New release

Changelist:

Jupyter notebook

1. Added intro (notebook name + what pipeline does) and hyperlinks to steps
2. Refactored imports - explained with comments, removed not necessary ones and reordered
3. Refactored too long (scrollable) lines
4. Renumbered major steps
5. Fixed babel warnings
6. Refactored method to divide clusters
7. Refactored method to convert pdb to orca
8. Refactored method to extract Orca energies

Docker image

1. Removed unnecessary software packages
2. Added init.sh script which initialises the environment for computation
3. Reduced size from 7GB to ~2.7GB

Other

1. Added Orca documentation
2. Added Gromacs documentation
3. Modularised ParmtSNEcv package to individual image