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protocols::swa::rna::StepWiseRNA_ResidueSampler Member List

This is the complete list of members for protocols::swa::rna::StepWiseRNA_ResidueSampler, including all inherited members.

allow_base_pair_only_centroid_screen_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
allow_bulge_at_chainbreak_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
allow_syn_pyrimidine_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
apply(core::pose::Pose &pose_to_visualize)protocols::swa::rna::StepWiseRNA_ResidueSamplervirtual
protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap)protocols::moves::Movervirtual
apply_bulge_variant(core::pose::Pose &pose, core::Real const &delta_atr_score)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
assert_no_virt_ribose_sampling_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
atr_rep_screening_scorefxn_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
base_centroid_screener_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
bin_size_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
build_pose_from_scratch_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
centroid_screen_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Chain_break_screening(core::pose::Pose &chain_break_screening_pose, core::scoring::ScoreFunctionOP const &constraint_scorefxn)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Chain_break_screening_general(core::pose::Pose &chain_break_screening_pose, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, core::Size const five_prime_res)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
chainbreak_scorefxn_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
clear_info()protocols::moves::Moverinlinevirtual
clone() const protocols::moves::Movervirtual
cluster_pose_data_list(utility::vector1< pose_data_struct2 > &pose_data_list)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
cluster_rmsd_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
combine_long_loop_mode_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Copy_CCD_torsions(core::pose::Pose &pose, core::pose::Pose const &template_pose) const protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Copy_CCD_torsions_general(core::pose::Pose &pose, core::pose::Pose const &template_pose, core::Size const five_prime_res, core::Size const three_prime_res) const protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
count_data_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
create()protocols::moves::Movervirtual
create_rotamer_string(core::pose::Pose const &pose) const protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
create_tag(std::string const prestring, StepWiseRNA_RotamerGenerator_WrapperOP const &rotamer_generator) const protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
create_torsion_value_string(core::Real const &torsion_value) const protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
current_score_cutoff_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
debug_eplison_south_sugar_mode_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
distinguish_pucker_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
do_not_sample_multiple_virtual_sugar_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
exclude_alpha_beta_gamma_sampling_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
extra_anti_chi_rotamer_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
extra_beta_rotamer_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
extra_epsilon_rotamer_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
extra_syn_chi_rotamer_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
fast_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Filters_map typedefprotocols::moves::Mover
finer_sampling_at_chain_closure_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
floating_base_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
floating_base_sampling(core::pose::Pose &pose, FloatingBaseChainClosureJobParameter const &prev_sugar_FB_JP)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
fresh_instance() const protocols::moves::Movervirtual
Full_atom_van_der_Waals_screening(core::pose::Pose &current_pose_screen, core::Real const &base_rep_score, core::Real const &base_atr_score, core::Real &delta_rep_score, core::Real &delta_atr_score, core::Size const &gap_size, bool const &Is_internal)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Full_atom_van_der_Waals_screening_REPLICATE(core::pose::Pose &current_pose_screen, core::Real const &base_rep_score, core::Real const &base_atr_score, core::Real &delta_rep_score, core::Real &delta_atr_score, core::Size const &gap_size, bool const &Is_internal)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
get_additional_output()protocols::moves::Movervirtual
get_base_atr_rep_score(core::pose::Pose const &pose, core::Real &base_atr_score, core::Real &base_rep_score)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
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_name() const protocols::swa::rna::StepWiseRNA_ResidueSamplervirtual
get_native_pose() const protocols::moves::Mover
get_pose_data_list()protocols::swa::rna::StepWiseRNA_ResidueSampler
get_reference_stub(core::Size const reference_res, core::pose::Pose const &pose) const protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
get_type() const protocols::moves::Moverinline
include_syn_chi_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
include_torsion_value_in_tag_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
info()protocols::moves::Moverinlinevirtual
info() const protocols::moves::Moverinlinevirtual
initialize_o2star_green_packer(core::pose::Pose &pose)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
initialize_o2star_packer_task(core::pose::Pose const &pose)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
initialize_scorefunctions()protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
integration_test_mode_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Is_current_sugar_virtual(core::pose::Pose const &pose) const protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Is_five_prime_chain_break_sugar_virtual(core::pose::Pose const &pose) const protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Is_previous_sugar_virtual(core::pose::Pose const &pose) const protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Is_three_prime_chain_break_sugar_virtual(core::pose::Pose const &pose) const protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
job_parameters_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
medium_fast_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Mover()protocols::moves::Mover
Mover(std::string const &type_name)protocols::moves::Mover
Mover(Mover const &other)protocols::moves::Mover
multiplier_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
name()protocols::moves::Moverinlinestatic
native_rmsd_screen_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
native_screen_rmsd_cutoff_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
num_pose_kept_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
o2star_green_packer_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
o2star_pack_scorefxn_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
o2star_pack_task_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
operator=(Mover const &other)protocols::moves::Mover
output_filename_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
output_pdb_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
output_pose_data_list(std::string const final_sampler_output_silent_file) const protocols::swa::rna::StepWiseRNA_ResidueSampler
