Simulation layer

Modules

• Simulation object
• Data objects
  • Data objects factory
  • Data objects
• Primitives
• Simulation variables
• Forces
  • Chain tether forces
  • Bond angle potential
  • Dihedral angle potentials
  • Chirality potential
  • Nonlocal function interface
  • Go-model native contacts potential
  • Electrostatic forces
  • Pauli exclusion forces
  • Pseudo-improper-dihedral custom potential
  • Quasi-adiabatic custom potential
• Kernels
  • Harmonic potential kernel
  • Lennard-Jones potential kernel
  • Shifted and truncated Lennard-Jones potential kernel
  • Sidechain Lennard-Jones potential kernel
• Verlet list
• Coordination stats
• Physical state object
• Integrators
  • Leapfrog integrator
  • Predictor-corrector integrator with Langevin noise
• Hooks
  • PDB export hook
  • Position diff hook
  • Progress bar hook