or more accessible. We hope this package will assist in advancing drug development and research efforts!


In which version of the Chem Package is ADMET included?

Hi Tom, apologies, it looks Oleksandra pulled the trigger a few days too soon :slight_smile: AdmeTox is a new plugin that will be released in a couple of days.

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Hello, is the package already available?
I’m using Chem version 1.6.15 but I can’t see ADME/TOX menue in Chem tab.


AdmeTox is a standalone package located in the Uncategorized section (Manage > Packages > Uncategorized). Currently, version 0.0.1 of AdmeTox is available.

We sincerely apologize for the inconvenience caused by the unavailability of the package you were expecting. Datagrok team is currently working on the remaining technical issues that are crucial for the successful release of the package. Our main focus is to ensure its stability and meet all the necessary requirements, which will ultimately enhance your experience with the product.
We deeply regret providing incorrect information about the package being available when it was not. It was an oversight on our part, and we understand the confusion it caused.
Please be assured that we will test the package and release its new version as soon as possible and will promptly update you with the revised information.


New substructure search functionality is available in the Chem package version 1.7.0.

We drastically improved the algorithm, and now it provides the following:

  • ability to filter datasets containing millions of molecules without memory overflow

  • 10 times faster consecutive searches against the same dataset. This is done by caching and reusing the pattern fingerprints

  • The first search results appear in just a split second, regardless of the dataset size. You do not have to wait for the entire dataset to be filtered before exploring the results.

  • Easy search process tracking with a search progress bar

There are two ways to run a substructure search:

  • Select Top menuChemSearchSubstructure Search...
  • Click Filter icon on a toolbox

In both cases, a filter opens on the right side of the table.

To conduct a search:

  1. Click on the Click to edit pane for the desired column. The molecule sketcher opens

  2. Sketch some substructure. The search starts immediately.

Clicking OK during the active search closes the sketcher, but the search continues. Clicking Cancel terminates the active search.
Additionally, you can modify the substructure during an active search, and the results will recalculate instantly.

Here is an example:


Hierarchical clustering for Molecules

Hierarchical clustering function from Dendrogram package now supports Molecule columns in various formats.
Users can also cluster Molecule columns alongside with numeric or Macromolecule(sequence) columns. In such cases, Distance matrices will be calculated for both, normalized and added together.
To run hierarchical clustering, Select Top menuChemAnalyzeHierarchical Clustering...
Then, select the column with molecules, choose the linkage method and press Ok.

Distance function:

First, for all molecules in the column, we calculate ‘Morgan Fingerprints’, which are 2048 bit vectors.
For distance function, we compare them using ‘Tanimoto similarity’ metric and build a distance matrix on each pair. This distance matrix then passes on to web assembly code for clustering. All this makes the process incredibly efficient and fast, taking less than 2 seconds on 1000 molecules.


We are thrilled to announce our latest update, Scaffold Tree integration with molecule fragments highlighting. This enhancement makes your data visualization experience even more user-friendly and intuitive.

To utilize this feature, we have introduced two icons:

  • Circle icon. Click to toggle the color on and off.

  • Palette icon. Click to open a convenient dialog with color picker. The icon allows you to apply or modify colors effortlessly.

In addition, we have outlined some important guidelines for you:

  • Color propagation. When you select or modify a color, it automatically extends to all child nodes. Keep in mind that more specific structures, closer to the leaves, take precedence.

  • Color inheritance. When you turn the color off, the node inherits its color from the parent.

Scaffolds are highlighted both in the column and viewer for the convenience.

For further information, please follow the link.

We believe, that with these enhancements, Scaffold Tree becomes an even more powerful tool for visualizing your data with precision and ease. Explore the new features and elevate your data visualization experience today!



New types of molecular search

Now we support multiple types of molecular search, which are:

  • Contains (search by substructure)
  • Not contains
  • Included in (search by superstructure)
  • Not included in
  • Exact (search by exact structure match)
  • Similar (search by similarity score)

To run the search:

  1. Click Filter icon on a toolbox. The filter panel opens. The default search type is Contains. Change the search type by selecting from a dropdown list.
  2. Click Click to edit pane for the desired column. The molecule sketcher opens
  3. Sketch some substructure. The search starts immediately.


This functionality is available in Chem package starting from version 1.8.0.