EKExceedsError
IntegrationFailError
Simulation
Simulation.RG()
Simulation.__init__()
Simulation.add_force()
Simulation.dist()
Simulation.do_block()
Simulation.get_data()
Simulation.get_scaled_data()
Simulation.init_positions()
Simulation.init_velocities()
Simulation.initialize()
Simulation.local_energy_minimization()
Simulation.print_stats()
Simulation.reinitialize()
Simulation.set_data()
Simulation.set_velocities()
Simulation.show()
fetch_block()
load()
rotation_matrix()
save()
HDF5Reporter
HDF5Reporter.__init__()
HDF5Reporter.continue_trajectory()
HDF5Reporter.dump_data()
HDF5Reporter.report()
list_URIs()
load_URI()
load_hdf5_file()
save_hdf5_file()
R2_scaling()
Rg2()
Rg2_matrix()
Rg2_scaling()
calculate_cistrans()
calculate_contacts()
contact_scaling()
generate_bins()
getLinkingNumber()
kabsch_msd()
kabsch_rmsd()
mutualSimplify()
ndarray_groupby_aggregate()
slope_contact_scaling()
smart_contacts()
streaming_ndarray_agg()
averageContacts()
averageContactsSimple()
binnedContactMap()
chunk()
filenameContactMap
filenameContactMap.__init__()
filenameContactMap.next()
filenameContactMapRepeat
filenameContactMapRepeat.__init__()
filenameContactMapRepeat.next()
findN()
indexing()
init()
monomerResolutionContactMap()
monomerResolutionContactMapSubchains()
simple_worker()
tonumpyarray()
triagToNormal()
worker()
angle_force()
constant_force_bonds()
cylindrical_confinement()
grosberg_angle()
grosberg_polymer_bonds()
grosberg_repulsive_force()
harmonic_bonds()
heteropolymer_SSW()
polynomial_repulsive()
pull_force()
selective_SSW()
smooth_square_well()
spherical_confinement()
spherical_well()
tether_particles()
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