Frag-pele

Flag included to choose between srun and mpirun command to run PELE. srun is set by default, but you can also use mpirun instead.

New features:
- Parameters of the core atoms close to the fragment are modified along with growing steps, until getting the completely grown ligand.
- Parameters of theta and phi angles are also modified (for fragment and core atoms).

Both changes allow us to reduce the amount of growing steps in order to speed up the simulation time, getting slightly less accurate results in complex systems (~20%) but with an increment up to 3 folds in speed, which is fundamental for screening large libraries.

Bugs solved:
- Sequential growing failed due to messing up folder movement. Fixed on PR 47
- Some bonds had NoneType Error because its distance was missing in the bond lengths dictionary. Fixed on PR 50
- Other small bugs have been corrected

Others:
- Argparse has been re-factorized and can be call via API.
- Tests have been improved.

- Flag to not check constants.py if desired

- Fix bug when simulation failing and staying inside the working folder

New update in FragPELE! We knew that the output folders and files could be confusing sometimes and difficult to interpret. In order to solve that, we have released FragPELE2.1.0.

Major changes:
- New reorganization of FragPELE results: 1 folder for each fragment-core combination 28 30
- New modes: only prepare and only grow. 37
- New flags added: Documents and Data symbolic links path 29

Minor changes:
- More hard-coded variables now are real variables.
- Small bugs corrected.

A new version of FragPELE is now available! We have done a lot of work to improve our ligand growing method and make it more suitable to be used in accordance with the real needs of the drug design market.

Major changes
* Force field parameters computation while growing. New parameters and equations applied.
* Growing onto heavy atoms: H not required anymore. More info 20
* Growing through BOND-LIKE selection. More info also in 20
* Fragments can be coupled through double and triple bonding. For more info 27
* More sampling options after growing: Explorative and personalized mode available. More info 18
* Backtracking of snapshots and connectivity: videos. Info: 31 32

You will find all the information about how to use the new implementations in the documentation.

Minor changes
* Clash threshold now is a variable argument. More info in 10
* Distance of newly created bonds is corrected accordingly with its atom type. For more info: 21
* Some folders have changed their names: "equilibration" simulation now is the "sampling" simulation.
* The documentation includes more info, such as the analysis tools.
* An automatic analysis is performed after the simulation, generating different CSV files with all the information for each sampling simulation. Additionally, the FragPELE score for each fragment is computed in a summary TSV file.

Bugs solved
* Terminal amides now won't change from cis to trans and vice-versa. 11
* Sometimes the instruction to select a specific H could be ignored. Now, this won't happen. 17

If you feel a special interest in all the changes performed, I strongly recommend you to read the closed issues section.

Greetings,

Carles Perez