Index

A

add_sources() (Allosteric method) add_targets() (Allosteric method)

Allosteric (class in physical_learning.allosteric_utils) animate() (Allosteric method) (Packing method)

C

color_plot() (Allosteric method)

compute_modes() (Elastic method) coordination() (Packing method)

D

distribution_plot() (Allosteric method)

E

Elastic (class in physical_learning.elastic_utils)

energy() (Elastic method)

G

generate() (Packing method)

get_clusters() (in module physical_learning.lammps_utils)

I

initialize() (Packing method)

L

load_run() (in module physical_learning.lammps_utils)

M

mean_square_displacement() (Elastic method) mode_plot() (Allosteric method)

mode_tile() (Allosteric method) module physical_learning.lammps_utils

P

Packing (class in physical_learning.packing_utils) physical_learning.lammps_utils module plot() (Allosteric method) (Packing method)

plot_network() (Elastic method) plot_source() (Allosteric method) plot_target() (Allosteric method)

R

read_data() (in module physical_learning.lammps_utils) read_dim() (in module physical_learning.lammps_utils) read_dump() (in module physical_learning.lammps_utils) read_log() (in module physical_learning.lammps_utils) reset_equilibrium() (Allosteric method) (Elastic method)

reset_init() (Elastic method) reset_view() (Elastic method) rigid_correction() (Elastic method) rotate() (Allosteric method) (Packing method) rotate_view() (Elastic method)

S

save() (Allosteric method) (Elastic method) (Packing method) set_axes() (Elastic method) set_frame() (Elastic method) (Packing method)

setup_run() (in module physical_learning.lammps_utils) solve() (Elastic method) strain() (Allosteric method) strain_map() (Allosteric method) strain_plot() (Allosteric method) strain_plot_thermal() (Allosteric method)

T

time_lapse() (Allosteric method)

W

write_job() (Allosteric method) write_lammps_data() (Allosteric method)

write_lammps_data_learning() (Allosteric method) write_lammps_input() (Allosteric method)