Index

A

aggregate_outputs_for_single_temp() (in module pydna_epbd.simulation.aggregate_outputs_and_write)

B

BubbleMonitor (class in pydna_epbd.monitors.bubble_monitor)

C

collect_at_iter() (pydna_epbd.monitors.all_monitors.Monitors method) (pydna_epbd.monitors.melting_and_fraction_monitor.MeltingAndFractionMonitor method) (pydna_epbd.monitors.monitor.Monitor method) collect_at_step() (pydna_epbd.monitors.all_monitors.Monitors method) (pydna_epbd.monitors.bubble_monitor.BubbleMonitor method) (pydna_epbd.monitors.coord_monitor.CoordMonitor method) (pydna_epbd.monitors.energy_monitor.EnergyMonitor method) (pydna_epbd.monitors.flipping_monitor.FlippingMonitor method) (pydna_epbd.monitors.flipping_monitor_verbose.FlippingMonitorVerbose method) (pydna_epbd.monitors.melting_and_fraction_many_monitor.MeltingAndFractionManyMonitor method) (pydna_epbd.monitors.melting_and_fraction_monitor.MeltingAndFractionMonitor method) (pydna_epbd.monitors.monitor.Monitor method)

collect_at_step_preheat() (pydna_epbd.monitors.all_monitors.Monitors method) (pydna_epbd.monitors.energy_monitor.EnergyMonitor method) (pydna_epbd.monitors.monitor.Monitor method) collect_at_temp() (pydna_epbd.monitors.monitor.Monitor method) CoordMonitor (class in pydna_epbd.monitors.coord_monitor) create_necessary_directories() (in module pydna_epbd.pickle_utils)

D

DNA (class in pydna_epbd.simulation.dna)

E

EnergyMonitor (class in pydna_epbd.monitors.energy_monitor)

execute() (pydna_epbd.simulation.mc_simulation.Simulation method)

F

FLIP_CUTOFF (pydna_epbd.monitors.flipping_monitor.FlippingMonitor attribute) (pydna_epbd.monitors.flipping_monitor_verbose.FlippingMonitorVerbose attribute)

FLIP_SIZES (pydna_epbd.monitors.flipping_monitor_verbose.FlippingMonitorVerbose attribute) FlippingMonitor (class in pydna_epbd.monitors.flipping_monitor) FlippingMonitorVerbose (class in pydna_epbd.monitors.flipping_monitor_verbose)

G

get_dimension() (in module pydna_epbd.pickle_utils)

I

init_temp() (pydna_epbd.simulation.mc_simulation.Simulation method)

InputConfigs (class in pydna_epbd.configs)

K

KB (pydna_epbd.monitors.energy_monitor.EnergyMonitor attribute)

L

load_pickle() (in module pydna_epbd.pickle_utils)

M

MAX_BUB_ELEM (pydna_epbd.monitors.bubble_monitor.BubbleMonitor attribute) MELT_FRACTION_SIZES (pydna_epbd.monitors.melting_and_fraction_many_monitor.MeltingAndFractionManyMonitor attribute) MELT_FRACTION_TIME_STEPS (pydna_epbd.monitors.melting_and_fraction_many_monitor.MeltingAndFractionManyMonitor attribute) MELT_FRACTION_TRESHOLD (pydna_epbd.monitors.melting_and_fraction_monitor.MeltingAndFractionMonitor attribute) MELT_FRACTION_TRESHOLDS (pydna_epbd.monitors.melting_and_fraction_many_monitor.MeltingAndFractionManyMonitor attribute) MeltingAndFractionManyMonitor (class in pydna_epbd.monitors.melting_and_fraction_many_monitor) MeltingAndFractionMonitor (class in pydna_epbd.monitors.melting_and_fraction_monitor) MIN_BUB_ELEM (pydna_epbd.monitors.bubble_monitor.BubbleMonitor attribute) module pydna_epbd pydna_epbd.configs pydna_epbd.input_reader pydna_epbd.monitors pydna_epbd.monitors.all_monitors pydna_epbd.monitors.bubble_monitor pydna_epbd.monitors.coord_monitor pydna_epbd.monitors.coord_monitor_verbose pydna_epbd.monitors.energy_monitor pydna_epbd.monitors.flipping_monitor pydna_epbd.monitors.flipping_monitor_verbose pydna_epbd.monitors.melting_and_fraction_many_monitor pydna_epbd.monitors.melting_and_fraction_monitor pydna_epbd.monitors.monitor pydna_epbd.pickle_utils pydna_epbd.run pydna_epbd.simulation pydna_epbd.simulation.aggregate_outputs_and_write pydna_epbd.simulation.constants pydna_epbd.simulation.dna pydna_epbd.simulation.mc_simulation pydna_epbd.simulation.simulation_steps pydna_epbd.version

Monitor (class in pydna_epbd.monitors.monitor) Monitors (class in pydna_epbd.monitors.all_monitors)

P

parse_args() (in module pydna_epbd.run) pydna_epbd module pydna_epbd.configs module pydna_epbd.input_reader module pydna_epbd.monitors module pydna_epbd.monitors.all_monitors module pydna_epbd.monitors.bubble_monitor module pydna_epbd.monitors.coord_monitor module pydna_epbd.monitors.coord_monitor_verbose module pydna_epbd.monitors.energy_monitor module pydna_epbd.monitors.flipping_monitor module pydna_epbd.monitors.flipping_monitor_verbose module

pydna_epbd.monitors.melting_and_fraction_many_monitor module pydna_epbd.monitors.melting_and_fraction_monitor module pydna_epbd.monitors.monitor module pydna_epbd.pickle_utils module pydna_epbd.run module pydna_epbd.simulation module pydna_epbd.simulation.aggregate_outputs_and_write module pydna_epbd.simulation.constants module pydna_epbd.simulation.dna module pydna_epbd.simulation.mc_simulation module pydna_epbd.simulation.simulation_steps module pydna_epbd.version module

R

random() (in module pydna_epbd.simulation.mc_simulation) read_all_sequences() (in module pydna_epbd.input_reader) read_configurations() (in module pydna_epbd.input_reader)

read_sequences_from_a_file() (in module pydna_epbd.input_reader) reset() (pydna_epbd.simulation.dna.DNA method) run_sequences() (in module pydna_epbd.simulation.simulation_steps) run_single_iteration() (in module pydna_epbd.simulation.simulation_steps)

S

save_as_pickle() (in module pydna_epbd.pickle_utils)

Simulation (class in pydna_epbd.simulation.mc_simulation)

T

TRESHOLD_SIZE (pydna_epbd.monitors.bubble_monitor.BubbleMonitor attribute)

TRESHOLDS (pydna_epbd.monitors.bubble_monitor.BubbleMonitor attribute)

U

update_state() (pydna_epbd.monitors.all_monitors.Monitors method) (pydna_epbd.monitors.monitor.Monitor method)