Rosetta Protocols  2014.35
protocols::farna::RNA_DeNovoProtocol Member List

This is the complete list of members for protocols::farna::RNA_DeNovoProtocol, including all inherited members.

add_chem_shift_info(core::io::silent::SilentStruct &silent_struct, core::pose::Pose const &const_pose) const protocols::farna::RNA_DeNovoProtocolprivate
add_number_base_pairs(core::pose::Pose const &pose_input, core::io::silent::SilentStruct &s) const protocols::farna::RNA_DeNovoProtocolprivate
add_number_native_base_pairs(core::pose::Pose &pose, core::io::silent::SilentStruct &s) const protocols::farna::RNA_DeNovoProtocolprivate
align_and_output_to_silent_file(core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag) const protocols::farna::RNA_DeNovoProtocol
all_lores_score_final_protocols::farna::RNA_DeNovoProtocolprivate
all_rna_fragments_protocols::farna::RNA_DeNovoProtocolprivate
all_rna_fragments_file_protocols::farna::RNA_DeNovoProtocolprivate
allow_bulge_protocols::farna::RNA_DeNovoProtocolprivate
allow_consecutive_bulges_protocols::farna::RNA_DeNovoProtocolprivate
allowed_bulge_res_protocols::farna::RNA_DeNovoProtocolprivate
apply(core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolvirtual
protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap)protocols::moves::Movervirtual
apply_chem_shift_data(core::pose::Pose &pose, std::string const out_file_tag)protocols::farna::RNA_DeNovoProtocolprivate
autofilter_protocols::farna::RNA_DeNovoProtocolprivate
autofilter_score_quantile_protocols::farna::RNA_DeNovoProtocolprivate
binary_rna_output_protocols::farna::RNA_DeNovoProtocolprivate
bps_moves_protocols::farna::RNA_DeNovoProtocolprivate
calc_rmsds(core::io::silent::SilentStruct &s, core::pose::Pose &pose, std::string const &out_file_tag) const protocols::farna::RNA_DeNovoProtocolprivate
chainbreak_weight_protocols::farna::RNA_DeNovoProtocolprivate
check_score_filter(core::Real const lores_score_, std::list< core::Real > &all_lores_score_)protocols::farna::RNA_DeNovoProtocolprivate
chem_shift_scorefxn_protocols::farna::RNA_DeNovoProtocolprivate
chunk_coverage_protocols::farna::RNA_DeNovoProtocolprivate
chunk_pdb_files_protocols::farna::RNA_DeNovoProtocolprivate
chunk_silent_files_protocols::farna::RNA_DeNovoProtocolprivate
clear_info()protocols::moves::Moverinlinevirtual
clone() const protocols::farna::RNA_DeNovoProtocolvirtual
close_loops_after_each_move_protocols::farna::RNA_DeNovoProtocolprivate
close_loops_at_end_protocols::farna::RNA_DeNovoProtocolprivate
close_loops_in_last_round_protocols::farna::RNA_DeNovoProtocolprivate
constraint_set_protocols::farna::RNA_DeNovoProtocolprivate
create()protocols::moves::Movervirtual
denovo_scorefxn_protocols::farna::RNA_DeNovoProtocolprivate
do_close_loops_protocols::farna::RNA_DeNovoProtocolprivate
do_random_moves(core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolprivate
dump_pdb_protocols::farna::RNA_DeNovoProtocolprivate
extra_minimize_chi_res_protocols::farna::RNA_DeNovoProtocolprivate
extra_minimize_res_protocols::farna::RNA_DeNovoProtocolprivate
figure_out_constraint_separation_cutoff(Size const r, Size const max_dist)protocols::farna::RNA_DeNovoProtocolprivate
filter_chain_closure_protocols::farna::RNA_DeNovoProtocolprivate
filter_chain_closure_distance_protocols::farna::RNA_DeNovoProtocolprivate
filter_chain_closure_halfway_protocols::farna::RNA_DeNovoProtocolprivate
filter_lores_base_pairs_protocols::farna::RNA_DeNovoProtocolprivate
filter_lores_base_pairs_early_protocols::farna::RNA_DeNovoProtocolprivate
Filters_map typedefprotocols::moves::Mover
final_score(core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolprivate
final_scorefxn_protocols::farna::RNA_DeNovoProtocolprivate
