Rosetta Protocols  2014.35
protocols::hybridization::FoldTreeHybridize Member List

This is the complete list of members for protocols::hybridization::FoldTreeHybridize, including all inherited members.

add_gap_constraints_to_pose(core::pose::Pose &pose, Loops const &chunks, int gap_edge_shift=0, Real stdev=0.1)protocols::hybridization::FoldTreeHybridize
add_hetatm_protocols::hybridization::FoldTreeHybridizeprivate
add_non_init_chunks_protocols::hybridization::FoldTreeHybridizeprivate
add_strand_pairing(core::scoring::dssp::Pairing const &pairing)protocols::hybridization::FoldTreeHybridizeprivate
add_strand_pairings()protocols::hybridization::FoldTreeHybridizeprivate
apply(core::pose::Pose &pose)protocols::hybridization::FoldTreeHybridizevirtual
protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap)protocols::moves::Movervirtual
auto_frag_insertion_weight(WeightedFragmentTrialMoverOP &frag_1mer_trial_mover, WeightedFragmentTrialMoverOP &small_frag_trial_mover, WeightedFragmentTrialMoverOP &big_frag_trial_mover)protocols::hybridization::FoldTreeHybridizeprivate
auto_frag_insertion_weight_protocols::hybridization::FoldTreeHybridizeprivate
big_frag_insertion_weight_protocols::hybridization::FoldTreeHybridizeprivate
center_of_mass(core::pose::Pose const &pose)protocols::hybridization::FoldTreeHybridize
chunk_insertion_weight_protocols::hybridization::FoldTreeHybridizeprivate
clear_info()protocols::moves::Moverinlinevirtual
clone() const protocols::hybridization::FoldTreeHybridizeprivatevirtual
create()protocols::moves::Movervirtual
cst_file_protocols::hybridization::FoldTreeHybridizeprivate
domain_assembly_protocols::hybridization::FoldTreeHybridizeprivate
filter_templates(std::set< core::Size > const &templates_to_remove)protocols::hybridization::FoldTreeHybridizeprivate
filter_templates_protocols::hybridization::FoldTreeHybridizeprivate
Filters_map typedefprotocols::moves::Mover
floating_pairs_protocols::hybridization::FoldTreeHybridizeprivate
foldtree_mover_protocols::hybridization::FoldTreeHybridizeprivate
FoldTreeHybridize()protocols::hybridization::FoldTreeHybridize
FoldTreeHybridize(core::Size const initial_template_index, utility::vector1< core::pose::PoseOP > const &template_poses, utility::vector1< core::Real > const &template_weights, utility::vector1< protocols::loops::Loops > const &template_chunks, utility::vector1< protocols::loops::Loops > const &template_contigs, core::fragment::FragSetOP fragments_small_in, core::fragment::FragSetOP fragments_big_in)protocols::hybridization::FoldTreeHybridize
frag_1mer_insertion_weight_protocols::hybridization::FoldTreeHybridizeprivate
frag_libs_1mer_protocols::hybridization::FoldTreeHybridizeprivate
frag_libs_big_protocols::hybridization::FoldTreeHybridizeprivate
frag_libs_small_protocols::hybridization::FoldTreeHybridizeprivate
frag_weight_aligned_protocols::hybridization::FoldTreeHybridizeprivate
fresh_instance() const protocols::hybridization::FoldTreeHybridizeprivatevirtual
gap_distance(Size Seq_gap)protocols::hybridization::FoldTreeHybridize
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_jump_anchors()protocols::hybridization::FoldTreeHybridizeprivate
get_last_move_status() const protocols::moves::Mover
get_name() const protocols::hybridization::FoldTreeHybridizevirtual
get_native_pose() const protocols::moves::Mover
get_pairings_jump_mover()protocols::hybridization::FoldTreeHybridizeprivate
get_pairings_residues()protocols::hybridization::FoldTreeHybridize
get_residue_weights_for_1mers(core::pose::Pose &pose)protocols::hybridization::FoldTreeHybridize
get_residue_weights_for_big_frags(core::pose::Pose &pose)protocols::hybridization::FoldTreeHybridize
get_residue_weights_for_small_frags(core::pose::Pose &pose)protocols::hybridization::FoldTreeHybridize
get_strand_pairs()protocols::hybridization::FoldTreeHybridizeinline
get_type() const protocols::moves::Moverinline
hetatm_prot_cst_weight_protocols::hybridization::FoldTreeHybridizeprivate
hetatm_self_cst_weight_protocols::hybridization::FoldTreeHybridizeprivate
hybridize_setup_protocols::hybridization::FoldTreeHybridizeprivate
increase_cycles_protocols::hybridization::FoldTreeHybridizeprivate
info()protocols::moves::Moverinlinevirtual
info() const protocols::moves::Moverinlinevirtual
init()protocols::hybridization::FoldTreeHybridize
initial_template_index_protocols::hybridization::FoldTreeHybridizeprivate
initialize_pose_by_templates_protocols::hybridization::FoldTreeHybridizeprivate
jump_frags_protocols::hybridization::FoldTreeHybridizeprivate
jump_sample_protocols::hybridization::FoldTreeHybridizeprivate
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
map_pdb_info_number(const core::pose::Pose &pose, core::Size pdb_res)protocols::hybridization::FoldTreeHybridizeprivate
max_registry_shift_protocols::hybridization::FoldTreeHybridizeprivate
Mover()protocols::moves::Mover
Mover(std::string const &type_name)protocols::moves::Mover
Mover(Mover const &other)protocols::moves::Mover
name()protocols::moves::Moverinlinestatic
native_protocols::hybridization::FoldTreeHybridizeprivate
normalize_template_wts()protocols::hybridization::FoldTreeHybridizeprivate
operator=(Mover const &other)protocols::moves::Mover
overlap_chainbreaks_protocols::hybridization::FoldTreeHybridizeprivate
pairings_file_protocols::hybridization::FoldTreeHybridizeprivate
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(utility::tag::TagCOP const, basic::datacache::DataMap &, Filters_map const &, Movers_map const &, Pose const &)protocols::hybridization::FoldTreeHybridizeprivatevirtual
parse_state(SerializableState const &state)protocols::moves::Movervirtual
Pose typedefprotocols::moves::Mover
PoseCOP typedefprotocols::moves::Mover
random_sheets_protocols::hybridization::FoldTreeHybridizeprivate
realign_domains_protocols::hybridization::FoldTreeHybridizeprivate
register_options()protocols::moves::Moverinlinestatic
reinitialize_for_each_job() const protocols::moves::Movervirtual
reinitialize_for_new_input() const protocols::moves::Movervirtual
reset_status()protocols::moves::Mover
residue_max_registry_shift_protocols::hybridization::FoldTreeHybridizeprivate
residue_sample_abinitio_protocols::hybridization::FoldTreeHybridizeprivate
residue_sample_template_protocols::hybridization::FoldTreeHybridizeprivate
restore_original_foldtree(core::pose::Pose &pose)protocols::hybridization::FoldTreeHybridize
revert_loops_to_original(core::pose::Pose &pose, Loops loops)protocols::hybridization::FoldTreeHybridize
save_state(SerializableState &state)protocols::moves::Movervirtual
scorefxn_protocols::hybridization::FoldTreeHybridizeprivate
set_add_hetatm(bool add_hetatm_in, core::Real hetatm_self_cst_weight_in, core::Real hetatm_prot_cst_weight_in)protocols::hybridization::FoldTreeHybridizeinline
set_add_non_init_chunks(bool add_non_init_chunks_in)protocols::hybridization::FoldTreeHybridizeinline
set_auto_frag_insertion_weight(bool auto_frag_insertion_weight_in)protocols::hybridization::FoldTreeHybridizeinline
set_big_frag_insertion_weight(core::Real big_frag_insertion_weight_in)protocols::hybridization::FoldTreeHybridizeinline
set_chunk_insertion_weight(core::Real chunk_insertion_weight_in)protocols::hybridization::FoldTreeHybridizeinline
set_constraint_file(std::string cst_file_in)protocols::hybridization::FoldTreeHybridizeinline
set_current_job(protocols::jobdist::BasicJobCOP job)protocols::moves::Mover
set_current_tag(std::string const &new_tag)protocols::moves::Moverinline
set_domain_assembly(bool domain_assembly_in)protocols::hybridization::FoldTreeHybridizeinline
set_filter_templates(bool filter_templates_in)protocols::hybridization::FoldTreeHybridizeinline
set_frag_1mer_insertion_weight(core::Real frag_1mer_insertion_weight_in)protocols::hybridization::FoldTreeHybridizeinline
set_frag_weight_aligned(core::Real frag_weight_aligned_in)protocols::hybridization::FoldTreeHybridizeinline
set_increase_cycles(core::Real increase_cycles_in)protocols::hybridization::FoldTreeHybridizeinline
set_input_pose(PoseCOP pose)protocols::moves::Movervirtual
