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protocols::relax::ClassicRelax Class Reference

A functor class which implements the classic Rosetta++ pose_relax protocol. More...

#include <ClassicRelax.hh>

Inheritance diagram for protocols::relax::ClassicRelax:
Inheritance graph
[legend]

Public Types

typedef RelaxProtocolBase parent
 
- Public Types inherited from protocols::relax::RelaxProtocolBase
typedef moves::Mover parent
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 ClassicRelax (core::scoring::ScoreFunctionOP scorefxn_in)
 
 ClassicRelax (core::scoring::ScoreFunctionOP scorefxn_in, core::kinematics::MoveMapOP movemap)
 constructor taking both ScoreFunction and MoveMap More...
 
 ClassicRelax (ClassicRelax const &)
 
 ClassicRelax ()
 
 ~ClassicRelax () override
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void set_default (core::scoring::ScoreFunctionOP scorefxn_in)
 
void apply (core::pose::Pose &pose) override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_default (bool const use_default_movemap=true)
 
void set_default_minimizer ()
 
void set_default_moveset_phase1 ()
 
void set_default_moveset_phase2 ()
 
void set_default_moveset_phase3 ()
 
void set_lj_ramp_cycles (int param)
 
void set_lj_ramp_inner_cycles (int param)
 
void set_start_rep_weight (core::Real param)
 
void set_stage2_cycles (int cycles2)
 
void set_stage2_repack_period (int repack2)
 
void set_stage3_cycles (int cycles3)
 
void set_tolerance (core::Real new_tolerance)
 
void set_mc (moves::MonteCarloOP new_mc_)
 
void set_full_repack (protocols::minimization_packing::PackRotamersMoverOP new_pack_full_repack)
 
void set_rottrial (protocols::minimization_packing::RotamerTrialsMoverOP new_pack_rottrial)
 
void setPoseExtraScore (core::pose::Pose &pose)
 
void use_coarse_vdw ()
 
moves::MonteCarloOP get_mc (core::pose::Pose &pose)
 
protocols::checkpoint::CheckPointerget_checkpoints ()
 
- Public Member Functions inherited from protocols::relax::RelaxProtocolBase
 RelaxProtocolBase (core::scoring::ScoreFunctionOP)
 
 RelaxProtocolBase (std::string const &movername="RelaxProtocol")
 
 RelaxProtocolBase (std::string const &movername, core::scoring::ScoreFunctionOP)
 
 ~RelaxProtocolBase () override
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void apply_disulfides (core::pose::Pose &pose)
 
void set_defaults ()
 
void set_default_minimization_settings ()
 
void set_default_coordinate_settings ()
 
void set_default_movemap ()
 
core::kinematics::MoveMapCOP get_movemap () const
 
core::kinematics::MoveMapOP get_movemap ()
 
const
core::scoring::ScoreFunctionCOP 
get_scorefxn () const
 
core::pack::task::TaskFactoryOP
const & 
get_task_factory () const
 
bool cartesian () const
 
std::string min_type () const
 
core::Size max_iter () const
 
bool dry_run () const
 
bool constrain_relax_to_native_coords () const
 
bool constrain_relax_to_start_coords () const
 
bool constrain_coords () const
 
bool coord_constrain_sidechains () const
 
bool ramp_down_constraints () const
 
bool constrain_relax_segments () const
 
bool minimize_bond_lengths () const
 
bool minimize_bond_angles () const
 
void set_movemap (core::kinematics::MoveMapOP movemap)
 
void set_movemap_factory (core::select::movemap::MoveMapFactoryOP mm_factory)
 
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 
void set_task_factory (core::pack::task::TaskFactoryOP task_factory)
 
void cartesian (bool newval)
 Use cartesian (minimization step) More...
 
void min_type (std::string min_type)
 
void max_iter (core::Size max_iter)
 
void dry_run (bool setting)
 
void constrain_relax_to_native_coords (bool constrain_relax_to_native_coords)
 
void constrain_relax_to_start_coords (bool constrain_relax_to_start_coords)
 
void constrain_coords (bool constrain_coords)
 
void coord_constrain_sidechains (bool coord_constrain_sidechains)
 
void constrain_relax_segments (bool constrain_relax_segments)
 
void ramp_down_constraints (bool ramp_down_constraints)
 
void minimize_bond_lengths (bool minimize_bond_lengths)
 
void minimize_bond_angles (bool minimize_bond_angles)
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. More...
 
