Adaptivepele

Bug fixes:

- Fix compatibility with latest Cython version

Bug fixes:

- Fix compatibility issues with networkx

New features:

- Add script to run RMSD clustering from scratch
- Add filters for plotAdaptive script
- Add support for multiple control files

Bug fixes:

- Fix bug in pdb processing for MD simulation when no protein was present
- Fix bug extracting the ligand for MD in some weird edge cases

New features:

- Add equilibrationRotationRange, equilibrationTranslationRange and
equilibrationBoxRadius parameters to tune equilibration
performance
- Add support to correctly run simulations with PELE interstep reports and trajectories

Bug fixes:

- Fix bug reading the ligand information in the adaptiveSampling main,
which caused to set the equilibration box in the center of mass of the
whole system

New features:

- Use residue numbers and chain names in clustering, which makes possible
to run protein-protein simulations
- The plotAdaptive script now accepts a path to the simulation folder and
has an option to skip the first step, or a number of steps when plotting

Bug fixes:

- Fix bugs running MD simulations without ligand after the changes in
previous version

New features:

- Add annotations to plotAdaptive, which show the origin (epoch, trajectory and snapshot) of the plot points
- Parametrize more than one ligand in MD simulations
- Include confactors in MD simulations
- MD simulations can now be extended in time
- The plotAdaptive script now accepts a path to the simulation folder and
has an option to skip the first step when plotting

Bug fixes:

- Fix bug ignoring ligandName parameter in the simulation block

Behaviour changes from previous version:

- Modify plotAdaptive to generate the plots using matplotlib and not rely on gnuplot
- Raise separate and more informative errors for the cases of input file not existing, resname selection incorrect, input file in text file but not pdb and topology mismatching for binary files
- Constrain the heavy atoms in the minimization run at the begging of the
epochs in MD simulation, to preserve similiraty with the original
cluster