protocols::relax::FastRelax Member List

This is the complete list of members for protocols::relax::FastRelax, including all inherited members.

add_cst_files(std::string const cstfile)	protocols::relax::RelaxProtocolBase	inlineprotected
apply(core::pose::Pose &pose)	protocols::relax::FastRelax	virtual
protocols::relax::RelaxProtocolBase::apply(core::io::serialization::PipeMap &pmap)	protocols::moves::Mover	virtual
apply_disulfides(core::pose::Pose &pose)	protocols::relax::RelaxProtocolBase
batch_apply(std::vector< core::io::silent::SilentStructOP > &input_structs, core::scoring::constraints::ConstraintSetOP input_csts=NULL, core::Real decay_rate=0.5)	protocols::relax::FastRelax
cartesian() const	protocols::relax::RelaxProtocolBase	inline
cartesian(bool newval)	protocols::relax::RelaxProtocolBase	inline
checkpoints_	protocols::relax::FastRelax	private
clear_info()	protocols::moves::Mover	inlinevirtual
clone() const	protocols::relax::FastRelax	virtual
cmd_accept_to_best(const core::scoring::ScoreFunctionOP local_scorefxn, core::pose::Pose &pose, core::pose::Pose &best_pose, const core::pose::Pose &start_pose, core::Real &best_score, core::Size &accept_count)	protocols::relax::FastRelax	protected
constrain_coords() const	protocols::relax::RelaxProtocolBase	inline
constrain_coords(bool constrain_coords)	protocols::relax::RelaxProtocolBase	inline
constrain_relax_segments() const	protocols::relax::RelaxProtocolBase	inline
constrain_relax_segments(bool constrain_relax_segments)	protocols::relax::RelaxProtocolBase	inline
constrain_relax_to_native_coords() const	protocols::relax::RelaxProtocolBase	inline
constrain_relax_to_native_coords(bool constrain_relax_to_native_coords)	protocols::relax::RelaxProtocolBase	inline
constrain_relax_to_start_coords() const	protocols::relax::RelaxProtocolBase	inline
constrain_relax_to_start_coords(bool constrain_relax_to_start_coords)	protocols::relax::RelaxProtocolBase	inline
create()	protocols::moves::Mover	virtual
cst_files(core::Size const i) const	protocols::relax::RelaxProtocolBase	inlineprotected
default_repeats_	protocols::relax::FastRelax	private
dna_move_	protocols::relax::FastRelax	private
do_md(core::pose::Pose &pose, core::Real nstep, core::Real temp0, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn)	protocols::relax::FastRelax	protected
do_minimize(core::pose::Pose &pose, core::Real tolerance, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn)	protocols::relax::FastRelax	protected
dry_run() const	protocols::relax::RelaxProtocolBase	inline
dry_run(bool setting)	protocols::relax::RelaxProtocolBase	inline
dumpall_	protocols::relax::FastRelax	private
explicit_ramp_constraints() const	protocols::relax::RelaxProtocolBase	inline
FastRelax(core::Size standard_repeats=0)	protocols::relax::FastRelax
FastRelax(core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats=0)	protocols::relax::FastRelax
FastRelax(core::scoring::ScoreFunctionOP scorefxn_in, std::string const &script_file)	protocols::relax::FastRelax
FastRelax(core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats, const std::string &script_file)	protocols::relax::FastRelax
Filters_map typedef	protocols::moves::Mover
fix_omega() const	protocols::relax::RelaxProtocolBase	inlineprotected
fix_omega(bool fix_omega)	protocols::relax::RelaxProtocolBase	inlineprotected
force_nonideal_	protocols::relax::FastRelax	private
fresh_instance() const	protocols::relax::RelaxProtocolBase	inlinevirtual
get_additional_output()	protocols::moves::Mover	virtual
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_movemap()	protocols::relax::RelaxProtocolBase	inline
get_name() const	protocols::relax::FastRelax	virtual
get_native_pose() const	protocols::moves::Mover
get_scorefxn() const	protocols::relax::RelaxProtocolBase	inline
get_scorefxn()	protocols::relax::RelaxProtocolBase	inlineprotected
get_task_factory() const	protocols::relax::RelaxProtocolBase	inline
get_type() const	protocols::moves::Mover	inline
info()	protocols::moves::Mover	inlinevirtual
info() const	protocols::moves::Mover	inlinevirtual
initialize_movemap(core::pose::Pose const &pose, core::kinematics::MoveMap &movemap)	protocols::relax::RelaxProtocolBase	protected
last_proposal_density_ratio()	protocols::moves::Mover	inlinevirtual
limit_aroma_chi2() const	protocols::relax::RelaxProtocolBase	inlineprotected
max_iter() const	protocols::relax::RelaxProtocolBase	inline
max_iter(Size max_iter)	protocols::relax::RelaxProtocolBase	inline
min_type() const	protocols::relax::RelaxProtocolBase	inline
min_type(std::string min_type)	protocols::relax::RelaxProtocolBase	inline
minimize_bond_angles() const	protocols::relax::RelaxProtocolBase	inlineprotected
