Index

_

__init__() (polyzymd.builders.enzyme.EnzymeBuilder method) (polyzymd.builders.polymer.PolymerBuilder method) (polyzymd.builders.substrate.SubstrateBuilder method) (polyzymd.builders.system_builder.SystemBuilder method) (polyzymd.config.loader.ConfigLoader method) (polyzymd.simulation.continuation.ContinuationManager method) (polyzymd.simulation.runner.SimulationRunner method)

A

all_conformers (polyzymd.builders.substrate.SubstrateBuilder property)

apply_fdr_correction() (in module polyzymd.analyses.shared.multi_run_comparison)

B

build() (polyzymd.builders.enzyme.EnzymeBuilder method) (polyzymd.builders.polymer.PolymerBuilder method) (polyzymd.builders.substrate.SubstrateBuilder method) build_condition_pairs() (in module polyzymd.analyses.shared.multi_run_comparison) build_enzyme() (polyzymd.builders.system_builder.SystemBuilder method)

build_from_config() (polyzymd.builders.enzyme.EnzymeBuilder method) (polyzymd.builders.polymer.PolymerBuilder method) (polyzymd.builders.substrate.SubstrateBuilder method) (polyzymd.builders.system_builder.SystemBuilder method) build_polymers() (polyzymd.builders.system_builder.SystemBuilder method) build_substrate() (polyzymd.builders.system_builder.SystemBuilder method)

C

canonical_sequence() (in module polyzymd.builders.polymer) characters (polyzymd.builders.polymer.PolymerBuilder property) combine_solutes() (polyzymd.builders.system_builder.SystemBuilder method)

ConfigLoader (class in polyzymd.config.loader) conformer_index (polyzymd.builders.substrate.SubstrateBuilder property) ContinuationManager (class in polyzymd.simulation.continuation) create_interchange() (polyzymd.builders.system_builder.SystemBuilder method)

E

EnzymeBuilder (class in polyzymd.builders.enzyme)

export_to_gromacs() (polyzymd.builders.system_builder.SystemBuilder method)

F

filter_summaries_with_run() (in module polyzymd.analyses.shared.multi_run_comparison) format_anova_line() (in module polyzymd.analyses.shared.multi_run_formatting)

format_markdown_bullet() (in module polyzymd.analyses.shared.multi_run_formatting) format_pairwise_line() (in module polyzymd.analyses.shared.multi_run_formatting) from_config() (polyzymd.builders.system_builder.SystemBuilder class method)

G

generate_random_sequence() (in module polyzymd.builders.polymer) get_component_info() (polyzymd.builders.system_builder.SystemBuilder method) get_molecule() (polyzymd.builders.enzyme.EnzymeBuilder method)

get_n_conformers() (polyzymd.builders.substrate.SubstrateBuilder method) get_openmm_components() (polyzymd.builders.system_builder.SystemBuilder method) get_packing_info() (polyzymd.builders.polymer.PolymerBuilder method)

H

history (polyzymd.simulation.runner.SimulationRunner property)

I

interchange (polyzymd.builders.system_builder.SystemBuilder property)

L

length (polyzymd.builders.polymer.PolymerBuilder property) load() (polyzymd.config.loader.ConfigLoader method) load_checkpoint() (polyzymd.simulation.runner.SimulationRunner method)

load_config() (in module polyzymd.config.loader) load_config_dict() (in module polyzymd.config.loader) load_previous_state() (polyzymd.simulation.continuation.ContinuationManager method) loaded_molecules (polyzymd.builders.polymer.PolymerBuilder property)

M

make_ranked_markdown_header() (in module polyzymd.analyses.shared.multi_run_formatting) make_ranked_rows() (in module polyzymd.analyses.shared.multi_run_formatting) make_ranked_table_header() (in module polyzymd.analyses.shared.multi_run_formatting) make_section_title() (in module polyzymd.analyses.shared.multi_run_formatting) minimize() (polyzymd.simulation.runner.SimulationRunner method) module polyzymd.analyses.shared.multi_run_comparison polyzymd.analyses.shared.multi_run_formatting polyzymd.builders.enzyme polyzymd.builders.polymer polyzymd.builders.substrate polyzymd.builders.system_builder polyzymd.config.loader polyzymd.simulation.continuation polyzymd.simulation.runner

molecule (polyzymd.builders.substrate.SubstrateBuilder property)

P

pack_polymers() (polyzymd.builders.system_builder.SystemBuilder method) pdb_path (polyzymd.builders.enzyme.EnzymeBuilder property) PolymerBuilder (class in polyzymd.builders.polymer) polyzymd.analyses.shared.multi_run_comparison module polyzymd.analyses.shared.multi_run_formatting module polyzymd.builders.enzyme module polyzymd.builders.polymer module

polyzymd.builders.substrate module polyzymd.builders.system_builder module polyzymd.config.loader module polyzymd.simulation.continuation module polyzymd.simulation.runner module probabilities (polyzymd.builders.polymer.PolymerBuilder property)

Q

quantity_from_dict() (in module polyzymd.simulation.continuation)

R

run_equilibration() (polyzymd.simulation.runner.SimulationRunner method) run_equilibration_stage() (polyzymd.simulation.runner.SimulationRunner method)

run_production() (polyzymd.simulation.runner.SimulationRunner method) run_segment() (polyzymd.simulation.continuation.ContinuationManager method) run_staged_equilibration() (polyzymd.simulation.runner.SimulationRunner method)

S

save_config() (in module polyzymd.config.loader) save_history() (polyzymd.simulation.runner.SimulationRunner method) save_topology() (polyzymd.builders.system_builder.SystemBuilder method) sdf_path (polyzymd.builders.substrate.SubstrateBuilder property) segment_index (polyzymd.simulation.continuation.ContinuationManager property) sequence_counts (polyzymd.builders.polymer.PolymerBuilder property)

simulation (polyzymd.simulation.continuation.ContinuationManager property) (polyzymd.simulation.runner.SimulationRunner property) SimulationRunner (class in polyzymd.simulation.runner) solvate() (polyzymd.builders.system_builder.SystemBuilder method) solvated_topology (polyzymd.builders.system_builder.SystemBuilder property) SubstrateBuilder (class in polyzymd.builders.substrate) SystemBuilder (class in polyzymd.builders.system_builder)

T

topology (polyzymd.builders.enzyme.EnzymeBuilder property)

V

validate() (polyzymd.builders.enzyme.EnzymeBuilder method) (polyzymd.builders.polymer.PolymerBuilder method) (polyzymd.builders.substrate.SubstrateBuilder method)

W

working_dir (polyzymd.simulation.continuation.ContinuationManager property) (polyzymd.simulation.runner.SimulationRunner property)