frag_size_protocols::farna::RNA_DeNovoProtocolprivate
fresh_instance() const protocols::moves::Movervirtual
get_additional_output()protocols::moves::Movervirtual
get_current_job() const protocols::moves::Mover
get_current_tag() const protocols::moves::Moverinline
get_input_pose() const protocols::moves::Mover
get_last_move_status() const protocols::moves::Mover
get_moving_res(core::pose::Pose const &pose) const protocols::farna::RNA_DeNovoProtocolprivate
get_name() const protocols::farna::RNA_DeNovoProtocolvirtual
get_native_pose() const protocols::moves::Mover
get_type() const protocols::moves::Moverinline
heat_structure_protocols::farna::RNA_DeNovoProtocolprivate
hires_scorefxn_protocols::farna::RNA_DeNovoProtocolprivate
ignore_secstruct(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
ignore_secstruct_protocols::farna::RNA_DeNovoProtocolprivate
info()protocols::moves::Moverinlinevirtual
info() const protocols::moves::Moverinlinevirtual
initial_denovo_scorefxn_protocols::farna::RNA_DeNovoProtocolprivate
initialize_constraints(core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolprivate
initialize_lores_silent_file()protocols::farna::RNA_DeNovoProtocolprivate
initialize_movers(core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolprivate
initialize_scorefxn(core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolprivate
initialize_tag_is_done()protocols::farna::RNA_DeNovoProtocolprivate
input_res_protocols::farna::RNA_DeNovoProtocolprivate
jump_change_frequency(core::Real const value)protocols::farna::RNA_DeNovoProtocolinline
jump_change_frequency_protocols::farna::RNA_DeNovoProtocolprivate
jump_library_file_protocols::farna::RNA_DeNovoProtocolprivate
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
linear_chainbreak_weight_protocols::farna::RNA_DeNovoProtocolprivate
local_rna_low_resolution_potential_protocols::farna::RNA_DeNovoProtocolprivate
lores_score_early_protocols::farna::RNA_DeNovoProtocolprivate
lores_score_final_protocols::farna::RNA_DeNovoProtocolprivate
lores_scorefxn_protocols::farna::RNA_DeNovoProtocolprivate
lores_silent_file_protocols::farna::RNA_DeNovoProtocolprivate
m_Temperature_protocols::farna::RNA_DeNovoProtocolprivate
minimize_structure_protocols::farna::RNA_DeNovoProtocolprivate
minimizer_use_coordinate_constraints_protocols::farna::RNA_DeNovoProtocolprivate
monte_carlo_protocols::farna::RNA_DeNovoProtocolprivate
monte_carlo_cycles_protocols::farna::RNA_DeNovoProtocolprivate
monte_carlo_cycles_max_default_protocols::farna::RNA_DeNovoProtocolprivate
move_first_rigid_body_protocols::farna::RNA_DeNovoProtocolprivate
Mover()protocols::moves::Mover
Mover(std::string const &type_name)protocols::moves::Mover
Mover(Mover const &other)protocols::moves::Mover
name()protocols::moves::Moverinlinestatic
nstruct_protocols::farna::RNA_DeNovoProtocolprivate
operator=(Mover const &other)protocols::moves::Mover
output_filters_protocols::farna::RNA_DeNovoProtocolprivate
output_lores_silent_file(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
output_lores_silent_file_protocols::farna::RNA_DeNovoProtocolprivate
output_silent_struct(core::io::silent::SilentStruct &s, core::io::silent::SilentFileData &silent_file_data, std::string const &silent_file, core::pose::Pose &pose, std::string const out_file_tag, bool const score_only=false) const protocols::farna::RNA_DeNovoProtocolprivate
output_to_silent_file(core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag, bool const score_only=false) const protocols::farna::RNA_DeNovoProtocol
parse_def(utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)protocols::moves::Movervirtual
parse_my_tag(TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)protocols::moves::Movervirtual
