Awesome

CPSign API USAGE GUIDE

This repo is meant to give some basic examples on how to get up and running with CPSign using the Java API. For more information we also refer to CPSign readthedocs. It now also includes a basic tutorial on using the CLI found at CLI demo.

Currently supported versions

The mapping of CPSign version to Tag in this repository should be identical (except for an added prefix v). Not all versions of CPSign has updated examples and currently the following versions of CPSign have working examples:

Note that the API has not changed drastically, so these should suffice to get you up and running for most versions of CPSign.

Requirements

To run these examples on your own computer you need the following:

• Java of version 11 or newer
• Maven for package management

Examples

All examples can be found in the examples directory:

• ApplyDataTransformations : Uses CDK physicochemical descriptors and shows how to apply data transformations.
• GeneratePredictionImages : Shows how to generate prediction images and how to customize the produced images with custom elements such as titles, boards and legends.
• ListAvailableServices : Shows how to list configurable elements that are loaded using the java ServiceLoader class. These also represent classes that users themselves can extend with their own implementations.
• ManipulatingNumericalDatasets : Shows basic data-manipulation such as shuffling and splitting data.
• ParameterTuning : Show how to preform a grid search over hyper-parameters in order to tune these.
• ParsingChemicalFiles : Shows how to read data from SDF and CSV files.
• SettingDescriptors : Shows how to use non-default chemical descriptors, by picking from the IMolecularDescriptor implementations from the CDK library.
• StandardWorkflows : Shows how to instantiate a predictor model, load data to use for training, train it, predict a test example and how to save the predictor model.
• StandardWorkflowsNonChem : Does the same workflow as above, but for numerical (non-chemistry) input data.

Note that this project uses the pom.xml to configure version of CPSign and other test dependencies.

Who do I talk to?

Do you have any further issues, refer to the CPSign Documentation, file an issue on CPSign GitHub or contact Aros Bio info@arosbio.com