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

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

add_evaluation(evaluation::PoseEvaluatorOP ev)protocols::abinitio::Protocol
add_spanning_region(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitio
ALL_STAGES enum valueprotocols::abinitio::MembraneAbinitio
apply(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitiovirtual
protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap)protocols::moves::Movervirtual
apply_large_frags_protocols::abinitio::MembraneAbinitioprivate
BaseClass typedefprotocols::abinitio::Protocol
bQuickTest() const protocols::abinitio::MembraneAbinitioinline
bQuickTest_protocols::abinitio::MembraneAbinitioprivate
brute_move_large()protocols::abinitio::MembraneAbinitio
brute_move_large_protocols::abinitio::MembraneAbinitioprivate
brute_move_small()protocols::abinitio::MembraneAbinitio
brute_move_small_protocols::abinitio::MembraneAbinitioprivate
brute_move_small_top25()protocols::abinitio::MembraneAbinitio
brute_move_small_top25_protocols::abinitio::MembraneAbinitioprivate
centroid_scorefxn()protocols::abinitio::Protocolinline
checkpoint(core::pose::Pose &pose, std::string const &id)protocols::abinitio::MembraneAbinitiovirtual
checkpoint_protocols::abinitio::MembraneAbinitioprivate
checkpoint_ids_protocols::abinitio::MembraneAbinitioprivate
clear_checkpoints(void)protocols::abinitio::MembraneAbinitiovirtual
clear_info()protocols::moves::Moverinlinevirtual
clone() const protocols::abinitio::MembraneAbinitiovirtual
create()protocols::moves::Movervirtual
current_scorefxn() const protocols::abinitio::MembraneAbinitioprotected
current_scorefxn(core::scoring::ScoreFunction const &scorefxn)protocols::abinitio::MembraneAbinitioprotected
do_stage1_cycles(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitioprotectedvirtual
do_stage2_cycles(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitioprotectedvirtual
do_stage3_cycles(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitioprotectedvirtual
do_stage3b_cycles(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitioprotectedvirtual
do_stage4_cycles(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitioprotectedvirtual
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
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 protocols::abinitio::MembraneAbinitiovirtual
get_native_pose() const protocols::moves::Mover
get_tmh_inserted(core::pose::Pose const &pose) const protocols::abinitio::MembraneAbinitioprivate
get_type() const protocols::moves::Moverinline
info()protocols::moves::Moverinlinevirtual
info() const protocols::moves::Moverinlinevirtual
init(core::pose::Pose const &pose)protocols::abinitio::MembraneAbinitiovirtual
just_smooth_cycles() const protocols::abinitio::MembraneAbinitioinline
just_smooth_cycles_protocols::abinitio::MembraneAbinitioprivate
kinematics()protocols::abinitio::Protocolinline
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
mc()protocols::abinitio::MembraneAbinitioinline
mc() const protocols::abinitio::MembraneAbinitioinline
mc_protocols::abinitio::MembraneAbinitioprivate
mc_ptr()protocols::abinitio::MembraneAbinitioinlineprotected
MembraneAbinitio(simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_small_top25, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int)protocols::abinitio::MembraneAbinitio
MembraneAbinitio(core::fragment::FragSetCOP fragset_small, core::fragment::FragSetCOP fragset_small_top25, core::fragment::FragSetCOP fragset_large, core::kinematics::MoveMapCOP movemap)protocols::abinitio::MembraneAbinitio
MembraneEmbed_from_pose(core::pose::Pose const &) const protocols::abinitio::MembraneAbinitioprivate
MembraneTopology_from_pose(core::pose::Pose const &) const protocols::abinitio::MembraneAbinitioprivate
move_all_inserted(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitio
movemap()protocols::abinitio::MembraneAbinitio
movemap_protocols::abinitio::MembraneAbinitioprivate
Mover()protocols::moves::Mover
Mover(std::string const &type_name)protocols::moves::Mover
Mover(Mover const &other)protocols::moves::Mover
name()protocols::moves::Moverinlinestatic
nonconst_MembraneEmbed_from_pose(core::pose::Pose &) const protocols::abinitio::MembraneAbinitioprivate
nonconst_MembraneTopology_from_pose(core::pose::Pose &) const protocols::abinitio::MembraneAbinitioprivate
only_stage4_protocols::abinitio::MembraneAbinitioprivate
operator=(Mover const &other)protocols::moves::Mover
output_debug_structure(core::pose::Pose &pose, std::string prefix)protocols::abinitio::MembraneAbinitioprotectedvirtual
Parent typedefprotocols::abinitio::MembraneAbinitioprivate
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::MembraneAbinitioprotectedvirtual
prepare_loop_in_stage4(core::pose::Pose &, Size, Size)protocols::abinitio::MembraneAbinitioprotectedvirtual
prepare_stage1(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitioprotectedvirtual
prepare_stage2(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitioprotectedvirtual
