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The `optimizers` module: optimization of the model

The `optimizers` module provides a number of methods to optimize a model. The molecular pdf is optimized with respect to the selected coordinates, and the optimized coordinates are returned.

These optimizers are often used to implement the variable target function method, for example in the `automodel` and `loopmodel` classes. See Section 6.12 for an example.

Subsections

- conjugate_gradients() — optimize atoms given restraints, with CG
- quasi_newton() — optimize atoms with quasi-Newton minimization
- molecular_dynamics() — optimize atoms given restraints, with MD
- actions.write_structure() — write out the model coordinates
- actions.trace() — write out optimization energies, etc
- actions.charmm_trajectory() — write out a CHARMM trajectory
- User-defined optimizers