Code for computing cut-based free energy profiles, and optimal reaction coordinates within that framework.
This code employs scipy’s weave, so C/OMP compatability is required. Most machines should have this functionality by default.
> Choose best search method in optimize > Add functionality for saving/loading the state of VariableCoordinate
| contact_reaction_coordinate(trajectory, weights) | Computes a residue-contact based reaction coordinate. |
| VariableCoordinate(rxn_coordinate_function, ...) | Class that contains methods for calculating cut-based free energy profiles based on a reaction coordinate mapping that takes variable parameters. |
| CutCoordinate(counts, generators, reactant, ...) | Object containing methods for computing the cut-based free energy profiles of reaction coordinates. |