Index

_

__init__() (soursop.ssbme.BME method) (soursop.ssbme.BMECustom method) (soursop.ssbme.iBME method) (soursop.sscoper.COPER method) (soursop.sscoper.iCOPER method) (soursop.sspre.SSPRE method) (soursop.sstrajectory.SSTrajectory method)

B

BME (class in soursop.ssbme) BMECustom (class in soursop.ssbme)

BMECustomResult (class in soursop.ssbme) BMEResult (class in soursop.ssbme)

C

calculate_all_CA_distances() (soursop.ssprotein.SSProtein method) calculated_values (soursop.ssbme.BMECustomResult attribute) (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute) ccap (soursop.ssprotein.SSProtein attribute) chi2_limit (soursop.sscoper.COPERResult attribute) chi2_limit_scan() (in module soursop.sscoper) chi2_limits (soursop.sscoper.COPERScanResult attribute) chi_squared_final (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute) chi_squared_initial (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute) chi_squared_min (soursop.sscoper.COPERResult attribute) chi_squared_values (soursop.ssbme.ThetaScanResult attribute) (soursop.sscoper.COPERScanResult attribute) compute_dihedral_hellingers() (soursop.sssampling.SamplingQuality method)

compute_dihedral_rel_entropy() (soursop.sssampling.SamplingQuality method) compute_frac_helicity() (soursop.sssampling.SamplingQuality method) compute_J3_HN_HA() (in module soursop.ssnmr) compute_joint_hellinger_distance() (in module soursop.sssampling) compute_Nc() (in module soursop.sshdx) compute_Nh() (in module soursop.sshdx) compute_NOE_distances() (in module soursop.ssnmr) compute_pdf() (soursop.sssampling.SamplingQuality method) compute_protection_factors() (in module soursop.sshdx) compute_random_coil_chemical_shifts() (in module soursop.ssnmr) compute_series_of_histograms_along_axis() (soursop.sssampling.SamplingQuality method) constraint_chi_squared() (in module soursop.ssutils) COPER (class in soursop.sscoper) COPERResult (class in soursop.sscoper) COPERScanResult (class in soursop.sscoper) cost_final (soursop.ssbme.BMECustomResult attribute) cost_initial (soursop.ssbme.BMECustomResult attribute)

D

delta_S (soursop.sscoper.COPERResult attribute) diagnostics() (soursop.ssbme.BMECustomResult method) (soursop.ssbme.BMEResult method) (soursop.sscoper.COPERResult method)

E

entropy (soursop.sscoper.COPERResult attribute) entropy_initial (soursop.sscoper.COPERResult attribute)

experiment (soursop.ssbme.BMECustomResult attribute) ExperimentalObservable (class in soursop.ssutils)

F

feasible (soursop.sscoper.COPERResult attribute) feasible_mask (soursop.sscoper.COPERScanResult attribute) find_optimal_theta() (in module soursop.ssutils) fit() (soursop.ssbme.BME method) (soursop.ssbme.BMECustom method) (soursop.ssbme.iBME method) (soursop.sscoper.COPER method) (soursop.sscoper.iCOPER method)

fractional_helicity() (soursop.sssampling.SamplingQuality method)

