Index

_

__init__() (rna_predict.dcatools.DcaContact method) (rna_predict.dcatools.DcaFilterThreshold method) (rna_predict.simulation.Command method) (rna_predict.simulation.EvalData method) (rna_predict.simulation.RNAPrediction method) (rna_predict.sysconfig.SysConfig method)

A

align_structure() (in module rna_predict.pdbtools) apply() (rna_predict.dcatools.DcaFilter method) (rna_predict.dcatools.DcaFilterThreshold method)

assemble() (rna_predict.simulation.RNAPrediction method)

B

build_cst_info_from_dca_contacts() (in module rna_predict.dcatools)

C

check_config() (rna_predict.simulation.RNAPrediction method) check_dir_existence() (in module rna_predict.simulation) check_file_existence() (in module rna_predict.simulation) check_sysconfig() (rna_predict.sysconfig.SysConfig method) comma_separated_entries_to_dict() (in module rna_predict.utils)

comma_separated_ranges_to_list() (in module rna_predict.utils) Command (class in rna_predict.simulation) CONFIG_FILE (rna_predict.simulation.RNAPrediction attribute) create_helices() (rna_predict.simulation.RNAPrediction method) create_motifs() (rna_predict.simulation.RNAPrediction method)

D

DcaContact (class in rna_predict.dcatools) DcaException DcaFilter (class in rna_predict.dcatools)

DcaFilterThreshold (class in rna_predict.dcatools) delete_glob() (in module rna_predict.simulation)

E

edit_constraints() (rna_predict.simulation.RNAPrediction method) EvalData (class in rna_predict.simulation) evaluate() (rna_predict.simulation.RNAPrediction method) evaluate_custom() (rna_predict.simulation.RNAPrediction method) execute_command() (rna_predict.simulation.RNAPrediction method)

execute_command_and_capture() (rna_predict.simulation.RNAPrediction method) execute_commands() (rna_predict.simulation.RNAPrediction method) extract_models() (rna_predict.simulation.RNAPrediction method) extract_pdb() (rna_predict.simulation.RNAPrediction method)

F

filter_atoms() (in module rna_predict.pdbtools) filter_dca_data() (in module rna_predict.dcatools)

fix_atom_names_in_cst() (in module rna_predict.simulation)

G

get_atoms_for_res() (in module rna_predict.dcatools) get_atoms_for_res_sequence() (in module rna_predict.dcatools) get_center_of_res() (in module rna_predict.pdbtools) get_contact_distance_map() (in module rna_predict.dcatools) get_contact_distance_map_mean() (in module rna_predict.dcatools) get_contact_information_in_pdb_chain() (in module rna_predict.dcatools) get_csts() (rna_predict.simulation.RNAPrediction method) get_full_command() (rna_predict.simulation.Command method)

get_model_count() (rna_predict.simulation.EvalData method) get_model_count_in_silent_file() (in module rna_predict.simulation) get_models() (rna_predict.simulation.EvalData method) (rna_predict.simulation.RNAPrediction static method) get_pdb_by_code() (in module rna_predict.pdbtools) get_rosetta_function() (rna_predict.dcatools.DcaContact method) get_status() (rna_predict.simulation.RNAPrediction method) get_weighted_model_score() (rna_predict.simulation.EvalData static method)

L

load_config() (rna_predict.simulation.RNAPrediction method) load_from_cst() (rna_predict.simulation.EvalData static method)

load_from_file() (rna_predict.simulation.EvalData static method) load_sysconfig() (rna_predict.sysconfig.SysConfig method)

M

main() (in module rna_predict.main) make_constraints() (rna_predict.simulation.RNAPrediction method) merge_silent_files() (in module rna_predict.simulation)

mkdir_p() (in module rna_predict.utils) modify_config() (rna_predict.simulation.RNAPrediction method)

N

natural_sort_key() (in module rna_predict.simulation)

P

parse_cst_file() (rna_predict.simulation.RNAPrediction static method) parse_cst_name_and_filename() (rna_predict.simulation.RNAPrediction static method) parse_dca_data() (in module rna_predict.dcatools) parse_dca_filter_string() (rna_predict.simulation.RNAPrediction method) parse_pdb() (in module rna_predict.pdbtools) plot_clusters() (in module rna_predict.tools) plot_constraint_quality() (in module rna_predict.tools) plot_contact_atoms() (in module rna_predict.tools) plot_contact_distances() (in module rna_predict.tools) plot_contact_map() (in module rna_predict.tools)

plot_dca_contacts_in_pdb() (in module rna_predict.tools) plot_gdt() (in module rna_predict.tools) plot_pdb_comparison() (in module rna_predict.tools) plot_tp_rate() (in module rna_predict.tools) prepare() (rna_predict.simulation.RNAPrediction method) prepare_cst() (rna_predict.simulation.RNAPrediction method) print_config() (rna_predict.simulation.RNAPrediction method) print_models() (rna_predict.simulation.EvalData method) (rna_predict.simulation.RNAPrediction static method) print_status() (rna_predict.simulation.RNAPrediction method) print_sysconfig() (rna_predict.sysconfig.SysConfig method)

R

read_file_line_by_line() (in module rna_predict.utils) read_pdb_mapping_from_file() (in module rna_predict.dcatools) rna_predict (module) rna_predict.dcatools (module) rna_predict.main (module) rna_predict.pdbtools (module)

rna_predict.simulation (module) rna_predict.sysconfig (module) rna_predict.tools (module) rna_predict.utils (module) RNAPrediction (class in rna_predict.simulation)

S

save_config() (rna_predict.simulation.RNAPrediction method) save_to_file() (rna_predict.simulation.EvalData method) SimulationException

SysConfig (class in rna_predict.sysconfig) SYSCONFIG_FILE (rna_predict.sysconfig.SysConfig attribute) SYSCONFIG_LOCATION (rna_predict.sysconfig.SysConfig attribute)