Index

A

adaptive_walk_fixed() (in module RNAsketch)

adaptive_walk_optimization() (in module RNAsketch) add_cuts() (in module RNAsketch.State)

C

calculate_objective() (in module RNAsketch) calculate_objective_1() (in module RNAsketch) calculate_objective_2() (in module RNAsketch) calculate_objective_2_squared() (in module RNAsketch) classtype (RNAsketch.Design.Design attribute) (RNAsketch.Design.hotknotsDesign attribute) (RNAsketch.Design.nupackDesign attribute) (RNAsketch.Design.pkissDesign attribute) (RNAsketch.Design.vrnaDesign attribute) (RNAsketch.State.State attribute) (RNAsketch.State.hotknotsState attribute) (RNAsketch.State.nupackState attribute) (RNAsketch.State.pKissState attribute) (RNAsketch.State.vrnaState attribute)

constraint (RNAsketch.State.State attribute) constraint_generation_optimization() (in module RNAsketch) create_bp_table() (in module RNAsketch.State) cut_points (RNAsketch.State.State attribute)

D

Design (class in RNAsketch.Design)

dump_new_stack() (RNAsketch.RNARedPrintSampler.RPSampler method)

E

enforce_constraint (RNAsketch.State.State attribute) ensemble_defect (RNAsketch.Design.Design attribute) (RNAsketch.State.State attribute) eos (RNAsketch.Design.Design attribute) (RNAsketch.State.State attribute)

eos_diff_mfe (RNAsketch.Design.Design attribute) (RNAsketch.State.State attribute) eos_reached_mfe (RNAsketch.Design.Design attribute) (RNAsketch.State.State attribute)

G

gcweight (RNAsketch.RNARedPrintSampler.RPSampler attribute) get_Design() (in module RNAsketch.Design)

get_graph_properties() (in module RNAsketch) get_sequence() (RNAsketch.RNARedPrintSampler.RPSampler method)

H

hasLonelyPairs() (RNAsketch.Structure.RNAStructure method)

hotknotsDesign (class in RNAsketch.Design) hotknotsState (class in RNAsketch.State)

L

length (RNAsketch.Design.Design attribute) (RNAsketch.State.State attribute)

ligand (RNAsketch.State.State attribute)

M

mfe_energy (RNAsketch.Design.Design attribute) (RNAsketch.State.State attribute) mfe_structure (RNAsketch.Design.Design attribute) (RNAsketch.State.State attribute)

model (RNAsketch.RNARedPrintSampler.RPSampler attribute) multifold (RNAsketch.State.State attribute)

N

newState() (RNAsketch.Design.Design method) (RNAsketch.Design.hotknotsDesign method) (RNAsketch.Design.nupackDesign method) (RNAsketch.Design.pkissDesign method) (RNAsketch.Design.vrnaDesign method)

number_of_structures (RNAsketch.Design.Design attribute) nupackDesign (class in RNAsketch.Design) nupackState (class in RNAsketch.State)

P

pf_energy (RNAsketch.Design.Design attribute) (RNAsketch.State.State attribute) pf_structure (RNAsketch.Design.Design attribute) (RNAsketch.State.State attribute)

pkissDesign (class in RNAsketch.Design) pKissState (class in RNAsketch.State) pos (RNAsketch.Design.Design attribute) (RNAsketch.State.State attribute)

R

read_inp_file() (in module RNAsketch) read_input() (in module RNAsketch) read_input_additions() (in module RNAsketch) remove_cuts() (in module RNAsketch.State) removeLonelyPairs() (RNAsketch.Structure.RNAStructure method) reset() (RNAsketch.State.State method) resolvePKs() (RNAsketch.Structure.RNAStructure method)

revert_sequence() (RNAsketch.RNARedPrintSampler.RPSampler method) RNAsketch (module) RNAsketch.Design (module) RNAsketch.RNARedPrintSampler (module) RNAsketch.State (module) RNAsketch.Structure (module) RNAStructure (class in RNAsketch.Structure) RPSampler (class in RNAsketch.RNARedPrintSampler)

S

sample() (RNAsketch.RNARedPrintSampler.RPSampler method) sample_clocal() (RNAsketch.RNARedPrintSampler.RPSampler method) sample_count_unique_solutions() (in module RNAsketch) sample_plocal() (RNAsketch.RNARedPrintSampler.RPSampler method) sample_sequence() (in module RNAsketch) sequence (RNAsketch.Design.Design attribute)

set_history_size() (RNAsketch.RNARedPrintSampler.RPSampler method) set_sequence() (RNAsketch.RNARedPrintSampler.RPSampler method) simulated_annealing_optimization() (in module RNAsketch) State (class in RNAsketch.State) structure (RNAsketch.State.State attribute) structures (RNAsketch.Design.Design attribute)

T

temperature (RNAsketch.State.State attribute)

V

vrnaDesign (class in RNAsketch.Design)

vrnaState (class in RNAsketch.State)

W

weights (RNAsketch.RNARedPrintSampler.RPSampler attribute) write_csv() (RNAsketch.Design.Design method)

write_csv_header() (RNAsketch.Design.Design method) write_out() (RNAsketch.Design.Design method)