Index

_

__init__() (afrc.AnalyticalFRC method) (afrc.polymer_models.fjc.FreelyJointedChain method) (afrc.polymer_models.frc.FreelyRotatingChain method) (afrc.polymer_models.nudep_saw.NuDepSAW method) (afrc.polymer_models.saw.SAW method) (afrc.polymer_models.wlc.WormLikeChain method) (afrc.polymer_models.wlc2.WormLikeChain2 method)

A

afrc.ensemble module afrc.ensemble_report module

AnalyticalFRC (class in afrc) assessed (afrc.ensemble_report.EnsembleReport property)

B

bond_angle_cosine (afrc.ensemble_report.ModelExpectations attribute)

bond_length (afrc.ensemble_report.ModelExpectations attribute)

C

Check (class in afrc.ensemble_report) check_ensemble() (afrc.AnalyticalFRC method) (afrc.polymer_models.fjc.FreelyJointedChain method) (afrc.polymer_models.frc.FreelyRotatingChain method) (afrc.polymer_models.nudep_saw.NuDepSAW method) (afrc.polymer_models.saw.SAW method) (afrc.polymer_models.wlc.WormLikeChain method) (afrc.polymer_models.wlc2.WormLikeChain2 method)

checks (afrc.ensemble_report.EnsembleReport attribute) compare_ensemble_to_gaussian_model() (in module afrc.ensemble_report) compare_ensemble_to_model() (in module afrc.ensemble_report) context (afrc.ensemble_report.EnsembleReport attribute) contour_length_per_residue (afrc.ensemble_report.ModelExpectations attribute)

D

discrete_worm_like_chain_msd() (in module afrc.ensemble)

E

end_to_end_distribution (afrc.ensemble_report.ModelExpectations attribute)

end_to_end_label (afrc.ensemble_report.ModelExpectations attribute) EnsembleReport (class in afrc.ensemble_report)

F

failed (afrc.ensemble_report.EnsembleReport property) format() (afrc.ensemble_report.EnsembleReport method)

freely_rotating_chain_msd() (in module afrc.ensemble) FreelyJointedChain (class in afrc.polymer_models.fjc) FreelyRotatingChain (class in afrc.polymer_models.frc)

G

gaussian (afrc.ensemble_report.ModelExpectations attribute) gaussian_chain_factor() (in module afrc.ensemble) get_contact_fraction() (afrc.AnalyticalFRC method) get_contact_map() (afrc.AnalyticalFRC method) get_distance_map() (afrc.AnalyticalFRC method) get_end_to_end_distribution() (afrc.AnalyticalFRC method) (afrc.polymer_models.fjc.FreelyJointedChain method) (afrc.polymer_models.frc.FreelyRotatingChain method) (afrc.polymer_models.nudep_saw.NuDepSAW method) (afrc.polymer_models.saw.SAW method) (afrc.polymer_models.wlc.WormLikeChain method) (afrc.polymer_models.wlc2.WormLikeChain2 method) get_internal_scaling() (afrc.AnalyticalFRC method) get_interresidue_distance_distribution() (afrc.AnalyticalFRC method) get_mean_end_to_end_distance() (afrc.AnalyticalFRC method) (afrc.polymer_models.fjc.FreelyJointedChain method) (afrc.polymer_models.frc.FreelyRotatingChain method) (afrc.polymer_models.nudep_saw.NuDepSAW method) (afrc.polymer_models.saw.SAW method) (afrc.polymer_models.wlc.WormLikeChain method) (afrc.polymer_models.wlc2.WormLikeChain2 method) get_mean_hydrodynamic_radius() (afrc.AnalyticalFRC method)

get_mean_interresidue_distance() (afrc.AnalyticalFRC method) get_mean_interresidue_radius_of_gyration() (afrc.AnalyticalFRC method) get_mean_radius_of_gyration() (afrc.AnalyticalFRC method) (afrc.polymer_models.fjc.FreelyJointedChain method) (afrc.polymer_models.frc.FreelyRotatingChain method) (afrc.polymer_models.nudep_saw.NuDepSAW method) (afrc.polymer_models.saw.SAW method) (afrc.polymer_models.wlc2.WormLikeChain2 method) get_mean_squared_distance_map() (afrc.AnalyticalFRC method) (afrc.polymer_models.fjc.FreelyJointedChain method) (afrc.polymer_models.frc.FreelyRotatingChain method) (afrc.polymer_models.nudep_saw.NuDepSAW method) (afrc.polymer_models.saw.SAW method) (afrc.polymer_models.wlc.WormLikeChain method) (afrc.polymer_models.wlc2.WormLikeChain2 method) get_pre_profile() (afrc.AnalyticalFRC method) get_radius_of_gyration_distribution() (afrc.AnalyticalFRC method) get_root_mean_squared_end_to_end_distance() (afrc.polymer_models.fjc.FreelyJointedChain method) (afrc.polymer_models.frc.FreelyRotatingChain method) (afrc.polymer_models.nudep_saw.NuDepSAW method) (afrc.polymer_models.saw.SAW method) (afrc.polymer_models.wlc.WormLikeChain method) (afrc.polymer_models.wlc2.WormLikeChain2 method)

