Introduction

This package contains the scoring functions for REINVENT.

Installation

To install in REINVENT's environment either install from repo or use pip install reinvent-scoring for the latest official release.

Developing

Setup environment

You can use Conda to create an environment with all the necessary packages installed.

$ conda env create -f reinvent_scoring
[...]
$ conda activate reinvent_scoring

Run tests

The tests use the unittest package testing framework. Before you can run the tests make sure that you have created a config.jsonfile in the reinvent_scoring/configs directory. There is an example config in the same directory, which you can base your own config off of. Make sure that you set MAIN_TEST_PATH to a non-existent directory; it is where temporary files will be written during the tests; if it is set to an existing directory, that directory will be removed once the tests have finished.

Some tests require a proprietary OpenEye license; you have to set up a few things to make the tests read your license. The simple way is to just set the OE_LICENSE environment variable to the path of the file containing the license. If you just want to set the license in the reinvent_scoring Conda environment, it is a bit more complicated, but you only have to do it once.

(reinvent-scoring) $ cd $CONDA_PREFIX
$ mkdir -p etc/conda/activate.d
$ mkdir -p etc/conda/deactivate.d

Put the following in etc/conda/activate.d/env_vars.sh.

#!/bin/sh
export OE_LICENSE='</path/to/your/oe_license/file>'

And put the following in etc/conda/deactivate.d/env_vars.sh.

#!/bin/sh
unset OE_LICENSE

Once you have created the files, deactivate and re-activate the environment, and echo $OE_LICENSE should output the path to the license file.

Once you have created and configured your environment, you can run unittests by running

python main_test.py --unittests

If you have a valid Open eye license and other dependencie configured, like Icolos and AZDOCK - you can also run integration tests, by running command (remember to submit this configuration, since the default one is test):

python main_test.py --integration --base_config <path to your configuration>

Building

• Building: python setup.py sdist bdist_wheel
• Upload build to test: python -m twine upload --repository testpypi dist/*
• Upload build: python -m twine upload dist/*