gmseabra / elion

Elion

An AI-based workflow for drug lead optimization

Installation

Conda Environment

Use the environment file provided or the spec-file (created for RHEL8.0)

Using the environemnt.yml file

Following the instructions from Conda docs, here.

$ conda env create -f environment.yml

Using the spec file (RHEL 8)

Follow the instructions from the Conda docs, here.

$ conda create --name myenv --file spec-file.txt

Install Dependencies

$ cd to/project/folder/
$ conda activate elion
$ pip install --editable .
Obtaining file:///home/seabra/work/li/elion_dev/elion
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Installing backend dependencies ... done
  Preparing editable metadata (pyproject.toml) ... done
Building wheels for collected packages: elion
  Building editable for elion (pyproject.toml) ... done
  Created wheel for elion: filename=elion-0.0.1a0.dev0-0.editable-py3-none-any.whl size=1740 sha256=668210deaf00e7bfc611743297e6e4b3e9e34a0198673054b137d824c0212041
  Stored in directory: /tmp/pip-ephem-wheel-cache-4o96z9y9/wheels/6b/da/ed/4f4d89acdea49ea9a18ebf1b66b36cbaaee17ea8f4c0eccc96
Successfully built elion
Installing collected packages: elion
Successfully installed elion-0.0.1a0.dev0

Use

1. To get help information, type elion --help
2. Prepare an input file that controls the calculation to be done. By default, Elion looks for a file named input.yml. If you want to use any other name, just use the -i flag.
3. Run Elion with the command:

$ elion [-i input_file]

Extra Info

This project uses setuptools and runs in editable mode, as described here.

TO-DO

• input_reader.py (78): Restore the threshold values from the last iteration
• Property.py (185): Allow larger threshold jumps based on percentile
• Property.py (180): (bug) enforce threshold limit. Currenlty only works for increasing absolute thresholds.

elion's Issues

input_example.yml may have some problems

hi,
Your work is very meaningful and valuable, and I am very interested in it. However, during the reproduction process, I found that there seem to be some issues with this file input_example.yml,no Key 'Reward_function'