Welcome to Fragmenstein’s documentation!

Contents:

• Fragmenstein
  • Stitched molecules
  • Quick links:
  • Classes
    • Combine
    • Place
    • RDkit only and OpenMM
    • Examples
    • Demo data
  • Other features
  • Installation
    • Fragmenstein and dependencies
    • Requires Pyrosetta
  • Origin
  • Command line interface
    • Specific cases
  • Authors
  • See Also
• fragmenstein package
  • Subpackages
    • fragmenstein.monster package
      • Monster
      • fragmenstein.monster.bond_provenance module
      • fragmenstein.monster.positional_mapping module
      • fragmenstein.monster.unmerge_mapper module
      • fragmenstein.monster.mcs_mapping module
    • fragmenstein.igor package
      • Igor
      • fragmenstein.igor.pyrosetta_import submodule
    • fragmenstein.victor package
      • Victor
      • MinimalPDBParser
    • fragmenstein.walton package
      • Walton
    • MultiVictorPlacement class
      • MultiVictorPlacement
    • fragmenstein.laboratory package
      • Laboratory
    • fragmenstein.mpro package
      • MProVictor
      • fetch_postera()
      • read_postera()
    • fragmenstein.cli package
      • main()
    • fragmenstein.branding submodule
      • Module contents
    • fragmenstein.m_rmsd submodule
      • Module contents
    • fragmenstein.branding submodule
      • Module contents
  • Module contents
• Discussion
  • Covalent
  • Monster
  • Warheads
    • Untested backdoor
  • Combined RMSD
  • Work in progress
  • 3D Viewing
  • 1
  • 2
  • 3
  • X
  • Generalised potentials
  • Examples
    • Config
      • Logging
      • Pyrosetta
      • Output path
      • Hits
    • Template
    • Merge
    • Troubleshooting
      • Ligand not in template
      • Too many results
      • Inspect
      • Protonation
      • Hydrogen in hits
      • That is taken!
      • Equal solutions
    • Advanced
      • Warheads
      • Monster
    • Michelanglo
      • Waters
  • Victor
    • Combine vs. Place
    • Class attributes
    • Class methods
    • Example
    • Methods for inheritance
    • Coordinate constraint
  • Igor
  • Linking
    • Choosing
    • Joining
  • Covid and Fragmenstein
    • Custom class
    • Over-inspired problem
    • Regen data
  • 0.15 - 21/2/2024
    • Added
    • Changed
  • Logging
  • Error
  • Steps
  • Monster entrypoints
  • Names
  • Overlapping rings
  • Other
  • Prerequisite
    • Template
    • Compound extraction
  • Compound merger generation
  • Tabulate
  • Molecule properties
    • SDFile
    • Binary
    • Custom
  • Results reproducibility.
  • Three modes
  • Predicting new followups
  • Merging
  • Ring collapse
    • Nitty Gritty
  • Logging
  • Valence
  • Warhead harmonisation
  • Mad ones
  • Fused rings
  • Allenes
  • Code caveat
  • Fragmenstein
    • Description
    • Mapping modes
      • Full merging
      • Partial mapping
    • No merging
      • Comparison
    • Covalent
    • Knows its past
    • Projection
    • Placing
      • Imperfect projection
  • Custom mapping for Monster
    • SpecialCompareAtoms
    • Filters
    • Example
  • History
  • Mapping
  • Removing the ones that do not map equally
  • Fragmenstein — full merger
    • Algorithm
    • Merger
    • Elemental changes
    • Example
    • Issues to be aware of
      • Non-overlapping fragments
      • More than 4 templates
• Notes
  • Troubleshooting example
  • TRY-UNI-714a760b-6
  • Experiment: heavily distorted molecule
  • Resonance
  • Pipe dream
  • No PyRosetta
  • Experiment: GTP to GDP
  • Download HRAS GTP
  • Download
  • Save the apo structure
  • Colour
  • Classes calling classes
  • Red Herring test

Indices and tables

• Index

• Module Index

• Search Page