bool mover_is_unpublished () const override
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provide a list of authors and their e-mail addresses, as strings. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 

Static Public Member Functions

static void register_options ()
 
- Static Public Member Functions inherited from protocols::relax::RelaxProtocolBase
static void register_options ()
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Member Functions

void check_default_mc (core::pose::Pose &pose)
 
void check_default_full_repacker (core::pose::Pose &pose, core::kinematics::MoveMap &movemap)
 
void check_default_rottrial (core::pose::Pose &pose, core::kinematics::MoveMap &movemap)
 

Private Attributes

protocols::minimization_packing::MinMoverOP min_mover_
 
protocols::checkpoint::CheckPointer checkpoints_
 
moves::MonteCarloOP mc_
 
bool use_default_mc_
 
protocols::minimization_packing::PackRotamersMoverOP pack_full_repack_
 
bool use_default_pack_full_repack_
 
protocols::minimization_packing::RotamerTrialsMoverOP pack_rottrial_
 
bool use_default_pack_rottrial_
 
core::Real m_Temperature
 
core::Size nmoves_
 
core::Real energycut
 
std::string min_type
 
bool nb_list
 
core::Real min_tolerance
 
moves::MoverOP moveset_phase1_
 
moves::MoverOP moveset_phase2_
 
moves::MoverOP moveset_phase3_
 
int lj_ramp_cycles
 
int lj_ramp_inner_cycles
 
core::Real start_rep_weight
 
core::Real end_rep_weight
 
core::scoring::ScoreType st_rep_
 
core::scoring::ScoreType st_atr_
 
core::scoring::ScoreType st_sol_
 
int stage2_repack_period
 
int stage2_cycles
 
int stage3_cycles
 
float score_stage2_beginning
 
float score_stage2_quarter
 
float score_stage2_half
 
float score_stage2_end
 
float filter_stage2_beginning
 
float filter_stage2_quarter
 
float filter_stage2_half
 
float filter_stage2_end
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::relax::RelaxProtocolBase
core::scoring::ScoreFunctionOP get_scorefxn ()
 
bool fix_omega () const
 
int minimize_bondlength_subset () const
 
int minimize_bondangle_subset () const
 
bool limit_aroma_chi2 () const
 
std::string cst_files (core::Size const i) const
 
void fix_omega (bool fix_omega)
 
void minimize_bondangle_subset (int minimize_bondangle_subset)
 
void minimize_bondlength_subset (int minimize_bondlength_subset)
 
void initialize_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap)
 
void set_up_constraints (core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap)
 
void output_debug_structure (core::pose::Pose &pose, std::string prefix)
 
void add_cst_files (std::string const &cstfile)
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Detailed Description

A functor class which implements the classic Rosetta++ pose_relax protocol.

A functor class which implements the classic Rosetta++ pose_relax protocol

Todo:
Crank and Wobble Moves - however there's little evidence that they are essential

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::relax::ClassicRelax::ClassicRelax ( core::scoring::ScoreFunctionOP  scorefxn_in)
protocols::relax::ClassicRelax::ClassicRelax ( core::scoring::ScoreFunctionOP  scorefxn_in,
core::kinematics::MoveMapOP  movemap 
)
protocols::relax::ClassicRelax::ClassicRelax ( ClassicRelax const &  )
default
protocols::relax::ClassicRelax::ClassicRelax ( )
protocols::relax::ClassicRelax::~ClassicRelax ( )
overridedefault

Member Function Documentation

void protocols::relax::ClassicRelax::apply ( core::pose::Pose pose)
overridevirtual

Central Apply function

Implements protocols::moves::Mover.

