Luna

**Most important updates:**

1. **LUNA is much faster now**;
- Average speed improvement in comparison to the previous version varies from 124% to 284% among a set of 50 complexes;

2. New interaction type: metal coordination;

3. Improved standardization for residues at PDB files.

4. Residues coordinating metals are standardized differently. For instance, an OH from TYR will be considered deprotonated in these circumstances;

6. Metals and ligands are now standardized as well;

7. New classes to run DOCK6;

8. New classes to prepare ligands: add charges, add hydrogens, generate tautomers and stereoisomers at any pH, generate conformers, and minimize ligand structures;

9. Fixed some minor bugs;

**Most important updates:**

1. Now, the main LUNA script (run.py) provides full compatibility with all LUNA parameters;

2. Now, the main LUNA script (run.py) provides full integration between command lines and config files, where the order of precedence is **default LUNA config < config file provided through command line < command line modifiers**.

3. LUNA now saves config files to <WORKING_PATH>/configs so that config files can be shared between users for reproducibility.

4. Speeded up LUNA: we added a new cache system to store protein information to avoid the recomputation of protein information over and over again when the protein is the same across all entries. This is especially useful for docking/MD campaigns where the same protein is used for all ligands. **To activate it sets Project's parameter 'use_cache' to True**. This will not provide any gains if the protein structures are different across your list of entries.