G

gather_phi_reference_dihedrals() (soursop.sssampling.PrecomputedDihedralInterface method) gather_psi_reference_dihedrals() (soursop.sssampling.PrecomputedDihedralInterface method) generate_PRE_profile() (soursop.sspre.SSPRE method) get_acylindricity() (soursop.ssprotein.SSProtein method) get_all_SASA() (soursop.ssprotein.SSProtein method) get_all_to_all_2d_trj_comparison() (soursop.sssampling.SamplingQuality method) get_all_to_all_trj_comparisons() (soursop.sssampling.SamplingQuality method) get_amino_acid_sequence() (soursop.ssprotein.SSProtein method) get_angle_decay() (soursop.ssprotein.SSProtein method) get_angles() (soursop.ssprotein.SSProtein method) get_asphericity() (soursop.ssprotein.SSProtein method) get_bounds() (soursop.ssutils.ExperimentalObservable method) get_CA_index() (soursop.ssprotein.SSProtein method) get_clusters() (soursop.ssprotein.SSProtein method) get_contact_map() (soursop.ssprotein.SSProtein method) get_D_vector() (soursop.ssprotein.SSProtein method) get_degree_bins() (soursop.sssampling.SamplingQuality method) get_dihedral_mutual_information() (soursop.ssprotein.SSProtein method) get_distance_map() (soursop.ssprotein.SSProtein method) get_end_to_end_distance() (soursop.ssprotein.SSProtein method) get_end_to_end_vs_rg_correlation() (soursop.ssprotein.SSProtein method) get_gyration_tensor() (soursop.ssprotein.SSProtein method) get_hydrodynamic_radius() (soursop.ssprotein.SSProtein method) get_ibme_stats() (soursop.ssbme.iBME method) get_ibme_weights() (soursop.ssbme.iBME method) get_icoper_stats() (soursop.sscoper.iCOPER method) get_icoper_weights() (soursop.sscoper.iCOPER method) get_inter_residue_atomic_distance() (soursop.ssprotein.SSProtein method) get_inter_residue_COM_distance() (soursop.ssprotein.SSProtein method)

get_inter_residue_COM_vector() (soursop.ssprotein.SSProtein method) get_interchain_contact_map() (soursop.sstrajectory.SSTrajectory method) get_interchain_distance() (soursop.sstrajectory.SSTrajectory method) get_interchain_distance_map() (soursop.sstrajectory.SSTrajectory method) get_internal_scaling() (soursop.ssprotein.SSProtein method) get_internal_scaling_RMS() (soursop.ssprotein.SSProtein method) get_local_collapse() (soursop.ssprotein.SSProtein method) get_local_heterogeneity() (soursop.ssprotein.SSProtein method) get_local_to_global_correlation() (soursop.ssprotein.SSProtein method) get_multiple_CA_index() (soursop.ssprotein.SSProtein method) get_overall_asphericity() (soursop.sstrajectory.SSTrajectory method) get_overall_hydrodynamic_radius() (soursop.sstrajectory.SSTrajectory method) get_overall_radius_of_gyration() (soursop.sstrajectory.SSTrajectory method) get_overlap_concentration() (soursop.ssprotein.SSProtein method) get_polymer_scaled_distance_map() (soursop.ssprotein.SSProtein method) get_prolateness() (soursop.ssprotein.SSProtein method) get_Q() (soursop.ssprotein.SSProtein method) get_radius_of_gyration() (soursop.ssprotein.SSProtein method) get_regional_SASA() (soursop.ssprotein.SSProtein method) get_residue_atom_indices() (soursop.ssprotein.SSProtein method) get_residue_COM() (soursop.ssprotein.SSProtein method) get_residue_mass() (soursop.ssprotein.SSProtein method) get_RMSD() (soursop.ssprotein.SSProtein method) get_scaling_exponent() (soursop.ssprotein.SSProtein method) get_secondary_structure_BBSEG() (soursop.ssprotein.SSProtein method) get_secondary_structure_DSSP() (soursop.ssprotein.SSProtein method) get_sidechain_alignment_angle() (soursop.ssprotein.SSProtein method) get_site_accessibility() (soursop.ssprotein.SSProtein method) get_t() (soursop.ssprotein.SSProtein method)

H

hellinger_distance() (in module soursop.sssampling)

hellingers_distances() (soursop.sssampling.SamplingQuality method)

I

iBME (class in soursop.ssbme) ibme_iterations (soursop.ssbme.BMEResult attribute) iCOPER (class in soursop.sscoper)

icoper_iterations (soursop.sscoper.COPERResult attribute) initial_weights (soursop.ssbme.BMECustomResult attribute) (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute)

K

karplus() (in module soursop.ssnmr)

kl_divergence_values (soursop.ssbme.ThetaScanResult attribute) (soursop.sscoper.COPERScanResult attribute)

L

lambdas (soursop.ssbme.BMEResult attribute)

length (soursop.ssprotein.SSProtein attribute) (soursop.sstrajectory.SSTrajectory attribute)