M

mean_squared_distance_map() (in module afrc.ensemble) mean_squared_distances (afrc.ensemble_report.ModelExpectations attribute) model_name (afrc.ensemble_report.EnsembleReport attribute) (afrc.ensemble_report.ModelExpectations attribute)

ModelExpectations (class in afrc.ensemble_report) module afrc.ensemble afrc.ensemble_report

N

n_conformations (afrc.ensemble_report.EnsembleReport attribute) n_pair_conformations (afrc.ensemble_report.EnsembleReport attribute) n_residues (afrc.ensemble_report.EnsembleReport attribute)

name (afrc.ensemble_report.Check attribute) notes (afrc.ensemble_report.EnsembleReport attribute) (afrc.ensemble_report.ModelExpectations attribute) NuDepSAW (class in afrc.polymer_models.nudep_saw)

P

p_of_r_resolution (afrc.AnalyticalFRC attribute)

passed (afrc.ensemble_report.Check attribute) (afrc.ensemble_report.EnsembleReport property)

R

reference_re (afrc.ensemble_report.ModelExpectations attribute) reference_re_label (afrc.ensemble_report.ModelExpectations attribute)

reference_rg (afrc.ensemble_report.ModelExpectations attribute) reference_rg_label (afrc.ensemble_report.ModelExpectations attribute)

S

sample_conformations() (afrc.AnalyticalFRC method) (afrc.polymer_models.fjc.FreelyJointedChain method) (afrc.polymer_models.frc.FreelyRotatingChain method) (afrc.polymer_models.nudep_saw.NuDepSAW method) (afrc.polymer_models.saw.SAW method) (afrc.polymer_models.wlc.WormLikeChain method) (afrc.polymer_models.wlc2.WormLikeChain2 method) sample_end_to_end_distribution() (afrc.AnalyticalFRC method) (afrc.polymer_models.fjc.FreelyJointedChain method) (afrc.polymer_models.frc.FreelyRotatingChain method) (afrc.polymer_models.nudep_saw.NuDepSAW method) sample_freely_jointed_chain() (in module afrc.ensemble) sample_freely_rotating_chain() (in module afrc.ensemble) sample_gaussian_chain() (in module afrc.ensemble)

sample_inter_residue_distance_distribution() (afrc.AnalyticalFRC method) sample_radius_of_gyration_distribution() (afrc.AnalyticalFRC method) sample_worm_like_chain() (in module afrc.ensemble) save_conformations() (in module afrc.ensemble) save_ensemble() (afrc.AnalyticalFRC method) (afrc.polymer_models.fjc.FreelyJointedChain method) (afrc.polymer_models.frc.FreelyRotatingChain method) (afrc.polymer_models.nudep_saw.NuDepSAW method) (afrc.polymer_models.saw.SAW method) (afrc.polymer_models.wlc.WormLikeChain method) (afrc.polymer_models.wlc2.WormLikeChain2 method) SAW (class in afrc.polymer_models.saw) seq (afrc.AnalyticalFRC attribute) structural (afrc.ensemble_report.Check attribute) summary (afrc.ensemble_report.Check attribute)

V

values (afrc.ensemble_report.Check attribute)

W

worm_like_chain (afrc.AnalyticalFRC attribute) worm_like_chain_discretization() (in module afrc.ensemble) worm_like_chain_msd() (in module afrc.ensemble) WormLikeChain (class in afrc.polymer_models.wlc)

WormLikeChain2 (class in afrc.polymer_models.wlc2) write_ensemble() (in module afrc.ensemble) write_multimodel_pdb() (in module afrc.ensemble) write_pdb() (in module afrc.ensemble) write_xtc() (in module afrc.ensemble)