Discussion

Contents:

• Pythonic usage
  • Prerequisites
  • Classes
  • Combine
  • Place
  • RDkit only and OpenMM
    • Score
    • Interactions
    • E-amide isomerism
• Installation
  • Fragmenstein and dependencies
  • Requires Pyrosetta
    • Modern way
    • Details from former way
      • PLIP
• Examples
  • View
  • Monster
    • Demo data
  • Config
    • Logging
    • Pyrosetta
    • Output path
    • Hits
  • Template/receptor
  • Merge
  • Stitched monsters and analogues-by-catalogue
  • Subclassing
  • Troubleshooting
    • Ligand not in template
    • Too many results
    • Inspect
    • Protonation
    • Hydrogen in hits
    • That is taken!
    • Equal solutions
  • Advanced
    • Warheads
    • Monster
  • Michelanglo
    • Waters
• Workings
  • Overview
    • Manin routes of Fragmenstein
    • Features and functionality
    • Atomic mapping
  • Class hierarchy
  • Combination process
    • Linking process
    • Rectification process
  • Placement process
  • Minimisation process
  • Pipeline
  • ∆Gbind
  • History
  • Other features
• Number of parent hits
• Catalogue and fragment sociability
• Polycyclic compounds
• Angles
• Authors
• Command line interface
  • Utils
  • Monster combine
  • Monster place
  • Victor combine
  • Victor place
  • Laboratory and pipeline subcommands
    • Laboratory combine
    • Laboratory place
    • Pipeline
  • Environment variables
  • Example slurm script
• It is failing
• I do not know what parent hits to use
• I want to do something complicated
• Linkers
• Wrong tautomer
• Fragmenstein and sterically hindrance
• Large binding sites
• Logging
• Error
• Steps
• 0.15 - 21/2/2024
  • Added
  • Changed
• Linking
• Method
  • Choosing
• Cutoff
  • Linking
  • Linker atom
• Caveat
• Igor
• Covid and Fragmenstein
  • Custom class
  • Over-inspired problem
  • Regen data
• Work in progress
• Generalised potentials
• Combined RMSD
• Results reproducibility.
• Molecule properties
  • SDFile
  • Binary
  • Custom
• Victor
  • Combine vs. Place
  • Class attributes
  • Class methods
  • Example
  • Methods for inheritance
  • Coordinate constraint
• Prerequisite
  • Template
  • Compound extraction
• Compound merger generation
• Tabulate
• Covalent
• Monster
• Warheads
  • Untested backdoor
• 1
• 2
• 3
• X
• Monster entrypoints
• Names
• Overlapping rings
• Other
• 3D Viewing
• Custom mapping for Monster
  • SpecialCompareAtoms
  • Filters
  • Example
• Fragmenstein — full merger
  • Algorithm
  • Merger
  • Elemental changes
  • Example
  • Issues to be aware of
    • Non-overlapping fragments
    • More than 4 templates
• Removing the ones that do not map equally
• Predicting new followups
• Merging
• Ring collapse
  • Nitty Gritty
• Logging
• Valence
• Warhead harmonisation
• Mad ones
• Fused rings
• Allenes
• Code caveat
• Three modes
• History
• Mapping
• Fragmenstein
  • Description
  • Mapping modes
    • Full merging
      • Pros
      • Pro/Con
      • Cons
    • Partial mapping
      • Pros
      • Cons
  • No merging
    • Comparison
  • Covalent
  • Knows its past
  • Projection
  • Placing
    • Imperfect projection