Index

_

__init__() (PyMEMENTO.MEMENTO method)

C

cap_termini() (in module PyMEMENTO.pdb_util) change_boxsize() (in module PyMEMENTO.gmx_util)

create_ali_file() (in module PyMEMENTO.modeller_util) create_box() (in module PyMEMENTO.gmx_util) crop_top_to_itp() (in module PyMEMENTO.gmx_util)

E

edit_last_line() (in module PyMEMENTO.gmx_util)

embed_in_lipids() (in module PyMEMENTO.gmx_util)

F

find_best_path() (PyMEMENTO.MEMENTO method)

fix_residue_numbers() (in module PyMEMENTO.pdb_util)

G

generate_membrane_index() (in module PyMEMENTO.gmx_util) generate_posre() (in module PyMEMENTO.gmx_util)

get_cubic_boxsize() (in module PyMEMENTO.gmx_util) get_monitor_value_from_xtc() (in module PyMEMENTO.plumed_util)

M

make_models() (PyMEMENTO.MEMENTO method) MCPathSampler (class in PyMEMENTO.mc_path_sampling) MEMENTO (class in PyMEMENTO) minimize() (in module PyMEMENTO.gmx_util) minimize_boxes() (PyMEMENTO.MEMENTO method) module PyMEMENTO PyMEMENTO.gmx_util PyMEMENTO.mc_path_sampling PyMEMENTO.modeller_util PyMEMENTO.pdb_util PyMEMENTO.plumed_util

morph() (PyMEMENTO.MEMENTO method)

P

parse_indexkey_to_list() (in module PyMEMENTO.gmx_util) path_energy_function() (PyMEMENTO.mc_path_sampling.MCPathSampler method) pdb2gmx() (in module PyMEMENTO.gmx_util) prepare_boxes() (PyMEMENTO.MEMENTO method) prepare_umbrella_sampling() (PyMEMENTO.MEMENTO method) process_models() (PyMEMENTO.MEMENTO method) PyMEMENTO module PyMEMENTO.gmx_util module

PyMEMENTO.mc_path_sampling module PyMEMENTO.modeller_util module PyMEMENTO.pdb_util module PyMEMENTO.plumed_util module

R

run_modeller() (in module PyMEMENTO.modeller_util)

run_monte_carlo() (PyMEMENTO.mc_path_sampling.MCPathSampler method) run_one_replicate_of_mc() (in module PyMEMENTO.mc_path_sampling)

S

sample_path() (PyMEMENTO.mc_path_sampling.MCPathSampler method) sed() (in module PyMEMENTO.pdb_util) solvate_boxes() (PyMEMENTO.MEMENTO method)

solvate_ions() (in module PyMEMENTO.gmx_util) stretch_boxsize() (in module PyMEMENTO.gmx_util) stretch_relative() (in module PyMEMENTO.gmx_util)