parse_state(SerializableState const &state)protocols::moves::Movervirtual
Pose typedefprotocols::moves::Mover
PoseCOP typedefprotocols::moves::Mover
random_chunk_trial(core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolprivate
random_fragment_trial(core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolprivate
random_jump_trial(core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolprivate
randomize_rigid_body_orientations(core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolprivate
refine_from_silent_protocols::farna::RNA_DeNovoProtocolprivate
refine_pose_protocols::farna::RNA_DeNovoProtocolprivate
refine_pose_list_protocols::farna::RNA_DeNovoProtocolprivate
register_options()protocols::moves::Moverinlinestatic
reinitialize_for_each_job() const protocols::moves::Movervirtual
reinitialize_for_new_input() const protocols::moves::Movervirtual
relax_structure_protocols::farna::RNA_DeNovoProtocolprivate
reset_status()protocols::moves::Mover
rigid_body_mover_protocols::farna::RNA_DeNovoProtocolprivate
rna_chunk_library_protocols::farna::RNA_DeNovoProtocolprivate
rna_data_file_protocols::farna::RNA_DeNovoProtocolprivate
rna_data_reader_protocols::farna::RNA_DeNovoProtocolprivate
RNA_DeNovoProtocol(Size const nstruct, std::string const silent_file, bool const heat_structure=true, bool const minimize_structure=false, bool const relax_structure=false, bool const allow_bulge=false)protocols::farna::RNA_DeNovoProtocol
rna_fragment_mover_protocols::farna::RNA_DeNovoProtocolprivate
rna_loop_closer_protocols::farna::RNA_DeNovoProtocolprivate
rna_minimizer_protocols::farna::RNA_DeNovoProtocolprivate
RNA_move_trial(core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolprivate
rna_params_file_protocols::farna::RNA_DeNovoProtocolprivate
rna_relaxer_protocols::farna::RNA_DeNovoProtocolprivate
rna_structure_parameters_protocols::farna::RNA_DeNovoProtocolprivate
root_at_first_rigid_body_protocols::farna::RNA_DeNovoProtocolprivate
rounds_protocols::farna::RNA_DeNovoProtocolprivate
save_state(SerializableState &state)protocols::moves::Movervirtual
set_all_rna_fragments_file(std::string const file)protocols::farna::RNA_DeNovoProtocolinline
set_allow_consecutive_bulges(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_allowed_bulge_res(utility::vector1< core::Size > const &setting)protocols::farna::RNA_DeNovoProtocolinline
set_autofilter(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_binary_rna_output(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_bps_moves(Size const setting)protocols::farna::RNA_DeNovoProtocolinline
set_chainbreak_weight(core::Real setting)protocols::farna::RNA_DeNovoProtocolinline
set_chunk_pdb_files(utility::vector1< std::string > const &chunk_pdb_files)protocols::farna::RNA_DeNovoProtocolinline
set_chunk_silent_files(utility::vector1< std::string > const &chunk_silent_files)protocols::farna::RNA_DeNovoProtocolinline
set_close_loops(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_close_loops_after_each_move(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_current_job(protocols::jobdist::BasicJobCOP job)protocols::moves::Mover
set_current_tag(std::string const &new_tag)protocols::moves::Moverinline
set_dump_pdb(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_extra_minimize_chi_res(utility::vector1< core::Size > setting)protocols::farna::RNA_DeNovoProtocol
set_extra_minimize_res(utility::vector1< core::Size > setting)protocols::farna::RNA_DeNovoProtocol
set_filter_chain_closure(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_filter_chain_closure_distance(core::Real const setting)protocols::farna::RNA_DeNovoProtocolinline