prepare_stage3(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitioprotectedvirtual
prepare_stage4(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitioprotectedvirtual
print_debug(core::pose::Pose &pose)protocols::abinitio::MembraneAbinitio
Protocol()protocols::abinitio::Protocol
recover_checkpoint(core::pose::Pose &pose, std::string const &id)protocols::abinitio::MembraneAbinitiovirtual
register_options()protocols::abinitio::MembraneAbinitiostatic
reinitialize_for_each_job() const protocols::moves::Movervirtual
reinitialize_for_new_input() const protocols::moves::Movervirtual
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
score_stage1_protocols::abinitio::MembraneAbinitioprivate
score_stage2_protocols::abinitio::MembraneAbinitioprivate
score_stage3a_protocols::abinitio::MembraneAbinitioprivate
score_stage3b_protocols::abinitio::MembraneAbinitioprivate
score_stage4_protocols::abinitio::MembraneAbinitioprivate
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::Moverinline
set_current_weight(core::scoring::ScoreType type, core::Real setting)protocols::abinitio::MembraneAbinitioprotected
set_cycles(core::Real increase_cycles=1.0)protocols::abinitio::MembraneAbinitiovirtual
set_default_mc(core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn)protocols::abinitio::MembraneAbinitioprotectedvirtual
set_default_options()protocols::abinitio::MembraneAbinitioprotectedvirtual
set_default_scores()protocols::abinitio::MembraneAbinitioprotectedvirtual
set_defaults(core::pose::Pose const &pose)protocols::abinitio::MembraneAbinitioprotectedvirtual
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::MembraneAbinitio
set_movemap(core::kinematics::MoveMapCOP mm)protocols::abinitio::MembraneAbinitiovirtual
set_moves(simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small)protocols::abinitio::MembraneAbinitio
set_native_pose(PoseCOP pose)protocols::moves::Movervirtual
set_only_stage4(bool value)protocols::abinitio::MembraneAbinitioinline
set_score_weight(core::scoring::ScoreType, core::Real setting, StageID stage=ALL_STAGES)protocols::abinitio::MembraneAbinitiovirtual
set_silentout_file_name(std::string str)protocols::abinitio::Protocolinline
set_stage4_cycles(Size stage4_cycles_new)protocols::abinitio::MembraneAbinitioinline
set_trials()protocols::abinitio::MembraneAbinitioprotectedvirtual
set_type(std::string const &setting)protocols::moves::Moverinline
short_insert_region_protocols::abinitio::MembraneAbinitioprivate
show(std::ostream &output=std::cout) const protocols::moves::Movervirtual
smooth_move_small()protocols::abinitio::MembraneAbinitio
smooth_move_small_protocols::abinitio::MembraneAbinitioprivate
smooth_trial_small_protocols::abinitio::MembraneAbinitioprivate
stage1_cycles() const protocols::abinitio::MembraneAbinitioinline
stage1_cycles_protocols::abinitio::MembraneAbinitioprotected
stage2_cycles() const protocols::abinitio::MembraneAbinitioinline
stage2_cycles_protocols::abinitio::MembraneAbinitioprotected
stage2_mover(core::pose::Pose &pose, moves::TrialMoverOP trials_in)protocols::abinitio::MembraneAbinitioprotectedvirtual
stage3_cycles() const protocols::abinitio::MembraneAbinitioinline
stage3_cycles_protocols::abinitio::MembraneAbinitioprotected
stage3_mover(core::pose::Pose &pose, int lct1, int lct2, moves::TrialMoverOP trials_in)protocols::abinitio::MembraneAbinitioprotectedvirtual
stage4_cycles() const protocols::abinitio::MembraneAbinitioinline
stage4_cycles_protocols::abinitio::MembraneAbinitioprotected
stage4_mover(core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in)protocols::abinitio::MembraneAbinitioprotectedvirtual
STAGE_1 enum valueprotocols::abinitio::MembraneAbinitio
STAGE_2 enum valueprotocols::abinitio::MembraneAbinitio
STAGE_3a enum valueprotocols::abinitio::MembraneAbinitio
STAGE_3b enum valueprotocols::abinitio::MembraneAbinitio
STAGE_4 enum valueprotocols::abinitio::MembraneAbinitio
StageID enum nameprotocols::abinitio::MembraneAbinitio
start_from_centroid() const protocols::abinitio::Protocolinlinevirtual
Strings typedefprotocols::moves::Mover
TagCOP typedefprotocols::moves::Mover
temperature_protocols::abinitio::MembraneAbinitioprivate
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
total_trials() const protocols::abinitio::MembraneAbinitioinline
total_trials_protocols::abinitio::MembraneAbinitioprivate
trial_large()protocols::abinitio::MembraneAbinitioinlineprotected
trial_large_protocols::abinitio::MembraneAbinitioprivate
trial_small()protocols::abinitio::MembraneAbinitioinlineprotected
trial_small_protocols::abinitio::MembraneAbinitioprivate
trial_small_top25()protocols::abinitio::MembraneAbinitioinlineprotected
trial_small_top25_protocols::abinitio::MembraneAbinitioprivate
trial_smooth()protocols::abinitio::MembraneAbinitioinlineprotected
type() const protocols::moves::Moverinline
type(const std::string &type_in)protocols::moves::Moverinline
update_moves()protocols::abinitio::MembraneAbinitioprotectedvirtual
~Mover()protocols::moves::Movervirtual
~Protocol()protocols::abinitio::Protocolinline