References core::scoring::angle_constraint, protocols::relax::RelaxProtocolBase::apply_disulfides(), core::scoring::atom_pair_constraint, core::scoring::CA_rmsd(), check_default_full_repacker(), check_default_mc(), check_default_rottrial(), protocols::checkpoint::CheckPointer::checkpoint(), checkpoints_, core::pose::Pose::conformation(), core::scoring::coordinate_constraint, core::pose::Pose::data(), core::scoring::dihedral_constraint, end_rep_weight, core::scoring::fa_rep, filter_stage2_beginning, filter_stage2_quarter, protocols::moves::Mover::get_current_tag(), protocols::relax::RelaxProtocolBase::get_movemap(), protocols::moves::Mover::get_native_pose(), protocols::relax::RelaxProtocolBase::get_scorefxn(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::pose::symmetry::is_symmetric(), lj_ramp_cycles, lj_ramp_inner_cycles, core::pose::symmetry::make_symmetric_movemap(), mc_, min_mover_, moveset_phase2_, moveset_phase3_, pack_full_repack_, pack_rottrial_, protocols::relax::RelaxProtocolBase::ramp_down_constraints(), protocols::checkpoint::CheckPointer::recover_checkpoint(), core::pose::Pose::residue(), core::io::raw_data::ScoreMap::score_and_add_energies_to_map(), score_stage2_beginning, score_stage2_end, score_stage2_half, score_stage2_quarter, protocols::relax::RelaxProtocolBase::set_up_constraints(), setPoseExtraScore(), core::pose::Pose::size(), stage2_cycles, stage2_repack_period, stage3_cycles, start_rep_weight, and protocols::relax::TR().

void protocols::relax::ClassicRelax::check_default_full_repacker ( core::pose::Pose pose,
core::kinematics::MoveMap movemap 
)
private
void protocols::relax::ClassicRelax::check_default_mc ( core::pose::Pose pose)
private
void protocols::relax::ClassicRelax::check_default_rottrial ( core::pose::Pose pose,
core::kinematics::MoveMap movemap 
)
private
protocols::moves::MoverOP protocols::relax::ClassicRelax::clone ( ) const
overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

protocols::checkpoint::CheckPointer& protocols::relax::ClassicRelax::get_checkpoints ( )
inline
moves::MonteCarloOP protocols::relax::ClassicRelax::get_mc ( core::pose::Pose pose)

Accessors

References check_default_mc(), and mc_.

std::string protocols::relax::ClassicRelax::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

void protocols::relax::ClassicRelax::register_options ( )
static

registering of options that are relevant for AbrelaxApplication

References protocols::relax::RelaxProtocolBase::register_options().

void protocols::relax::ClassicRelax::set_default ( core::scoring::ScoreFunctionOP  scorefxn_in)
void protocols::relax::ClassicRelax::set_default ( bool const  use_default_movemap = true)
void protocols::relax::ClassicRelax::set_default_minimizer ( )
void protocols::relax::ClassicRelax::set_default_moveset_phase1 ( )

At stage 1 we're only doing small and shear moves

References protocols::relax::RelaxProtocolBase::get_movemap(), m_Temperature, moveset_phase1_, and nmoves_.

Referenced by set_default().

void protocols::relax::ClassicRelax::set_default_moveset_phase2 ( )

At stage 2 we're doing small, shear, wobble and crank moves (the latter two are works in progress)

References protocols::relax::RelaxProtocolBase::get_movemap(), m_Temperature, moveset_phase2_, and nmoves_.

Referenced by set_default().

void protocols::relax::ClassicRelax::set_default_moveset_phase3 ( )

At stage 3 we're only doing small and shear moves

References protocols::relax::RelaxProtocolBase::get_movemap(), m_Temperature, moveset_phase3_, and nmoves_.