minimize_bond_angles(bool minimize_bond_angles)	protocols::relax::RelaxProtocolBase	inlineprotected
minimize_bond_lengths() const	protocols::relax::RelaxProtocolBase	inlineprotected
minimize_bond_lengths(bool minimize_bond_lengths)	protocols::relax::RelaxProtocolBase	inlineprotected
minimize_bondangle_subset() const	protocols::relax::RelaxProtocolBase	inlineprotected
minimize_bondangle_subset(int minimize_bondangle_subset)	protocols::relax::RelaxProtocolBase	inlineprotected
minimize_bondlength_subset() const	protocols::relax::RelaxProtocolBase	inlineprotected
minimize_bondlength_subset(int minimize_bondlength_subset)	protocols::relax::RelaxProtocolBase	inlineprotected
movemap_tag_	protocols::relax::FastRelax	private
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=(Mover const &other)	protocols::moves::Mover
output_debug_structure(core::pose::Pose &pose, std::string prefix)	protocols::relax::RelaxProtocolBase	protected
parent typedef	protocols::relax::RelaxProtocolBase
parse_def(utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, protocols::moves::MoverCacheSP cache)	protocols::relax::FastRelax	virtual
parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)	protocols::relax::FastRelax	virtual
parse_state(SerializableState const &state)	protocols::moves::Mover	virtual
Pose typedef	protocols::moves::Mover
PoseCOP typedef	protocols::moves::Mover
ramady_	protocols::relax::FastRelax	private
ramady_cutoff_	protocols::relax::FastRelax	private
ramady_force_	protocols::relax::FastRelax	private
ramady_num_rebuild_	protocols::relax::FastRelax	private
ramady_rms_limit_	protocols::relax::FastRelax	private
ramp_down_constraints() const	protocols::relax::RelaxProtocolBase	inline
ramp_down_constraints(bool ramp_down_constraints)	protocols::relax::RelaxProtocolBase	inline
read_script_file(const std::string &script_file, core::Size standard_repeats=5)	protocols::relax::FastRelax	private
register_options()	protocols::relax::RelaxProtocolBase	static
reinitialize_for_each_job() const	protocols::moves::Mover	virtual
reinitialize_for_new_input() const	protocols::moves::Mover	virtual
RelaxProtocolBase(core::scoring::ScoreFunctionOP)	protocols::relax::RelaxProtocolBase
RelaxProtocolBase(std::string const &movername="RelaxProtocol")	protocols::relax::RelaxProtocolBase
RelaxProtocolBase(std::string const &movername, core::scoring::ScoreFunctionOP)	protocols::relax::RelaxProtocolBase
repack_	protocols::relax::FastRelax	private
reset_status()	protocols::moves::Mover
save_state(SerializableState &state)	protocols::moves::Mover	virtual
script_	protocols::relax::FastRelax	private
script_max_accept_	protocols::relax::FastRelax	private
set_constraint_weight(core::scoring::ScoreFunctionOP local_scorefxn, core::scoring::EnergyMap const &full_weights, core::Real const weight) const	protocols::relax::FastRelax	protectedvirtual
set_current_job(protocols::jobdist::BasicJobCOP job)	protocols::moves::Mover
set_current_tag(std::string const &new_tag)	protocols::moves::Mover	inline
set_default_coordinate_settings()	protocols::relax::RelaxProtocolBase
set_default_minimization_settings()	protocols::relax::RelaxProtocolBase
set_default_movemap()	protocols::relax::RelaxProtocolBase
set_defaults()	protocols::relax::RelaxProtocolBase
set_force_nonideal(bool val)	protocols::relax::FastRelax	inline
set_input_pose(PoseCOP pose)	protocols::moves::Mover	virtual
set_last_move_status(MoverStatus status)	protocols::moves::Mover	protected
set_movemap(core::kinematics::MoveMapOP movemap)	protocols::relax::RelaxProtocolBase	inline
set_native_pose(PoseCOP pose)	protocols::moves::Mover	virtual
set_scorefxn(core::scoring::ScoreFunctionOP scorefxn)	protocols::relax::RelaxProtocolBase	inline
set_script_to_batchrelax_default(core::Size standard_repeats=0)	protocols::relax::FastRelax
set_task_factory(core::pack::task::TaskFactoryOP task_factory)	protocols::relax::RelaxProtocolBase	inline
set_to_default()	protocols::relax::FastRelax
set_up_constraints(core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap)	protocols::relax::RelaxProtocolBase	protected
show(std::ostream &output=std::cout) const	protocols::moves::Mover	virtual
Strings typedef	protocols::moves::Mover
symmetric_rmsd_	protocols::relax::FastRelax	private
TagCOP typedef	protocols::moves::Mover
test_cycles_	protocols::relax::FastRelax	private
test_move(Pose &pose)	protocols::moves::Mover	inlinevirtual
type() const	protocols::moves::Mover	inline
type(const std::string &type_in)	protocols::moves::Mover	inline
~FastRelax()	protocols::relax::FastRelax	virtual
~Mover()	protocols::moves::Mover	virtual
~RelaxProtocolBase()	protocols::relax::RelaxProtocolBase