Index

A

add_force() (oxdna_simulation.Simulation method) add_force_file() (oxdna_simulation.Simulation method) add_observable() (oxdna_simulation.Simulation method)

add_protein_par() (oxdna_simulation.Simulation method) align() (oxdna_simulation.OxdnaAnalysisTools method) Analysis (class in oxdna_simulation) angle() (oxdna_simulation.OxdnaAnalysisTools method)

B

BaseUmbrellaSampling (class in umbrella_sampling) build() (oxdna_simulation.Simulation method)

build_equlibration_runs() (umbrella_sampling.ComUmbrellaSampling method) build_production_runs() (umbrella_sampling.ComUmbrellaSampling method)

C

centroid() (oxdna_simulation.OxdnaAnalysisTools method) chunk_convergence_analysis() (umbrella_sampling.WhamAnalysis method) com_distance() (oxdna_simulation.OxdnaAnalysisTools method) com_force() (oxdna_simulation.Force static method)

ComUmbrellaSampling (class in umbrella_sampling) concat_all_system_traj() (oxdna_simulation.GenerateReplicas method) conformational_entropy() (oxdna_simulation.OxdnaAnalysisTools method) convergence_analysis() (umbrella_sampling.WhamAnalysis method) current_step() (oxdna_simulation.Analysis method)

D

data_truncated_convergence_analysis() (umbrella_sampling.WhamAnalysis method) decimate() (oxdna_simulation.OxdnaAnalysisTools method)

determine_cv_sign() (oxdna_simulation.OxdnaAnalysisTools method) deviations() (oxdna_simulation.OxdnaAnalysisTools method) distance() (oxdna_simulation.Observable static method)

F

Force (class in oxdna_simulation)

force_energy() (oxdna_simulation.Observable static method)

G

GenerateReplicas (class in oxdna_simulation) get_conf() (oxdna_simulation.Analysis method)

get_conf_count() (oxdna_simulation.Analysis method) get_init_conf() (oxdna_simulation.Analysis method) get_last_conf() (oxdna_simulation.Analysis method)

H

harmonic_trap() (oxdna_simulation.Force static method)

hb_list() (oxdna_simulation.Observable static method)

I

input_file() (oxdna_simulation.Simulation method)

K

kinetic_energy() (oxdna_simulation.Observable static method)

M

make_sequence_dependant() (oxdna_simulation.Simulation method) mean() (oxdna_simulation.OxdnaAnalysisTools method) minify() (oxdna_simulation.OxdnaAnalysisTools method)

morse() (oxdna_simulation.Force static method) multisystem_replica() (oxdna_simulation.GenerateReplicas method) mutual_trap() (oxdna_simulation.Force static method)

O

Observable (class in oxdna_simulation)

oxDNA_PDB() (oxdna_simulation.OxdnaAnalysisTools method) OxdnaAnalysisTools (class in oxdna_simulation)

P

particle_position() (oxdna_simulation.Observable static method) pca() (oxdna_simulation.OxdnaAnalysisTools method)

plot_energy() (oxdna_simulation.Analysis method) potential_energy() (oxdna_simulation.Observable static method)

Q

queue_sim() (oxdna_simulation.SimulationManager method)

R

radius_of_gyration() (oxdna_simulation.OxdnaAnalysisTools method) rate_umbrella_forces() (umbrella_sampling.ComUmbrellaSampling method) repulsion_plane() (oxdna_simulation.Force static method)

repulsion_sphere() (oxdna_simulation.Force static method) rotating_harmonic_trap() (oxdna_simulation.Force static method) run() (oxdna_simulation.SimulationManager method) run_wham() (umbrella_sampling.WhamAnalysis method)

S

Simulation (class in oxdna_simulation) SimulationManager (class in oxdna_simulation) skew_force() (oxdna_simulation.Force static method)

start_nvidia_cuda_mps_control() (oxdna_simulation.SimulationManager method) string() (oxdna_simulation.Force static method) subset_trajectory() (oxdna_simulation.OxdnaAnalysisTools method)

U

umbrella_forces() (umbrella_sampling.ComUmbrellaSampling method)

V

view_conf() (oxdna_simulation.Analysis method)

view_init() (oxdna_simulation.Analysis method) view_last() (oxdna_simulation.Analysis method)

W

wham_run() (umbrella_sampling.BaseUmbrellaSampling method)

WhamAnalysis (class in umbrella_sampling) worker_manager() (oxdna_simulation.SimulationManager method)