parin_favorite_output_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
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(TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)protocols::moves::Movervirtual
parse_state(SerializableState const &state)protocols::moves::Movervirtual
PBP_clustering_at_chain_closure_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
perform_o2star_pack_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Pose typedefprotocols::moves::Mover
pose_data_list_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
Pose_selection_by_full_score(utility::vector1< pose_data_struct2 > &pose_data_list, core::pose::Pose &current_pose, std::string const &tag)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
PoseCOP typedefprotocols::moves::Mover
previous_floating_base_chain_closure(core::pose::Pose &viewer_pose, FloatingBaseChainClosureJobParameter const &FB_job_params, std::string const name)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
rebuild_bulge_mode_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
register_options()protocols::moves::Moverinlinestatic
reinitialize_CCD_torsions_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
reinitialize_for_each_job() const protocols::moves::Movervirtual
reinitialize_for_new_input() const protocols::moves::Movervirtual
rep_cutoff_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
reset_status()protocols::moves::Mover
sample_both_sugar_base_rotamer_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
sample_o2star_hydrogen(core::pose::Pose &pose, core::pose::Pose &pose_with_original_HO2star_torsion)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
sample_ONLY_multiple_virtual_sugar_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
sampling_scorefxn_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
save_state(SerializableState &state)protocols::moves::Movervirtual
scorefxn_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
set_allow_base_pair_only_centroid_screen(bool const setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_allow_bulge_at_chainbreak(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_allow_syn_pyrimidine(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_assert_no_virt_ribose_sampling(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_base_centroid_screener(StepWiseRNA_BaseCentroidScreenerOP &screener)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_centroid_screen(bool const setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_cluster_rmsd(core::Real const &setting)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_combine_long_loop_mode(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_current_job(protocols::jobdist::BasicJobCOP job)protocols::moves::Mover
set_current_tag(std::string const &new_tag)protocols::moves::Moverinline
set_debug_eplison_south_sugar_mode(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_distinguish_pucker(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_do_not_sample_multiple_virtual_sugar(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_exclude_alpha_beta_gamma_sampling(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_extra_anti_chi_rotamer(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_extra_beta_rotamer(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_extra_epsilon_rotamer(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_extra_syn_chi_rotamer(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_fast(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_finer_sampling_at_chain_closure(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_floating_base(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_include_syn_chi(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_include_torsion_value_in_tag(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_input_pose(PoseCOP pose)protocols::moves::Movervirtual
set_integration_test_mode(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_last_move_status(MoverStatus status)protocols::moves::Moverprotected
set_medium_fast(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_native_pose(PoseCOP pose)protocols::moves::Movervirtual
set_native_rmsd_screen(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_native_screen_rmsd_cutoff(core::Real const &setting)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_num_pose_kept(core::Size const &num_pose_kept)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_output_filename(std::string const &output_filename)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_output_pdb(bool const setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_parin_favorite_output(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_PBP_clustering_at_chain_closure(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_perform_o2star_pack(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_rebuild_bulge_mode(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_reinitialize_CCD_torsions(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_sample_both_sugar_base_rotamer(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_sample_ONLY_multiple_virtual_sugar(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_scorefxn(core::scoring::ScoreFunctionOP const &scorefxn)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_silent_file(std::string const &setting)protocols::swa::rna::StepWiseRNA_ResidueSampler
set_user_input_VDW_bin_screener(StepWiseRNA_VDW_Bin_ScreenerOP const &user_input_VDW_bin_screener)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_VDW_atr_rep_screen(bool const setting)protocols::swa::rna::StepWiseRNA_ResidueSamplerinline
set_verbose(bool const &setting)protocols::swa::rna::StepWiseRNA_ResidueSampler
sfd_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
silent_file_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
silent_file_data()protocols::swa::rna::StepWiseRNA_ResidueSampler
standard_sampling(core::pose::Pose &pose, utility::vector1< pose_data_struct2 > &pose_data_list, std::string const sugar_tag)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
standard_sampling_WRAPPER(core::pose::Pose &pose, FloatingBaseChainClosureJobParameter const &prev_sugar_FB_JP, FloatingBaseChainClosureJobParameter const &curr_sugar_FB_JP, FloatingBaseChainClosureJobParameter const &five_prime_CB_sugar_FB_JP, FloatingBaseChainClosureJobParameter const &three_prime_CB_sugar_FB_JP)protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
StepWiseRNA_ResidueSampler(StepWiseRNA_JobParametersCOP &job_parameters_)protocols::swa::rna::StepWiseRNA_ResidueSampler
Strings typedefprotocols::moves::Mover
TagPtr typedefprotocols::moves::Mover
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
type() const protocols::moves::Moverinline
type(const std::string &type_in)protocols::moves::Moverinline
Update_pose_data_list(std::string const &tag, utility::vector1< pose_data_struct2 > &pose_data_list, core::pose::Pose const &current_pose, core::Real const &current_score) const protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
use_green_packer_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
user_input_VDW_bin_screener_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
VDW_atr_rep_screen_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
verbose_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
working_rmsd_res_protocols::swa::rna::StepWiseRNA_ResidueSamplerprivate
~Mover()protocols::moves::Movervirtual
~StepWiseRNA_ResidueSampler()protocols::swa::rna::StepWiseRNA_ResidueSampler
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