set_last_move_status(MoverStatus status)protocols::moves::Moverprotected
set_loops_to_virt_ala(core::pose::Pose &pose, Loops loops)protocols::hybridization::FoldTreeHybridize
set_max_registry_shift(core::Size max_registry_shift_in)protocols::hybridization::FoldTreeHybridizeinline
set_native_pose(PoseCOP pose)protocols::moves::Movervirtual
set_pairings_file(std::string pairings_file_in)protocols::hybridization::FoldTreeHybridizeinline
set_random_sheets(utility::vector1< core::Size > random_sheets_in)protocols::hybridization::FoldTreeHybridizeinline
set_scorefunction(core::scoring::ScoreFunctionOP const scorefxn)protocols::hybridization::FoldTreeHybridizeinline
set_sheets(utility::vector1< core::Size > sheets_in)protocols::hybridization::FoldTreeHybridizeinline
set_small_frag_insertion_weight(core::Real small_frag_insertion_weight_in)protocols::hybridization::FoldTreeHybridizeinline
set_stage1_1_cycles(core::Size stage1_1_cycles_in)protocols::hybridization::FoldTreeHybridizeinline
set_stage1_2_cycles(core::Size stage1_2_cycles_in)protocols::hybridization::FoldTreeHybridizeinline
set_stage1_3_cycles(core::Size stage1_3_cycles_in)protocols::hybridization::FoldTreeHybridizeinline
set_stage1_4_cycles(core::Size stage1_4_cycles_in)protocols::hybridization::FoldTreeHybridizeinline
set_task_factory(core::pack::task::TaskFactoryOP task_factory_in)protocols::hybridization::FoldTreeHybridize
set_top_n_big_frag(core::Size top_n_big_frag_in)protocols::hybridization::FoldTreeHybridizeinline
set_top_n_small_frag(core::Size top_n_small_frag_in)protocols::hybridization::FoldTreeHybridizeinline
set_type(std::string const &setting)protocols::moves::Moverinline
set_user_csts(utility::vector1< core::Size > user_csts_in)protocols::hybridization::FoldTreeHybridizeinline
setup_foldtree(core::pose::Pose &pose)protocols::hybridization::FoldTreeHybridize
setup_for_parser()protocols::hybridization::FoldTreeHybridize
setup_scorefunctions(core::scoring::ScoreFunctionOP score0, core::scoring::ScoreFunctionOP score1, core::scoring::ScoreFunctionOP score2, core::scoring::ScoreFunctionOP score5, core::scoring::ScoreFunctionOP score3)protocols::hybridization::FoldTreeHybridize
sheets_protocols::hybridization::FoldTreeHybridizeprivate
show(std::ostream &output=std::cout) const protocols::moves::Movervirtual
small_frag_insertion_weight_protocols::hybridization::FoldTreeHybridizeprivate
ss_chunks_pose_protocols::hybridization::FoldTreeHybridizeprivate
stage1_1_cycles_protocols::hybridization::FoldTreeHybridizeprivate
stage1_2_cycles_protocols::hybridization::FoldTreeHybridizeprivate
stage1_3_cycles_protocols::hybridization::FoldTreeHybridizeprivate
stage1_4_cycles_protocols::hybridization::FoldTreeHybridizeprivate
strand_pairings_template_indices_protocols::hybridization::FoldTreeHybridizeprivate
strand_pairs_protocols::hybridization::FoldTreeHybridizeprivate
Strings typedefprotocols::moves::Mover
superimpose_strand_pairings_to_templates(core::pose::Pose &pose)protocols::hybridization::FoldTreeHybridizeprivate
TagCOP typedefprotocols::moves::Mover
target_sequence_protocols::hybridization::FoldTreeHybridizeprivate
task_factory_protocols::hybridization::FoldTreeHybridizeprivate
template_chunks_protocols::hybridization::FoldTreeHybridizeprivate
template_contigs_protocols::hybridization::FoldTreeHybridizeprivate
template_poses_protocols::hybridization::FoldTreeHybridizeprivate
template_wts_protocols::hybridization::FoldTreeHybridizeprivate
templates_with_incorrect_strand_pairings_protocols::hybridization::FoldTreeHybridizeprivate
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
top_n_big_frag_protocols::hybridization::FoldTreeHybridizeprivate
top_n_small_frag_protocols::hybridization::FoldTreeHybridizeprivate
translate_virt_to_CoM(core::pose::Pose &pose)protocols::hybridization::FoldTreeHybridize
type() const protocols::moves::Moverinline
type(const std::string &type_in)protocols::moves::Moverinline
user_csts_protocols::hybridization::FoldTreeHybridizeprivate
~Mover()protocols::moves::Movervirtual