cctbx.geometry_restraints.energies module

class cctbx.geometry_restraints.energies.energies(sites_cart, unit_cell=None, bond_proxies=None, nonbonded_proxies=None, nonbonded_function=None, angle_proxies=None, dihedral_proxies=None, reference_coordinate_proxies=None, reference_dihedral_manager=None, ncs_dihedral_manager=None, den_manager=None, chirality_proxies=None, planarity_proxies=None, parallelity_proxies=None, bond_similarity_proxies=None, ramachandran_manager=None, external_energy_function=None, compute_gradients=True, gradients=None, disable_asu_cache=False, normalization=False, extension_objects=[])

Bases: energies

angle_deviations()

angle_deviations_weighted()

angle_deviations_z()

Calculate rmsz of angles deviations

Compute rmsz, the Root-Mean-Square of the z-scors for a set of data using z_i = {x_i - mu / sigma} and rmsz = sqrt(mean(z*z))

Compute rmsz, the Root-Mean-Square of the z-scors for a set of data using z_i = {x_i - mu / sigma} and rmsz = sqrt(mean(z*z)) x_i: atcual bond angle mu: geometry restraints mean sigma: geometry restraints standard deviation z_i: z-score for bond i z: array of z_i

The sigma and the (x_i - mu) are model constrains, geometry restraints. They function extracts from self, not calculated from data.

Returns:

a_rmsz: rmsz, root mean square of the z-scors of all angles a_z_min/max: min/max values of z-scors

bond_deviations()

bond_deviations_weighted()

bond_deviations_z()

Calculate rmsz of bond deviations

Compute rmsz, the Root-Mean-Square of the z-scors for a set of data using z_i = {x_i - mu / sigma} and rmsz = sqrt(mean(z*z)) x_i: atcual bond length mu: geometry restraints mean sigma: geometry restraints standard deviation z_i: z-score for bond i z: array of z_i

The sigma and the (x_i - mu) are model constrains, geometry restraints. This function extracts from self, not calculated from data.

Returns:

b_rmsz: rmsz, root mean square of the z-scors of all bonds b_z_min/max: min/max abolute values of z-scors

chirality_deviations()

dihedral_deviations()

get_angle_outliers(sites_cart, sigma_threshold=4)

get_bond_outliers(sites_cart, sigma_threshold=4)

get_chirality_outliers(sites_cart, sigma_threshold=4)

get_dihedral_outliers(sites_cart, sigma_threshold=4)

get_filtered_n_angle_proxies()

get_filtered_n_bond_proxies()

get_filtered_n_dihedral_proxies()

get_filtered_n_planarity_proxies()

nonbonded_deviations()

nonbonded_distances()

parallelity_deviations()

planarity_deviations()

reference_dihedral_deviations()

show(f=None, prefix='')