boltzkit.evaluation.molecular_eval

Classes

BondAngleEval

BondLengthEval

DihedralAngleEval

TicaEval

TorsionMarginalEval

class boltzkit.evaluation.molecular_eval.TorsionMarginalEval[source]

Bases: Evaluation

requirements: list[Literal['samples_true', 'samples_pred', 'true_samples_target_log_prob', 'pred_samples_target_log_prob', 'true_samples_model_log_prob', 'pred_samples_model_log_prob']] = ['samples_pred', 'samples_true']
__init__(topology: ~mdtraj.core.topology.Topology, vis_mode: ~boltzkit.utils.histogram.VisualizationMode = <function plot_as_log_density>, include_pdf: bool = True, include_true_histograms: bool = True, include_pred_histograms: bool = True, histogram_metrics: tuple[~boltzkit.evaluation.sample_based.histogram_comparison.HistogramMetric] = [<function get_histogram_fwd_kullback_leibler>])[source]
class boltzkit.evaluation.molecular_eval.BondAngleEval[source]

Bases: Evaluation

requirements: list[Literal['samples_true', 'samples_pred', 'true_samples_target_log_prob', 'pred_samples_target_log_prob', 'true_samples_model_log_prob', 'pred_samples_model_log_prob']] = ['samples_pred', 'samples_true']
__init__(topology: ~mdtraj.core.topology.Topology, z_matrix: list[tuple[int, int, int, int]], vis_mode: ~boltzkit.utils.histogram.VisualizationMode = <function plot_as_log_density>, include_pdfs: bool = True, include_true_histograms: bool = False, include_pred_histograms: bool = False)[source]
class boltzkit.evaluation.molecular_eval.DihedralAngleEval[source]

Bases: Evaluation

requirements: list[Literal['samples_true', 'samples_pred', 'true_samples_target_log_prob', 'pred_samples_target_log_prob', 'true_samples_model_log_prob', 'pred_samples_model_log_prob']] = ['samples_pred', 'samples_true']
__init__(topology: ~mdtraj.core.topology.Topology, z_matrix: list[tuple[int, int, int, int]], vis_mode: ~boltzkit.utils.histogram.VisualizationMode = <function plot_as_log_density>, include_pdfs: bool = True, include_true_histograms: bool = False, include_pred_histograms: bool = False, histogram_metrics: tuple[~boltzkit.evaluation.sample_based.histogram_comparison.HistogramMetric] = [<function get_histogram_fwd_kullback_leibler>], include_individual_hist_metrics: bool = False, include_aggregated_hist_metrics: bool = True)[source]
class boltzkit.evaluation.molecular_eval.TicaEval[source]

Bases: Evaluation

requirements: list[Literal['samples_true', 'samples_pred', 'true_samples_target_log_prob', 'pred_samples_target_log_prob', 'true_samples_model_log_prob', 'pred_samples_model_log_prob']] = ['samples_pred', 'samples_true']
__init__(topology: Topology, tica_model: TicaModelWithLengthScale | TransferOperatorModel, vis_mode: VisualizationMode = <function plot_as_log_density>, include_pdf: bool = True, include_true_histogram: bool = True, include_pred_histogram: bool = True, plot_pred_in_true_range: bool = True)[source]
class boltzkit.evaluation.molecular_eval.BondLengthEval[source]

Bases: Evaluation

requirements: list[Literal['samples_true', 'samples_pred', 'true_samples_target_log_prob', 'pred_samples_target_log_prob', 'true_samples_model_log_prob', 'pred_samples_model_log_prob']] = ['samples_pred', 'samples_true']
__init__(topology: ~mdtraj.core.topology.Topology, z_matrix: list[tuple[int, int, int, int]], vis_mode: ~boltzkit.utils.histogram.VisualizationMode = <function plot_as_density>, include_pdfs: bool = True, include_true_histograms: bool = False, include_pred_histograms: bool = False, max_histogram_bond_length: float | None = None)[source]