Calculators and Predictors in Playground

Version 1.2

This documentation gives a short introduction to Chemaxon's Playground.

What is Playground?

Playground is an easy-to-use web application that allows scientists to access Chemaxon's physico-chemical property calculators/predictors and analyse the results in an interactive way.

Demo site

You can try the latest Playground version on our demo site.

Playground walk-through

The welcome page

The welcome page of Playground has a MarvinJS canvas where you can immediately start drawing your molecules. We have also pre-selected some example molecules to get you started without drawing.

Next to the drawing canvas you can find the Explore Calculations menu where you can select and set the order of the available calculations and predictions.

Result windows

Once an input molecule is created, the calculation and prediction result windows appear under the Explore Calculations menu. The calculation results are automatically updated if the input molecule is modified on the canvas.

You can remove any window from the result windows by clicking on the Close button.

It is also possible to download the result of the calculations in an SD file for each window by clicking on the Export result in SDF button.

pKa

The pKa window displays predicted properties related to ionization: the strongest acidic and basic pKa values, the microspecies and their distribution plots.

You can get a full-screen view of the molecule with the predicted pKa values by clicking on the Ionization panel of the window. You can do the same with any of the microspecies by clicking on them.

Hovering over a predicted pKa value, the given value gets highlighted next to its functional group in the molecule.

Hovering over a single microform, the microform appears in the Ionization Panel while only the distribution plot of that microform is shown.

Scrolling through the microspecies plots as the pH is changing, the major microspecies and only the dominant microspecies at the actual pH value are shown. The distribution percentages of the displayed microspecies are also shown.

To set the pH to a given value use the Highlight pH box.

Solubility

The Solubility window displays the predicted intrinsic solubility and the pH-dependent solubility plot. Scrolling through the plot the solubility value at the actual pH is also displayed. To set the pH to a given value use the Highlight pH box.

Lipophilicity

The Lipophilicity window displays the predicted logP and the pH-dependent logD plot. Scrolling through the plot the logD value at the actual pH is also displayed. To set the pH to a given value use the Highlight pH box.

Basic Properties

The Basic Properties window displays basic physico-chemical properties important for chemists in their daily work. Scrolling through the list of properties, the actual property and its calculated value(s) get highlighted.

hERG

The hERG window displays the predicted hERG pActivity value and its applicability domain. Scrolling through the most similar molecules from the training set, their position on the Similarity-pActivity chart gets highlighted.

You can read the details of the hERG prediction here.

Comparing results for multiple molecules

Playground also supports comparing prediction results for multiple molecules by plotting them with different colours.

Note: Comparing results for the pKa calculation is not supported as displaying many microspecies plots for multiple molecules would cause too much complexity in visualising the results. pKa and microspecies plots are calculated and displayed only for the largest structure on the canvas.

Licensing

To run a calculation or prediction in Playground you need a valid MarvinJS and the corresponding valid Calculators licenses. You can read about MarvinJS licensing here and check the licensing of the Calculators here.

Note: The license files (marvin4js-license.cxl and license.cxl ) must be stored in the .chemaxon (Unix) or chemaxon (Windows) sub-directory of the user’s home directory.

Installation guide

Playground can be installed and run via Docker or a downloadable ZIP package.

Installation via Docker

To install Playground via Docker please follow the instructions below:

Download and install Docker to your computer.
Create a Chemaxon account and generate an API key.
Once Docker is installed on your computer, login with it to the ChemAxon hub with the following command:

echo <API-KEY> | docker login -u <E-MAIL> --password-stdin hub.chemaxon.com

Once you are logged in, download the playground.sh script and run it. The images will be automatically downloaded during the first run.

If you successfully follow the steps above, Playground will start in your browser.

Note 1: The Playground script contains the docker pull command, so there is no need to run it directly. Note 2: You might need to add executing permission to the Playground script to be able to run it on your OS. Note 3: Before running the script it is recommended to check the validity of the relevant Chemaxon licenses.

Installation via a ZIP package

The minimum requirement is Java 1.8 or versions above.
Download the ZIP package of Playground to your computer from here.
You can directly run the playground.sh (on Linux or Mac OS) or the playground.bat (on Win) script after unzipping the package.

Release notes (History of changes)

Playground v. 1.0:

Calculations related to ionization (pKa, microspecies distribution and major microspecies at a certain pH) are available
Calculations related to aqueous solubility (intrinsic logS and logS at a certain pH) are available
Calculations related to lipophilicity (logP and logD at a certain pH value) are available
SDF export for all calculations
Supporting multi-fragment calculations (except for pKa)

Playground v. 1.1:

Calculating basic properties (e.g. molecular weight, molecular formula) are available
A .bat script is available in the ZIP package for Win users
From this version the ZIP distribution can be run with Java 14 and Java 15.

Playground v. 1.2:

hERG prediction and its applicability domain are available