Milestone: User Requests

This milestone includes various wanted features from currently open issues.

Linked Issues:

• Include guards
  #244

• Clean up unused variables
  #253

• Bringing back option to output a logfile
  #164

• Implementing B and Si parameters
  #171

• Support re-scoring of multi-ligand PDBQT
  #327

• Local optimizer (--local_only) with direct interactions instead of grids
  #67
  #232

• Computing unbound energies with direct interactions instead of grids
  #362

• Allow manipulation of scoring function with custom coefficients
  #103

• Allow definition of additional parameters (for metal, unsupported elements, etc.)
  #322

• Flexible hydrated docking
  #275