update amberff usage & other improvements

[David-Araripe]

Sorry for the large PR, but this includes all the changes to be introduced on the QligFEPv2 paper. From now on, let's work with smaller PR's since that makes it easier to track the different changes. Current changes include:

• Update AmberFF parameters including N and C terminus;
• Update Q's aminoacid reading from pdb to 4 characters to enable proper N & C termini detection
• Include a new method for choosing ligand-ligand restraints, based on kartograf
• Water droplet density adjusted dynamically depending on lipid atom presence (Fixes for membrane proteins qligfep#19)
• Add class for doing MCS-based ligand alignment.
• Better support for random seed setting.
  • Now, if the user passes a specific random seed to the run, the same seed will vary according to the replicate number (run 1 with seed X, run 2 with seed Y...)
• FEP_submit.sh supports replicate-based job re-submission
• qligfep_analyze now also calculates metrics with cinnabar, providing the 95% CI interval of the calculated metrics
• job sumission scheme uses slurm job arrays
• New tutorial including available parameters for the restraint setting
• Water molecule cloud dynamically adjusted to remove HOH making steric clashes with the ligand
  • The distance threshold for this function can also be controlled in the command line by adjusting the water_thresh parameter.
• Support for creating custom FF.prm & FF.lib files that include parametrized co-factors
• Automatic detection of cystein bonds

To improve:

• Current tutorial doesn't cover dynamic visualization of the restraints, though it's supported in the code
• Currently, adjusting water_thresh won't make a distinction between the ligand and the POPC atoms. It would be beneficial to have a different treatment to these atom types
• There's no current support for doing a local runs, without depending on slurm job arrays. This is something to be improved in the future
• Remove the INPUTS files in favor of string advanced formatting
• Though we have a class for doing alingment, there's no current example notebook on how to work with it. It would be nice to have a "new target" in the tutorial section to show the user how to work with it