Optimisation
============

A package of the optimisation classes used in `CGExplore`.

Energy calculators
------------------

- :doc:`CGOMMSinglePoint <_autosummary/cgexplore.optimisation.CGOMMSinglePoint>`

Geometry optimisations
----------------------

- :doc:`CGOMMOptimizer <_autosummary/cgexplore.optimisation.CGOMMOptimizer>`

Dynamics
--------

- :doc:`CGOMMDynamics <_autosummary/cgexplore.optimisation.CGOMMDynamics>`
- :doc:`OMMTrajectory <_autosummary/cgexplore.optimisation.OMMTrajectory>`


Modular functions for geometry optimisation workflows
-----------------------------------------------------

Note that variations of these exist in `the scram module <scram.html>`_ and
`the system optimisation module <systems_optimisation.html>`_, which will be
redeveloped in the future.


- :doc:`optimise_ligand <_autosummary/cgexplore.utilities.optimise_ligand>`
- :doc:`run_constrained_optimisation <_autosummary/cgexplore.utilities.run_constrained_optimisation>`
- :doc:`run_optimisation <_autosummary/cgexplore.utilities.run_optimisation>`
- :doc:`run_soft_md_cycle <_autosummary/cgexplore.utilities.run_soft_md_cycle>`
- :doc:`shift_beads <_autosummary/cgexplore.utilities.shift_beads>`
- :doc:`soften_forcefield <_autosummary/cgexplore.utilities.soften_forcefield>`
- :doc:`yield_near_models <_autosummary/cgexplore.utilities.yield_near_models>`
- :doc:`yield_shifted_models <_autosummary/cgexplore.utilities.yield_shifted_models>`