set_filter_chain_closure_halfway(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_filter_lores_base_pairs(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_filter_lores_base_pairs_early(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_input_pose(PoseCOP pose)protocols::moves::Movervirtual
set_input_res(utility::vector1< Size > const &input_res)protocols::farna::RNA_DeNovoProtocolinline
set_jump_library_file(std::string const jump_library_file)protocols::farna::RNA_DeNovoProtocolinline
set_last_move_status(MoverStatus status)protocols::moves::Moverprotected
set_linear_chainbreak_weight(core::Real setting)protocols::farna::RNA_DeNovoProtocolinline
set_lores_scorefxn(std::string const &lores_scorefxn)protocols::farna::RNA_DeNovoProtocolinline
set_minimizer_use_coordinate_constraints(Size const setting)protocols::farna::RNA_DeNovoProtocolinline
set_monte_carlo_cycles(Size const setting)protocols::farna::RNA_DeNovoProtocolinline
set_move_first_rigid_body(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_native_pose(PoseCOP pose)protocols::moves::Movervirtual
set_output_filters(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_refine_pose(Size const setting)protocols::farna::RNA_DeNovoProtocolinline
set_refine_pose_list(utility::vector1< core::pose::PoseOP > const &setting)protocols::farna::RNA_DeNovoProtocol
set_rna_data_file(std::string const file)protocols::farna::RNA_DeNovoProtocolinline
set_rna_params_file(std::string const file)protocols::farna::RNA_DeNovoProtocolinline
set_root_at_first_rigid_body(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_rounds(Size const setting)protocols::farna::RNA_DeNovoProtocolinline
set_staged_constraints(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
set_suppress_bp_constraint(core::Real const setting)protocols::farna::RNA_DeNovoProtocolinline
set_temperature(core::Real const setting)protocols::farna::RNA_DeNovoProtocolinline
set_type(std::string const &setting)protocols::moves::Moverinline
set_vall_torsions_file(std::string const file)protocols::farna::RNA_DeNovoProtocolinline
set_vary_bond_geometry(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
setup_monte_carlo_cycles(core::pose::Pose const &pose)protocols::farna::RNA_DeNovoProtocolprivate
setup_rigid_body_mover(core::pose::Pose const &pose, core::Size const r)protocols::farna::RNA_DeNovoProtocolprivate
show(std::ostream &output=std::cout) const protocols::farna::RNA_DeNovoProtocolvirtual
silent_file_protocols::farna::RNA_DeNovoProtocolprivate
simple_rmsd_cutoff_relax(bool const setting)protocols::farna::RNA_DeNovoProtocolinline
simple_rmsd_cutoff_relax_protocols::farna::RNA_DeNovoProtocolprivate
staged_constraints_protocols::farna::RNA_DeNovoProtocolprivate
Strings typedefprotocols::moves::Mover
suppress_bp_constraint_protocols::farna::RNA_DeNovoProtocolprivate
tag_is_done_protocols::farna::RNA_DeNovoProtocolprivate
TagCOP typedefprotocols::moves::Mover
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
titrate_stack_bonus_protocols::farna::RNA_DeNovoProtocolprivate
type() const protocols::moves::Moverinline
type(const std::string &type_in)protocols::moves::Moverinline
update_denovo_scorefxn_weights(Size const r)protocols::farna::RNA_DeNovoProtocolprivate
update_frag_size(Size const r)protocols::farna::RNA_DeNovoProtocolprivate
update_pose_constraints(Size const r, core::pose::Pose &pose)protocols::farna::RNA_DeNovoProtocolprivate
use_chem_shift_data_protocols::farna::RNA_DeNovoProtocolprivate
user_defined_cycles_protocols::farna::RNA_DeNovoProtocolprivate
vary_bond_geometry_protocols::farna::RNA_DeNovoProtocolprivate
~Mover()protocols::moves::Movervirtual
~RNA_DeNovoProtocol()protocols::farna::RNA_DeNovoProtocol