RBFENetworkMap

Plan Relative Binding Free Energy perturbation networks from RDKit molecules.

Given a series of ligands, the package returns a scored, tunable network of alchemical transformations. Every transformation carries a common-core / soft-core partition that satisfies the constraint the whole package is organised around: a transformation has at most one connected soft-core region per side.

Guide

• Quickstart
  • Installation
  • Example data
  • Plan a network
  • Ligands must be co-posed
  • Aligning ligands
• Soft-core repair
  • The constraint
  • The algorithm
  • Why closure size is the cost
  • Termination
  • Rejection
  • The ring cascade is real
  • Auditing a repair
• Scoring
  • Reject versus bad score
  • The linear scorer
  • Other scorers
• Network selection
  • Adaptive pair evaluation
  • The guarantee, stated exactly
  • Cycles
  • Path length
  • Counterpoised (CBFE) edges
  • Clustered planning
  • Reproducing a released behaviour
  • Intermediate ligands
  • Knob precedence
  • Why the n_edges conflict is a hard error
  • Edge budget
  • Diagnostics
  • Cost in machine time
  • Importing an existing map
  • Other planners
• Surgery and replanning
  • Appending a ligand
  • Deleting an edge
  • Merging and concatenating
  • Cyclizing a component
  • Diagnostics-driven replanning
• Intermediate ligands
  • Read this first
  • The generators
  • Posing, and the only thing that certifies it
  • Provenance
  • What leaves the package
  • Tuning
• The Tyk2 variant matrix
  • Which topologies are worth running
  • Optimal design buys precision, not accuracy
  • What soft-core consistency changes for an Amber setup
  • What --cbfe costs, and why the planner never reaches for it
  • What the stranded-core repair changed
  • A known gap in budget allocation
• Command line
  • plan
  • Ligand alignment
  • score
  • replan
  • inspect
  • diagnose
  • report
  • plugins
• Graphical interface
  • The form is the command line
  • What it shows you that the command line cannot
  • Why a second run is faster
  • Running it on a cluster
  • Options
  • What it does not do
• Plugins
  • Lazy registration
  • Writing a mapper
  • Registering it
  • Exporters: the hook into other programs

Reference

• API reference
  • Core
  • Plugins
  • Input and output
  • Visualization
  • Command-line interface
  • Graphical interface

Indices

• Index

• Module Index