Index

A

align_structures() (in module analyze_foldamers.ensembles.cluster) analyze_foldamers.ensembles.cluster module analyze_foldamers.ensembles.cluster_torsion module analyze_foldamers.parameters.angle_distributions module, [1], [2]

analyze_foldamers.parameters.bond_distributions module analyze_foldamers.parameters.helical_fitting module analyze_foldamers.utilities.snapshot module

C

calc_2d_distribution() (in module analyze_foldamers.parameters.angle_distributions) calc_bond_angle_distribution() (in module analyze_foldamers.parameters.angle_distributions) calc_bond_length_distribution() (in module analyze_foldamers.parameters.bond_distributions) calc_ramachandran() (in module analyze_foldamers.parameters.angle_distributions)

calc_torsion_distribution() (in module analyze_foldamers.parameters.angle_distributions) calculate_p2() (in module analyze_foldamers.parameters.helical_fitting) cluster_torsions_DBSCAN() (in module analyze_foldamers.ensembles.cluster_torsion) cluster_torsions_KMedoids() (in module analyze_foldamers.ensembles.cluster_torsion) concatenate_trajectories() (in module analyze_foldamers.ensembles.cluster)

F

filter_distances() (in module analyze_foldamers.ensembles.cluster)

fit_ramachandran_data() (in module analyze_foldamers.parameters.angle_distributions)

G

get_cluster_medoid_positions_DBSCAN() (in module analyze_foldamers.ensembles.cluster) get_cluster_medoid_positions_KMedoids() (in module analyze_foldamers.ensembles.cluster) get_cluster_medoid_positions_OPTICS() (in module analyze_foldamers.ensembles.cluster) get_helical_data() (in module analyze_foldamers.parameters.helical_fitting)

get_helical_parameters() (in module analyze_foldamers.parameters.helical_fitting) get_representative_structures() (in module analyze_foldamers.ensembles.cluster) get_rmsd_matrix() (in module analyze_foldamers.ensembles.cluster) get_torsion_matrix() (in module analyze_foldamers.ensembles.cluster_torsion)

M

make_cluster_distance_plots() (in module analyze_foldamers.ensembles.cluster) make_silhouette_plot() (in module analyze_foldamers.ensembles.cluster) module analyze_foldamers.ensembles.cluster analyze_foldamers.ensembles.cluster_torsion analyze_foldamers.parameters.angle_distributions, [1], [2] analyze_foldamers.parameters.bond_distributions analyze_foldamers.parameters.helical_fitting analyze_foldamers.utilities.snapshot

O

orient_along_z_axis() (in module analyze_foldamers.parameters.helical_fitting)

S

show_helical_fit() (in module analyze_foldamers.parameters.helical_fitting)

T

take_snapshot() (in module analyze_foldamers.utilities.snapshot)

W

write_medoids_to_file() (in module analyze_foldamers.ensembles.cluster)