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protocols::abinitio::ClassicAbinitio Member List

This is the complete list of members for protocols::abinitio::ClassicAbinitio, including all inherited members.

add_evaluation(evaluation::PoseEvaluatorOP ev)protocols::abinitio::Protocol
ALL_STAGES enum valueprotocols::abinitio::ClassicAbinitio
apply(core::pose::Pose &pose) overrideprotocols::abinitio::ClassicAbinitiovirtual
apply_large_frags_protocols::abinitio::ClassicAbinitioprivate
BaseClass typedefprotocols::abinitio::Protocol
bQuickTest() const protocols::abinitio::ClassicAbinitioinline
bQuickTest_protocols::abinitio::ClassicAbinitioprivate
brute_move_large()protocols::abinitio::ClassicAbinitio
brute_move_large_protocols::abinitio::ClassicAbinitioprivate
brute_move_small()protocols::abinitio::ClassicAbinitio
brute_move_small_protocols::abinitio::ClassicAbinitioprivate
bSkipStage1_protocols::abinitio::ClassicAbinitio
bSkipStage2_protocols::abinitio::ClassicAbinitio
bSkipStage3_protocols::abinitio::ClassicAbinitio
bSkipStage4_protocols::abinitio::ClassicAbinitio
bSkipStage5_protocols::abinitio::ClassicAbinitio
centroid_scorefxn()protocols::abinitio::Protocolinline
ClassicAbinitio(simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int)protocols::abinitio::ClassicAbinitio
ClassicAbinitio(core::fragment::FragSetCOP fragset_small, core::fragment::FragSetCOP fragset_large, core::kinematics::MoveMapCOP movemap)protocols::abinitio::ClassicAbinitio
ClassicAbinitio(ClassicAbinitio const &src)protocols::abinitio::ClassicAbinitio
clear_info()protocols::moves::Moverinlinevirtual
clone() const overrideprotocols::abinitio::ClassicAbinitiovirtual
close_chbrk_protocols::abinitio::ClassicAbinitioprivate
create()protocols::moves::Movervirtual
current_scorefxn() const protocols::abinitio::ClassicAbinitioprotected
current_scorefxn(core::scoring::ScoreFunction const &scorefxn)protocols::abinitio::ClassicAbinitioprotected
do_stage1_cycles(core::pose::Pose &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
do_stage2_cycles(core::pose::Pose &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
do_stage3_cycles(core::pose::Pose &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
do_stage4_cycles(core::pose::Pose &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
do_stage5_cycles(core::pose::Pose &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
evaluate_pose(core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const protocols::abinitio::Protocol
evaluator()protocols::abinitio::Protocolinline
fresh_instance() const protocols::moves::Movervirtual
fullatom_scorefxn()protocols::abinitio::Protocolinline
get_additional_output()protocols::moves::Movervirtual
get_checkpoints()protocols::abinitio::Protocolinlinevirtual
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 overrideprotocols::abinitio::ClassicAbinitiovirtual
get_native_pose() const protocols::moves::Mover
get_self_ptr() const protocols::moves::Moverinline
get_self_ptr()protocols::moves::Moverinline
get_self_weak_ptr() const protocols::moves::Moverinline
get_self_weak_ptr()protocols::moves::Moverinline
get_type() const protocols::moves::Moverinline
info()protocols::moves::Moverinlinevirtual
info() const protocols::moves::Moverinlinevirtual
init(core::pose::Pose const &pose) overrideprotocols::abinitio::ClassicAbinitiovirtual
just_smooth_cycles() const protocols::abinitio::ClassicAbinitioinline
just_smooth_cycles_protocols::abinitio::ClassicAbinitioprivate
kinematics()protocols::abinitio::Protocolinline
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
mc()protocols::abinitio::ClassicAbinitioinline
mc() const protocols::abinitio::ClassicAbinitioinline
mc_protocols::abinitio::ClassicAbinitioprivate
mc_ptr()protocols::abinitio::ClassicAbinitioprotected
movemap()protocols::abinitio::ClassicAbinitio
movemap_protocols::abinitio::ClassicAbinitioprivate
Mover()protocols::moves::Mover
Mover(std::string const &type_name)protocols::moves::Mover
name()protocols::moves::Moverinlinestatic