Referenced by set_default().

void protocols::relax::ClassicRelax::set_full_repack ( protocols::minimization_packing::PackRotamersMoverOP  new_pack_full_repack)
void protocols::relax::ClassicRelax::set_lj_ramp_cycles ( int  param)
inline

Set options from outside

References lj_ramp_cycles.

void protocols::relax::ClassicRelax::set_lj_ramp_inner_cycles ( int  param)
inline

References lj_ramp_inner_cycles.

void protocols::relax::ClassicRelax::set_mc ( moves::MonteCarloOP  new_mc_)

References mc_, and use_default_mc_.

void protocols::relax::ClassicRelax::set_rottrial ( protocols::minimization_packing::RotamerTrialsMoverOP  new_pack_rottrial)
void protocols::relax::ClassicRelax::set_stage2_cycles ( int  cycles2)
inline

References stage2_cycles.

void protocols::relax::ClassicRelax::set_stage2_repack_period ( int  repack2)
inline

References stage2_repack_period.

void protocols::relax::ClassicRelax::set_stage3_cycles ( int  cycles3)
inline

References stage3_cycles.

void protocols::relax::ClassicRelax::set_start_rep_weight ( core::Real  param)
inline

References start_rep_weight.

void protocols::relax::ClassicRelax::set_tolerance ( core::Real  new_tolerance)
void protocols::relax::ClassicRelax::setPoseExtraScore ( core::pose::Pose pose)
void protocols::relax::ClassicRelax::use_coarse_vdw ( )
inline

Member Data Documentation

protocols::checkpoint::CheckPointer protocols::relax::ClassicRelax::checkpoints_
private

Referenced by apply().

core::Real protocols::relax::ClassicRelax::end_rep_weight
private

Referenced by apply(), and set_default().

core::Real protocols::relax::ClassicRelax::energycut
private
float protocols::relax::ClassicRelax::filter_stage2_beginning
private

Referenced by apply(), and set_default().

float protocols::relax::ClassicRelax::filter_stage2_end
private

Referenced by set_default().

float protocols::relax::ClassicRelax::filter_stage2_half
private

Referenced by set_default().

float protocols::relax::ClassicRelax::filter_stage2_quarter
private

Referenced by apply(), and set_default().

int protocols::relax::ClassicRelax::lj_ramp_cycles
private
int protocols::relax::ClassicRelax::lj_ramp_inner_cycles
private
core::Real protocols::relax::ClassicRelax::m_Temperature
private
moves::MonteCarloOP protocols::relax::ClassicRelax::mc_
private
protocols::minimization_packing::MinMoverOP protocols::relax::ClassicRelax::min_mover_
private

Referenced by apply(), and set_default_minimizer().

core::Real protocols::relax::ClassicRelax::min_tolerance
private
std::string protocols::relax::ClassicRelax::min_type
private
moves::MoverOP protocols::relax::ClassicRelax::moveset_phase1_
private
moves::MoverOP protocols::relax::ClassicRelax::moveset_phase2_
private
moves::MoverOP protocols::relax::ClassicRelax::moveset_phase3_
private
bool protocols::relax::ClassicRelax::nb_list
private
core::Size protocols::relax::ClassicRelax::nmoves_
private
protocols::minimization_packing::PackRotamersMoverOP protocols::relax::ClassicRelax::pack_full_repack_
private
protocols::minimization_packing::RotamerTrialsMoverOP protocols::relax::ClassicRelax::pack_rottrial_
private
float protocols::relax::ClassicRelax::score_stage2_beginning
private
float protocols::relax::ClassicRelax::score_stage2_end
private
float protocols::relax::ClassicRelax::score_stage2_half
private
float protocols::relax::ClassicRelax::score_stage2_quarter
private
core::scoring::ScoreType protocols::relax::ClassicRelax::st_atr_
private

Referenced by set_default(), and use_coarse_vdw().

core::scoring::ScoreType protocols::relax::ClassicRelax::st_rep_
private

Referenced by set_default(), and use_coarse_vdw().

core::scoring::ScoreType protocols::relax::ClassicRelax::st_sol_
private

Referenced by set_default(), and use_coarse_vdw().

int protocols::relax::ClassicRelax::stage2_cycles
private
int protocols::relax::ClassicRelax::stage2_repack_period
private
int protocols::relax::ClassicRelax::stage3_cycles
private
core::Real protocols::relax::ClassicRelax::start_rep_weight
private
bool protocols::relax::ClassicRelax::use_default_mc_
private
bool protocols::relax::ClassicRelax::use_default_pack_full_repack_
private
bool protocols::relax::ClassicRelax::use_default_pack_rottrial_
private

Referenced by ClassicRelax().


The documentation for this class was generated from the following files: