Valid subpocket connections

[paulaju]

• define valid subpocket connections
• adjust subpocket definitions (centers) such that invalid connections are avoided
• minimum fragment size = 3
• reimplement fix_small_fragments function such that any minimum size can be given as input
• introduce X pool for fragments that are not close to any subpocket center
• refactoring of final fragmentation (more modular)
• fix FP-B1 and FP-B2 connections:
  1. if FP close to GA: assign FP fragment to GA
  2. if not: assign B1/2 fragment to X pool
• discard ligands not occupying AP
• discard remaining ligands with invalid subpocket connections