operator=(ClassicAbinitio const &src)protocols::abinitio::ClassicAbinitioprivate
output_debug_structure(core::pose::Pose &pose, std::string prefix) overrideprotocols::abinitio::ClassicAbinitioprotectedvirtual
pack_rotamers_protocols::abinitio::ClassicAbinitioprivate
Parent typedefprotocols::abinitio::ClassicAbinitioprivate
parse_my_tag(TagCOP tag, basic::datacache::DataMap &data)protocols::moves::Movervirtual
Pose typedefprotocols::moves::Mover
PoseCOP typedefprotocols::moves::Mover
prepare_loop_in_stage3(core::pose::Pose &, core::Size, core::Size)protocols::abinitio::ClassicAbinitioprotectedvirtual
prepare_loop_in_stage4(core::pose::Pose &, core::Size, core::Size)protocols::abinitio::ClassicAbinitioprotectedvirtual
prepare_stage1(core::pose::Pose &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
prepare_stage2(core::pose::Pose &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
prepare_stage3(core::pose::Pose &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
prepare_stage4(core::pose::Pose &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
prepare_stage5(core::pose::Pose &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
Protocol()protocols::abinitio::Protocol
provide_citation_info(basic::citation_manager::CitationCollectionList &) const protocols::moves::Movervirtual
recover_low(core::pose::Pose &pose, StageID stage)protocols::abinitio::ClassicAbinitioprotected
recover_low_stages_protocols::abinitio::ClassicAbinitio
register_options()protocols::abinitio::ClassicAbinitiostatic
reinitialize_for_each_job() const protocols::moves::Movervirtual
reinitialize_for_new_input() const protocols::moves::Movervirtual
replace_scorefxn(core::pose::Pose &pose, StageID stage, core::Real intra_stage_progress)protocols::abinitio::ClassicAbinitioprotectedvirtual
reset_status()protocols::moves::Mover
return_centroid() const protocols::abinitio::Protocolinlinevirtual
return_centroid(bool setting)protocols::abinitio::Protocolinlinevirtual
score_stage1_protocols::abinitio::ClassicAbinitioprivate
score_stage2_protocols::abinitio::ClassicAbinitioprivate
score_stage3a_protocols::abinitio::ClassicAbinitioprivate
score_stage3b_protocols::abinitio::ClassicAbinitioprivate
score_stage4_protocols::abinitio::ClassicAbinitioprivate
score_stage4rot_protocols::abinitio::ClassicAbinitioprivate
score_stage4rot_sc_protocols::abinitio::ClassicAbinitioprivate
score_stage5_protocols::abinitio::ClassicAbinitioprivate
set_centroid_scorefxn(core::scoring::ScoreFunctionOP sfxn)protocols::abinitio::Protocolinline
set_current_job(protocols::jobdist::BasicJobCOP job)protocols::moves::Mover
set_current_tag(std::string const &new_tag)protocols::moves::Moverinlinevirtual
set_current_weight(core::scoring::ScoreType type, core::Real setting)protocols::abinitio::ClassicAbinitioprotected
set_cycles(core::Real increase_cycles=1.0)protocols::abinitio::ClassicAbinitiovirtual
set_default_mc(core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn)protocols::abinitio::ClassicAbinitioprotectedvirtual
set_default_options()protocols::abinitio::ClassicAbinitioprotectedvirtual
set_default_scores()protocols::abinitio::ClassicAbinitioprotectedvirtual
set_defaults(core::pose::Pose const &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
set_evaluation(evaluation::MetaPoseEvaluatorOP ev)protocols::abinitio::Protocol
set_fullatom_scorefxn(core::scoring::ScoreFunctionOP sfxn)protocols::abinitio::Protocolinline
set_input_pose(PoseCOP pose)protocols::moves::Movervirtual
set_kinematics(abinitio::KinematicControlOP kc)protocols::abinitio::Protocolinline
set_last_move_status(MoverStatus status)protocols::moves::Moverprotected
set_mc(moves::MonteCarloOP)protocols::abinitio::ClassicAbinitio
set_movemap(core::kinematics::MoveMapCOP mm)protocols::abinitio::ClassicAbinitiovirtual
set_moves(simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small)protocols::abinitio::ClassicAbinitio
set_native_pose(PoseCOP pose)protocols::moves::Movervirtual
set_score_weight(core::scoring::ScoreType, core::Real setting, StageID stage=ALL_STAGES)protocols::abinitio::ClassicAbinitiovirtual