M

mean_delta_G_kT (soursop.sscoper.COPERResult attribute) message (soursop.ssbme.BMECustomResult attribute) (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute) metadata (soursop.ssbme.BMECustomResult attribute) (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute)

method (soursop.ssbme.ThetaScanResult attribute) (soursop.sscoper.COPERScanResult attribute) module soursop.sshdx soursop.ssnmr soursop.sssampling

N

n_frames (soursop.ssprotein.SSProtein attribute) (soursop.sstrajectory.SSTrajectory attribute) n_iterations (soursop.ssbme.BMECustomResult attribute) (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute)

n_proteins (soursop.sstrajectory.SSTrajectory attribute) n_residues (soursop.ssprotein.SSProtein attribute) ncap (soursop.ssprotein.SSProtein attribute) noe_ensemble_average() (in module soursop.ssnmr)

O

observables (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute) offset (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute)

optimal_chi2_limit (soursop.sscoper.COPERScanResult attribute) optimal_idx (soursop.ssbme.ThetaScanResult attribute) (soursop.sscoper.COPERScanResult attribute) optimal_theta (soursop.ssbme.ThetaScanResult attribute)

P

phi (soursop.ssbme.BMECustomResult attribute) (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute) phi_values (soursop.ssbme.ThetaScanResult attribute) (soursop.sscoper.COPERScanResult attribute) PrecomputedDihedralInterface (class in soursop.sssampling) predict() (soursop.ssbme.BME method) (soursop.ssbme.BMECustom method) (soursop.ssbme.BMECustomResult method) (soursop.ssbme.BMEResult method) (soursop.ssbme.iBME method) (soursop.sscoper.COPER method) (soursop.sscoper.COPERResult method) (soursop.sscoper.iCOPER method)

print_diagnostics() (soursop.ssbme.BMECustomResult method) (soursop.ssbme.BMEResult method) (soursop.sscoper.COPERResult method) print_residues() (soursop.ssprotein.SSProtein method) print_summary() (soursop.ssbme.ThetaScanResult method) (soursop.sscoper.COPERScanResult method)

Q

quality_plot() (soursop.sssampling.SamplingQuality method)

R

ref_pdfs() (soursop.sssampling.SamplingQuality method) rel_entropy() (in module soursop.sssampling) relative_entropy() (in module soursop.ssutils) reset_cache() (soursop.ssprotein.SSProtein method)

resid_with_CA (soursop.ssprotein.SSProtein attribute) residue_index_list (soursop.ssprotein.SSProtein attribute) results (soursop.ssbme.ThetaScanResult attribute) (soursop.sscoper.COPERScanResult attribute)

S

sample_angles() (soursop.sssampling.PrecomputedDihedralInterface method) SamplingQuality (class in soursop.sssampling) scale (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute) scan_chi2_limit() (soursop.sscoper.COPER method) (soursop.sscoper.iCOPER method) scan_theta() (soursop.ssbme.BME method) (soursop.ssbme.BMECustom method) (soursop.ssbme.iBME method) soursop.sshdx module

soursop.ssnmr module soursop.sssampling module SSPRE (class in soursop.sspre) SSProtein (class in soursop.ssprotein) SSTrajectory (class in soursop.sstrajectory) success (soursop.ssbme.BMECustomResult attribute) (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute)

T

theta (soursop.ssbme.BMECustomResult attribute) (soursop.ssbme.BMEResult attribute) theta_scan() (in module soursop.ssbme)

theta_values (soursop.ssbme.ThetaScanResult attribute) ThetaScanResult (class in soursop.ssbme) trj_pdfs() (soursop.sssampling.SamplingQuality method)

V

validate_reweighting_inputs() (in module soursop.ssutils)

validate_weights() (in module soursop.ssutils)

W

weighted_corr() (in module soursop.ssutils) weighted_linear_regression() (in module soursop.ssutils) weighted_mean() (in module soursop.ssutils) weighted_rms() (in module soursop.ssutils)

weighted_std() (in module soursop.ssutils) weights (soursop.ssbme.BMECustomResult attribute) (soursop.ssbme.BMEResult attribute) (soursop.sscoper.COPERResult attribute)