add_additional_low_resolution_step(protocols::moves::MoverOP additional_low_resolution_mover) | protocols::docking::DockingProtocol | |
add_additional_task_operaration(core::pack::task::operation::TaskOperationOP task_operation) | protocols::docking::DockingProtocol | |
add_jump(core::Size const jump_number) | protocols::docking::DockingProtocol | inline |
apply(core::pose::Pose &pose) | protocols::docking::stateless::SaneDockingProtocol | virtual |
clear_info() | protocols::moves::Mover | inlinevirtual |
clone() const | protocols::docking::DockingProtocol | virtual |
create() | protocols::moves::Mover | virtual |
docking_highres_mover() const | protocols::docking::DockingProtocol | |
docking_lowres_mover() const | protocols::docking::DockingProtocol | |
DockingProtocol() | protocols::docking::DockingProtocol | |
DockingProtocol(Size const rb_jump_in, bool const low_res_protocol_only=false, bool const docking_local_refine=false, bool const autofoldtree=true, core::scoring::ScoreFunctionOP docking_score_low=core::scoring::ScoreFunctionOP(NULL), core::scoring::ScoreFunctionOP docking_score_high=core::scoring::ScoreFunctionOP(NULL)) | protocols::docking::DockingProtocol | |
DockingProtocol(DockJumps const movable_jumps, bool const low_res_protocol_only=false, bool const docking_local_refine=false, bool const autofoldtree=true, core::scoring::ScoreFunctionOP docking_score_low=core::scoring::ScoreFunctionOP(NULL), core::scoring::ScoreFunctionOP docking_score_high=core::scoring::ScoreFunctionOP(NULL)) | protocols::docking::DockingProtocol | |
DockingProtocol(DockingProtocol const &rhs) | protocols::docking::DockingProtocol | |
Filters_map typedef | protocols::moves::Mover | |
fresh_instance() const | protocols::docking::DockingProtocol | virtual |
get_additional_output() | protocols::moves::Mover | virtual |
get_additional_task_operarations() | protocols::docking::DockingProtocol | |
get_current_job() const | protocols::moves::Mover | |
get_current_tag() const | protocols::moves::Mover | inline |
get_input_pose() const | protocols::moves::Mover | |
get_last_move_status() const | protocols::moves::Mover | |
get_name() const | protocols::docking::stateless::SaneDockingProtocol | virtual |
get_native_pose() const | protocols::moves::Mover | |
get_self_ptr() const | protocols::moves::Mover | inline |
get_self_ptr() | protocols::moves::Mover | inline |
get_self_weak_ptr() const | protocols::moves::Mover | inline |
get_self_weak_ptr() | protocols::moves::Mover | inline |
get_type() const | protocols::moves::Mover | inline |
info() | protocols::moves::Mover | inlinevirtual |
info() const | protocols::moves::Mover | inlinevirtual |
last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
movable_jumps() | protocols::docking::DockingProtocol | inline |
movable_jumps() const | protocols::docking::DockingProtocol | inline |
Mover() | protocols::moves::Mover | |
Mover(std::string const &type_name) | protocols::moves::Mover | |
Mover(Mover const &other) | protocols::moves::Mover | |
name() | protocols::moves::Mover | inlinestatic |
operator=(DockingProtocol const &rhs) | protocols::docking::DockingProtocol | |
protocols::moves::Mover::operator=(Mover const &other) | protocols::moves::Mover | |
parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) | protocols::docking::DockingProtocol | virtual |
partners() const | protocols::docking::DockingProtocol | inline |
perturber() const | protocols::docking::DockingProtocol | |
Pose typedef | protocols::moves::Mover | |
PoseCOP typedef | protocols::moves::Mover | |
register_options() | protocols::docking::DockingProtocol | static |
reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
reinitialize_for_new_input() const | protocols::docking::DockingProtocol | virtual |
reset_status() | protocols::moves::Mover | |
set_additional_task_operarations(utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations) | protocols::docking::DockingProtocol | |
set_autofoldtree(bool const autofoldtree) | protocols::docking::DockingProtocol | inline |
set_cst_weight(core::Real const cst_weight) | protocols::docking::DockingProtocol | |
set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
set_default() | protocols::docking::DockingProtocol | |
set_design(bool const design) | protocols::docking::DockingProtocol | inline |
set_dock_min(bool const dock_min) | protocols::docking::DockingProtocol | |
set_docking_highres_mover(protocols::docking::DockingHighResOP docking_highres_mover) | protocols::docking::DockingProtocol | |
set_docking_local_refine(bool const docking_local_refine) | protocols::docking::DockingProtocol | |
set_ensemble1(std::string const &ensemble1) | protocols::docking::DockingProtocol | inline |
set_ensemble2(std::string const &ensemble2) | protocols::docking::DockingProtocol | inline |
set_highres_scorefxn(core::scoring::ScoreFunctionOP docking_scorefxn_high) | protocols::docking::DockingProtocol | |
set_highres_scorefxn(core::scoring::ScoreFunctionOP docking_scorefxn_high, core::scoring::ScoreFunctionOP docking_scorefxn_pack) | protocols::docking::DockingProtocol | |
set_highres_scorefxn(core::scoring::ScoreFunctionOP docking_scorefxn_high, core::scoring::ScoreFunctionOP docking_scorefxn_pack, core::scoring::ScoreFunctionOP docking_scorefxn_output) | protocols::docking::DockingProtocol | |
set_ignore_default_docking_task(bool const ignore_default_docking_task) | protocols::docking::DockingProtocol | inline |
set_inner_cycles(core::Size inner_cycles) | protocols::docking::DockingProtocol | inline |
set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
set_interface_definition_task_operation(protocols::toolbox::task_operations::InterfaceTaskOperationOP interface_definition) | protocols::docking::DockingProtocol | |
set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
set_low_res_protocol_only(bool const low_res_protocol_only) | protocols::docking::DockingProtocol | |
set_lowres_scorefxn(core::scoring::ScoreFunctionOP docking_scorefxn_low) | protocols::docking::DockingProtocol | |
set_movable_jumps(DockJumps const jump_numbers) | protocols::docking::DockingProtocol | inline |
set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
set_no_filters(bool no_filters) | protocols::docking::DockingProtocol | |
set_outer_cycles(core::Size outer_cycles) | protocols::docking::DockingProtocol | inline |
set_partners(std::string const &partners) | protocols::docking::DockingProtocol | inline |
set_recover_sidechains_filename(std::string const &file) | protocols::docking::DockingProtocol | inline |
set_reporting(bool report) | protocols::docking::DockingProtocol | inline |
set_rt_min(bool rt_min) | protocols::docking::DockingProtocol | |
set_sc_min(bool sc_min) | protocols::docking::DockingProtocol | |
set_task_factory(core::pack::task::TaskFactoryOP task_factory) | protocols::docking::DockingProtocol | inline |
set_type(std::string const &setting) | protocols::moves::Mover | inline |
set_use_constraints(bool const use_csts) | protocols::docking::DockingProtocol | |
set_use_legacy_protocol(bool const use_legacy_protocol) | protocols::docking::DockingProtocol | |
show(std::ostream &out=std::cout) const | protocols::docking::DockingProtocol | virtual |
Strings typedef | protocols::moves::Mover | |
sync_objects_with_flags() | protocols::docking::DockingProtocol | |
TagCOP typedef | protocols::moves::Mover | |
task_factory() | protocols::docking::DockingProtocol | inline |
test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
to_all_atom() const | protocols::docking::DockingProtocol | |
to_centroid() const | protocols::docking::DockingProtocol | |
type() const | protocols::moves::Mover | inline |
type(const std::string &type_in) | protocols::moves::Mover | inline |
~DockingProtocol() | protocols::docking::DockingProtocol | |
~Mover() | protocols::moves::Mover | virtual |