SiMGen example molecules

Examples of structures generated using SiMGen.

• Macrocycles, including their generation trajectories.
• Small molecules.
• Baseline comparison of molecules generated via the linear interpolation mentioned in the paper.
• Structures generated for analysing SiMGen's performance in an unconditional setting. (simgen_unconditional_gen_*, performance_table.ipynb for generating the table).
• Structures generated for the size sweep experiment, and their analysis. (simgen_size_sweep_*)
• Binders generated with SiMGen for the Octa-Acid cage. Includes original and redocked examples. (oa_simgen_filtered.zip and oa_redocked.zip)
• Examples of molecules generated with MolDiff and SiMGen guidance (with/without score and importance sampling guidance). E_inv (the log density) used to generate the violin plots is also included for all structures. (guided_moldiff_examples.tar.gz)

Note, some of these used an older version of the MACE-OFF models so a slight adjustment of the restorative force parameters might be necessary.

The interactive version at https://zndraw.icp.uni-stuttgart.de/ will always have the latest stable version.