set_silentout_file_name(std::string str)protocols::abinitio::Protocolinline
set_skip_stage1(bool setting)protocols::abinitio::ClassicAbinitioinline
set_skip_stage2(bool setting)protocols::abinitio::ClassicAbinitioinline
set_stage4_cycles(core::Size stage4_cycles_new)protocols::abinitio::ClassicAbinitioinline
set_trials()protocols::abinitio::ClassicAbinitioprotectedvirtual
set_type(std::string const &setting)protocols::moves::Moverinline
set_use_trRosetta_constraints(bool const setting)protocols::abinitio::Protocol
short_insert_region_protocols::abinitio::ClassicAbinitioprivate
show(std::ostream &output=std::cout) const protocols::moves::Movervirtual
smooth_move_small()protocols::abinitio::ClassicAbinitio
smooth_move_small_protocols::abinitio::ClassicAbinitioprivate
smooth_trial_small_protocols::abinitio::ClassicAbinitioprivate
smooth_trial_small_pack_protocols::abinitio::ClassicAbinitioprivate
stage1_cycles() const protocols::abinitio::ClassicAbinitioinline
stage1_cycles_protocols::abinitio::ClassicAbinitioprotected
stage1_mover(core::pose::Pose &pose, moves::TrialMoverOP trials_in)protocols::abinitio::ClassicAbinitioprotectedvirtual
stage2_cycles() const protocols::abinitio::ClassicAbinitioinline
stage2_cycles_protocols::abinitio::ClassicAbinitioprotected
stage2_mover(core::pose::Pose &pose, moves::TrialMoverOP trials_in)protocols::abinitio::ClassicAbinitioprotectedvirtual
stage3_cycles() const protocols::abinitio::ClassicAbinitioinline
stage3_cycles_protocols::abinitio::ClassicAbinitioprotected
stage3_mover(core::pose::Pose &pose, int lct1, int lct2, moves::TrialMoverOP trials_in)protocols::abinitio::ClassicAbinitioprotectedvirtual
stage4_cycles() const protocols::abinitio::ClassicAbinitioinline
stage4_cycles_protocols::abinitio::ClassicAbinitioprotected
stage4_cycles_pack_rate_protocols::abinitio::ClassicAbinitioprotected
stage4_mover(core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in)protocols::abinitio::ClassicAbinitioprotectedvirtual
stage4rot_mover(core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in)protocols::abinitio::ClassicAbinitioprotectedvirtual
stage5_cycles() const protocols::abinitio::ClassicAbinitioinline
stage5_cycles_protocols::abinitio::ClassicAbinitioprotected
stage5_mover(core::pose::Pose &pose, moves::TrialMoverOP trials_in)protocols::abinitio::ClassicAbinitioprotectedvirtual
STAGE_1 enum valueprotocols::abinitio::ClassicAbinitio
STAGE_2 enum valueprotocols::abinitio::ClassicAbinitio
STAGE_3a enum valueprotocols::abinitio::ClassicAbinitio
STAGE_3b enum valueprotocols::abinitio::ClassicAbinitio
STAGE_4 enum valueprotocols::abinitio::ClassicAbinitio
STAGE_4rot enum valueprotocols::abinitio::ClassicAbinitio
STAGE_5 enum valueprotocols::abinitio::ClassicAbinitio
StageID enum nameprotocols::abinitio::ClassicAbinitio
start_from_centroid() const protocols::abinitio::Protocolinlinevirtual
Strings typedefprotocols::moves::Mover
supports_trRosetta_constraints() const overrideprotocols::abinitio::ClassicAbinitiovirtual
TagCOP typedefprotocols::moves::Mover
temperature_protocols::abinitio::ClassicAbinitioprivate
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
total_trials() const protocols::abinitio::ClassicAbinitioinline
total_trials_protocols::abinitio::ClassicAbinitioprivate
trial_large()protocols::abinitio::ClassicAbinitioprotected
trial_large_protocols::abinitio::ClassicAbinitioprivate
trial_small()protocols::abinitio::ClassicAbinitioprotected
trial_small_protocols::abinitio::ClassicAbinitioprivate
trial_small_pack_protocols::abinitio::ClassicAbinitioprivate
trial_smooth()protocols::abinitio::ClassicAbinitioprotected
type(const std::string &type_in)protocols::moves::Moverinline
type() const protocols::moves::Moverinline
update_moves()protocols::abinitio::ClassicAbinitioprotectedvirtual
use_trRosetta_constraints() const protocols::abinitio::Protocolinline
~ClassicAbinitio() overrideprotocols::abinitio::ClassicAbinitio
~Protocol() override=defaultprotocols::abinitio::Protocol
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