fit_priors.py

mlcg_tk.scripts.fit_priors.compute_statistics(dataset_name, names, tag, save_dir, stride, batch_size, prior_tag, prior_builders, embedding_map, statistics_tag=None, device='cpu', save_figs=True, save_sample_statistics=False, weights_template_fn=None, mol_num_batches=1)[source]

Computes structural features and accumulates statistics on dataset samples

Parameters:

  • dataset_name (str) – Name given to specific dataset

  • names (List[str]) – List of sample names

  • tag (str) – Label given to all output files produced from dataset

  • save_dir (str) – Path to directory from which input will be loaded and to which output will be saved

  • stride (int) – Integer by which to stride frames

  • batch_size (int) – Number of frames to take per batch

  • prior_tag (str) – String identifying the specific combination of prior terms

  • prior_builders (List[PriorBuilder]) – List of PriorBuilder objects and their corresponding parameters

  • embedding_map (CGEmbeddingMap) – Mapping object

  • statistics_tag (Optional[str]) – String differentiating parameters used for statistics computation

  • device (str) – Device on which to run delta force calculations

  • save_sample_statistics (bool) – If true, will save individual list of prior builders with accumulated statistics of one molecule

  • save_figs (bool) – Whether to plot histograms of computed statistics

  • weights_template_fn (Optional[str]) – Template file location of weights to use for accumulating statistics

  • mol_num_batches (Optional[int]) – If greater than 1, will save each molecule data into the specified number of batches that will be treated as different samples

mlcg_tk.scripts.fit_priors.fit_priors(save_dir, prior_tag, embedding_map, temperature)[source]

Fits potential energy estimates to computed statistics

Parameters:

  • save_dir (str) – Path to directory from which input will be loaded and to which output will be saved

  • prior_tag (str) – String identifying the specific combination of prior terms

  • embedding_map (CGEmbeddingMap) – Mapping object

  • temperature (float) – Temperature from which beta value will be computed