Rosetta Protocols  2014.35
protocols::abinitio::KinematicAbinitio Member List

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

add_evaluation(evaluation::PoseEvaluatorOP ev)protocols::abinitio::Protocol
ALL_STAGES enum valueprotocols::abinitio::ClassicAbinitio
apply(core::pose::Pose &pose)protocols::abinitio::KinematicAbinitiovirtual
protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap)protocols::moves::Movervirtual
BaseClass typedefprotocols::abinitio::Protocol
bIgnoreSequenceSeparation(bool setting)protocols::abinitio::FoldConstraintsinlineprotected
bIgnoreSequenceSeparation()protocols::abinitio::FoldConstraintsinlineprotected
bOverlapChainbreaks_protocols::abinitio::KinematicAbinitioprivate
bQuickTest() const protocols::abinitio::ClassicAbinitioinline
bRampChainbreaks_protocols::abinitio::KinematicAbinitioprivate
brute_move_large()protocols::abinitio::ClassicAbinitio
brute_move_small()protocols::abinitio::ClassicAbinitio
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 protocols::abinitio::KinematicAbinitioinlinevirtual
closure_protocol(loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol)protocols::abinitio::KinematicAbinitioinline
closure_protocol_protocols::abinitio::KinematicAbinitioprivate
constraints()protocols::abinitio::FoldConstraintsinlineprotected
create()protocols::moves::Movervirtual
create_bb_moves(core::pose::Pose &pose, moves::MoverOP std_moves, bool bLargeWobble, core::Real crank_up_angle)protocols::abinitio::KinematicAbinitioprivate
create_jump_moves(moves::MoverOP stdmove)protocols::abinitio::KinematicAbinitioprivate
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::FoldConstraintsprotectedvirtual
do_stage2_cycles(core::pose::Pose &pose)protocols::abinitio::FoldConstraintsprotectedvirtual
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
dump_jump_log(core::pose::Pose &pose, std::string const &file_name)protocols::abinitio::KinematicAbinitioprivate
evaluate_pose(core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const protocols::abinitio::Protocol
evaluator()protocols::abinitio::Protocolinline
Filters_map typedefprotocols::moves::Mover
FoldConstraints(simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy)protocols::abinitio::FoldConstraints
FoldConstraints(core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap)protocols::abinitio::FoldConstraints
FoldConstraints(FoldConstraints const &src)protocols::abinitio::FoldConstraints
fresh_instance() const protocols::moves::Movervirtual
full_constraint_set_protocols::abinitio::KinematicAbinitioprivate
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 protocols::abinitio::KinematicAbinitiovirtual
get_native_pose() const protocols::moves::Mover
get_type() const protocols::moves::Moverinline
info()protocols::moves::Moverinlinevirtual
info() const protocols::moves::Moverinlinevirtual
init(core::pose::Pose const &pose)protocols::abinitio::ClassicAbinitiovirtual
just_smooth_cycles() const protocols::abinitio::ClassicAbinitioinline
KinematicAbinitio(simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy)protocols::abinitio::KinematicAbinitio
KinematicAbinitio(core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap)protocols::abinitio::KinematicAbinitio
kinematics()protocols::abinitio::Protocolinline
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
max_seq_sep_fudge() const protocols::abinitio::FoldConstraintsinlineprotected
max_seq_sep_fudge(core::Real setting)protocols::abinitio::FoldConstraintsinlineprotected
mc()protocols::abinitio::ClassicAbinitioinline
mc() const protocols::abinitio::ClassicAbinitioinline
mc_ptr()protocols::abinitio::ClassicAbinitioprotected
min_move()protocols::abinitio::FoldConstraintsinlineprotected
min_trial(core::pose::Pose &pose)protocols::abinitio::FoldConstraintsprotected
movemap()protocols::abinitio::ClassicAbinitio
Mover()protocols::moves::Mover
Mover(std::string const &type_name)protocols::moves::Mover
Mover(Mover const &other)protocols::moves::Mover
name()protocols::moves::Moverinlinestatic
protocols::abinitio::Protocol::operator=(Mover const &other)protocols::moves::Mover
output_debug_structure(core::pose::Pose &pose, std::string prefix)protocols::abinitio::ClassicAbinitioprotectedvirtual
Parent typedefprotocols::abinitio::KinematicAbinitioprivate
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
prepare_loop_in_stage3(core::pose::Pose &, Size, Size)protocols::abinitio::KinematicAbinitiovirtual
prepare_loop_in_stage4(core::pose::Pose &, Size, Size)protocols::abinitio::KinematicAbinitiovirtual
prepare_stage1(core::pose::Pose &pose)protocols::abinitio::KinematicAbinitiovirtual
prepare_stage2(core::pose::Pose &pose)protocols::abinitio::KinematicAbinitiovirtual
prepare_stage3(core::pose::Pose &pose)protocols::abinitio::KinematicAbinitiovirtual
prepare_stage4(core::pose::Pose &pose)protocols::abinitio::FoldConstraintsprotectedvirtual
prepare_stage5(core::pose::Pose &pose)protocols::abinitio::ClassicAbinitioprotectedvirtual
Protocol()protocols::abinitio::Protocol
recover_low(core::pose::Pose &pose, StageID stage)protocols::abinitio::ClassicAbinitioprotected
recover_low_stages_protocols::abinitio::ClassicAbinitio
register_options()protocols::abinitio::KinematicAbinitiostatic
reinitialize_for_each_job() const protocols::moves::Movervirtual
reinitialize_for_new_input() const protocols::moves::Movervirtual
replace_scorefxn(core::pose::Pose &pose, StageID, core::Real intra_stage_progress)protocols::abinitio::KinematicAbinitioprotectedvirtual
reset_status()protocols::moves::Mover
return_centroid() const protocols::abinitio::Protocolinlinevirtual
return_centroid(bool setting)protocols::abinitio::Protocolinlinevirtual
save_state(SerializableState &state)protocols::moves::Movervirtual
set_centroid_scorefxn(core::scoring::ScoreFunctionOP sfxn)protocols::abinitio::Protocolinline
set_constraint_weight(core::Real setting)protocols::abinitio::FoldConstraintsinline
set_current_job(protocols::jobdist::BasicJobCOP job)protocols::moves::Mover
set_current_tag(std::string const &new_tag)protocols::moves::Moverinline
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::KinematicAbinitioprotectedvirtual
set_default_scores()protocols::abinitio::KinematicAbinitioprotectedvirtual
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_max_seq_sep(core::pose::Pose &pose, Size setting)protocols::abinitio::KinematicAbinitiovirtual
set_mc(moves::MonteCarloOP)protocols::abinitio::ClassicAbinitio
set_min_move(protocols::simple_moves::MinMoverOP mm)protocols::abinitio::FoldConstraintsprotected
set_movemap(core::kinematics::MoveMapCOP mm)protocols::abinitio::FoldConstraintsprotectedvirtual
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_seq_sep_stage1(core::Real setting)protocols::abinitio::FoldConstraintsinlineprotected
set_seq_sep_stage3(core::Real setting)protocols::abinitio::FoldConstraintsinlineprotected
set_show_viol_level(core::Size setting)protocols::abinitio::FoldConstraintsinline
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(Size stage4_cycles_new)protocols::abinitio::ClassicAbinitioinline
set_trials()protocols::abinitio::ClassicAbinitioprotectedvirtual
set_type(std::string const &setting)protocols::moves::Moverinline
setup_default_min_move()protocols::abinitio::FoldConstraintsprotectedvirtual
show(std::ostream &output=std::cout) const protocols::moves::Movervirtual
smooth_move_small()protocols::abinitio::ClassicAbinitio
stage1_cycles() const protocols::abinitio::ClassicAbinitioinline
stage1_cycles_protocols::abinitio::ClassicAbinitioprotected
stage1_mover(core::pose::Pose &pose, moves::TrialMoverOP trials_in)protocols::abinitio::KinematicAbinitiovirtual
stage2_cycles() const protocols::abinitio::ClassicAbinitioinline
stage2_cycles_protocols::abinitio::ClassicAbinitioprotected
stage2_mover(core::pose::Pose &pose, moves::TrialMoverOP trials_in)protocols::abinitio::KinematicAbinitiovirtual
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::KinematicAbinitiovirtual
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::KinematicAbinitiovirtual
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
TagCOP typedefprotocols::moves::Mover
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
total_res(core::pose::Pose const &pose) const protocols::abinitio::FoldConstraintsprotected
total_trials() const protocols::abinitio::ClassicAbinitioinline
trial_large()protocols::abinitio::ClassicAbinitioprotected
trial_small()protocols::abinitio::ClassicAbinitioprotected
trial_smooth()protocols::abinitio::ClassicAbinitioprotected
type() const protocols::moves::Moverinline
type(const std::string &type_in)protocols::moves::Moverinline
update_moves()protocols::abinitio::ClassicAbinitioprotectedvirtual
~ClassicAbinitio()protocols::abinitio::ClassicAbinitio
~FoldConstraints()protocols::abinitio::FoldConstraints
~KinematicAbinitio()protocols::abinitio::KinematicAbinitio
~Mover()protocols::moves::Movervirtual
~Protocol()protocols::abinitio::Protocolinline