TSCoDe - Transition State Conformational Docker

• Introduction
  • What it is
  • What it does
  • How the embedding works
  • How the ensemble refinement works
  • Extra features
• Installation
  • XTB (recommended for FF/SE)
  • ORCA (optional, recommended for DFT)
  • Gaussian (optional)
  • MOPAC2016 (optional, deprecated)
  • Openbabel
  • TSCoDe
• Usage
  • Input formatting
    • Operators
    • Embedding runs
    • Pairings
  • Good practice and suggested options (work in progress)
• Operators and keywords
  • Operators
  • Keywords
• Examples
  • 1. Generation of a 3D structure from SMILES, conformational search and refinement
  • 1. Trimolecular input
  • 2. Atropisomer rotation
  • 3. Peptide-substrate binding mode
  • 4. Complex embedding with internal and external constraints
• License
• TSCoDe
  • setup module
  • tscode package
    • Subpackages
    • Submodules
    • tscode.algebra module
    • tscode.ase_manipulations module
    • tscode.atropisomer_module module
    • tscode.automep module
    • tscode.dispy_test module
    • tscode.docker module
    • tscode.embedder module
    • tscode.embedder_options module
    • tscode.embeds module
    • tscode.errors module
    • tscode.graph_manipulations module
    • tscode.hypermolecule_class module
    • tscode.modify_settings module
    • tscode.mprof module
    • tscode.multiembed module
    • tscode.nci module
    • tscode.operators module
    • tscode.optimization_methods module
    • tscode.parameters module
    • tscode.pka module
    • tscode.profiler module
    • tscode.pt module
    • tscode.python_functions module
    • tscode.quotes module
    • tscode.reactive_atoms_classes module
    • tscode.run module
    • tscode.settings module
    • tscode.solvents module
    • tscode.tests module
    • tscode.torsion_module module
    • tscode.utils module
    • Module contents