Creating and Applying Molecule Filters

The cheminformatics floes provide several floes for creating and applying molecular filters. This tutorial describes how to use these floes.

Floes used in this Tutorial

The floes used in this tutorial are:

  • Dataset Filtering – Create Custom Filter

  • Dataset Filtering – Custom or Built-in Filter Types

Create a Custom Filter

The Dataset Filtering – Create Custom Filter floe is designed to output an OEMolProp filter file that can be used in a subsequent script or floe.

Filter Customization

To start construction of the filter file, the floe can take a base OEMolProp filter, choosing from the built-in Lead, Drug, Blockbuster, or PAINS filter. Any further parameter settings that are selected will override parameters from this base file.

Custom filter lines can also be added in the Custom String to Add to Base Filter parameter. Any other settings set elsewhere in the floe parameters that conflict with these settings will override these strings.

Filter Customization

Filter Customization Settings

Parameter Settings

The many available OEMolProp parameters are sorted into groups based on their function. In each parameter description, the capitalized parameter corresponds to the keyword that is written into the filter file, along with the provided setting. If a setting isn’t specified in the UI, nothing is written to the filter file for that setting. For more details on each parameter, search for the parameter keyword in the OEMolProp documentation.

Filter Customization

Ring System Filter Parameters

Functional Group Parameters

There are many functional groups maximums that can be added to the filter as rules. These correspond to the maximum occurrences of the functional groups allowed in the molecule. For details on these functional groups, refer to the OEMolProp documentation.

Functional Groups

Functional Group Settings

Create Custom Filter Floe Output

The floe will output a file with extension .txt that contains the custom filter based on the settings. This file can now be input into the Dataset Filtering – Custom or Built-in Filter Types Floe.

Run a Custom Filter

The filter floe can take the filter output from the Create Custom Filter Floe, or any other custom filter file, in the following input parameter. The Use Custom Filter parameter must be set to On for the floe to use this custom input file.

Custom Filter File Input

Input Custom Filter File


Due to the sheer number of potential parameters in the Create Custom Filter Floe, it is possible that this floe will create an invalid filter file. If the output filter file does not work in a subsequent script or floe, please refer to the documentation for OEMolProp to troubleshoot. It is likely that only a few adjustments will be required to fix the filter file.