Stereogeneration

Studying the effects of including stereisomeric information in generative models for molecules.

Benchmarks:

• Rediscovery benchmark
• Docking score
• CD Spectra

Preliminaries

Be sure to allow binaries to be executable. This includes

stereogeneration/docking/smina.static
~/bin/stda/g_spec
~/bin/stda/stda_v1.6.3
~/bin/stda/xtb4stda

otherwise there will be errors in using cd and docking fitnesses.

Using the models

Virutal environment used created using

./make_cc_env.sh

JANUS

Go into janus folder.

See main.py for running JANUS (with and without stereoinformation). Add custom fitness function in this file. The fitness currently assumes the use of 1 core (modification is necessary).

Use the submission scripts for stereo vs. non-stereo runs:

sbatch submit_nonstereo.sh  # submit_stereo.sh

REINVENT

Go into reinvent folder.