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protocols::relax::RelaxProtocolBase Class Reference

#include <RelaxProtocolBase.hh>

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Public Types

typedef moves::Mover parent
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 		Filters_map
 
typedef std::list< std::string > Strings
 

Public Member Functions

 RelaxProtocolBase (core::scoring::ScoreFunctionOP)
 
 RelaxProtocolBase (std::string const &movername="RelaxProtocol")
 
 RelaxProtocolBase (std::string const &movername, core::scoring::ScoreFunctionOP)
 
 ~RelaxProtocolBase ()
 
virtual protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_defaults ()
 
void set_default_minimization_settings ()
 
void set_default_coordinate_settings ()
 
void set_default_movemap ()
 
void minimize_bond_lengths (bool setting)
 
void minimize_bond_angles (bool setting)
 
void minimize_bondlength_subset (int setting)
 
void minimize_bondangle_subset (int setting)
 
bool minimize_bond_lengths () const
 
bool minimize_bond_angles () const
 
int minimize_bondlength_subset () const
 
int minimize_bondangle_subset () const
 
bool constrain_relax_to_native_coords () const
 
bool constrain_relax_to_start_coords () const
 
bool constrain_coords () const
 
bool explicit_ramp_constraints () const
 
bool ramp_down_constraints () const
 
bool constrain_relax_segments () const
 
bool limit_aroma_chi2 () const
 
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 ramp_down_constraints (bool ramp_down_constraints)
 
void constrain_relax_segments (bool constrain_relax_segments)
 
void cartesian (bool newval)
 
bool cartesian () const
 
core::kinematics::MoveMapOP get_movemap ()
 
void set_movemap (core::kinematics::MoveMapOP movemap)
 
void set_min_type (std::string min_type)
 
void set_scorefxn (core::scoring::ScoreFunctionOP score)
 
const
core::scoring::ScoreFunctionCOP 		get_scorefxn () const
 
void set_task_factory (core::pack::task::TaskFactoryOP taskf)
 
core::pack::task::TaskFactoryOP
const & 		get_task_factory () const
 
void set_dry_run (bool setting)
 
bool dry_run () const
 
void apply_disulfides (core::pose::Pose &pose)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Mover & operator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void apply (Pose &)=0
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
virtual std::string get_name () const =0
 Each derived class must specify its name. The class name. More...
 
std::string get_type () const
 
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...
 
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 Strings & info ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 this function informs 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
 this function informs 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Static Public Member Functions

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 

Protected Member Functions

void initialize_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap)
 
core::scoring::ScoreFunctionOP get_scorefxn ()
 
void set_up_constraints (core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap)
 
void output_debug_structure (core::pose::Pose &pose, std::string prefix)
 
- 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...
 

Protected Attributes

bool constrain_relax_to_native_coords_
 
bool constrain_relax_to_start_coords_
 
bool constrain_coords_
 
bool coord_constrain_sidechains_
 
bool explicit_ramp_constraints_
 
bool ramp_down_constraints_
 
bool constrain_relax_segments_
 
std::string min_type_
 
bool cartesian_
 Do cartesian-space minimization? More...
 
bool limit_aroma_chi2_
 

Private Attributes

bool minimize_bond_lengths_
 
bool minimize_bond_angles_
 
int minimize_bondangle_subset_
 
int minimize_bondlength_subset_
 
core::kinematics::MoveMapOP movemap_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::pack::task::TaskFactoryOP task_factory_
 task factory for packer ( used only FastRelax as of 11/05/2010 ) More...
 
bool dry_run_
 Is this a dry run (i.e. do no cycles) More...
 

Detailed Description

Definition at line 43 of file RelaxProtocolBase.hh.

Member Typedef Documentation

typedef moves::Mover protocols::relax::RelaxProtocolBase::parent

Definition at line 45 of file RelaxProtocolBase.hh.

Constructor & Destructor Documentation

protocols::relax::RelaxProtocolBase::RelaxProtocolBase ( core::scoring::ScoreFunctionOP  score_in)

Definition at line 94 of file RelaxProtocolBase.cc.

References set_defaults().

protocols::relax::RelaxProtocolBase::RelaxProtocolBase ( std::string const &  movername = "RelaxProtocol")

Definition at line 102 of file RelaxProtocolBase.cc.

References set_defaults().

protocols::relax::RelaxProtocolBase::RelaxProtocolBase ( std::string const &  movername,
core::scoring::ScoreFunctionOP  score_in 
)

Definition at line 110 of file RelaxProtocolBase.cc.

References set_defaults().

protocols::relax::RelaxProtocolBase::~RelaxProtocolBase ( )

Definition at line 119 of file RelaxProtocolBase.cc.

Member Function Documentation

void protocols::relax::RelaxProtocolBase::apply_disulfides ( core::pose::Pose &  pose)

Definition at line 348 of file RelaxProtocolBase.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), movemap_, and core::pose::Pose::total_residue().

Referenced by protocols::relax::MiniRelax::apply(), protocols::relax::ClassicRelax::apply(), and protocols::relax::FastRelax::apply().

void protocols::relax::RelaxProtocolBase::cartesian ( bool  newval)
inline

Definition at line 108 of file RelaxProtocolBase.hh.

References cartesian_.

bool protocols::relax::RelaxProtocolBase::cartesian ( ) const
inline

Definition at line 109 of file RelaxProtocolBase.hh.

References cartesian_.

Referenced by protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::FastRelax::parse_def(), and protocols::relax::FastRelax::parse_my_tag().

bool protocols::relax::RelaxProtocolBase::constrain_coords ( ) const
inline

Definition at line 83 of file RelaxProtocolBase.hh.

References constrain_coords_.

Referenced by protocols::relax::FastRelax::apply(), and constrain_coords().

void protocols::relax::RelaxProtocolBase::constrain_coords ( bool  constrain_coords)
inline

Definition at line 96 of file RelaxProtocolBase.hh.

References constrain_coords(), and constrain_coords_.

bool protocols::relax::RelaxProtocolBase::constrain_relax_segments ( ) const
inline

Definition at line 86 of file RelaxProtocolBase.hh.

References constrain_relax_segments_.

Referenced by constrain_relax_segments().

void protocols::relax::RelaxProtocolBase::constrain_relax_segments ( bool  constrain_relax_segments)
inline

Definition at line 103 of file RelaxProtocolBase.hh.

References constrain_relax_segments(), and constrain_relax_segments_.

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords ( ) const
inline

Definition at line 81 of file RelaxProtocolBase.hh.

References constrain_relax_to_native_coords_.

Referenced by constrain_relax_to_native_coords().

void protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords ( bool  constrain_relax_to_native_coords)
inline

Definition at line 90 of file RelaxProtocolBase.hh.

References constrain_relax_to_native_coords(), and constrain_relax_to_native_coords_.

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords ( ) const
inline

Definition at line 82 of file RelaxProtocolBase.hh.

References constrain_relax_to_start_coords_.

Referenced by constrain_relax_to_start_coords().

void protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords ( bool  constrain_relax_to_start_coords)
inline

Definition at line 93 of file RelaxProtocolBase.hh.

References constrain_relax_to_start_coords(), and constrain_relax_to_start_coords_.

bool protocols::relax::RelaxProtocolBase::dry_run ( ) const
inline

Definition at line 127 of file RelaxProtocolBase.hh.

References dry_run_.

Referenced by protocols::relax::FastRelax::apply(), and protocols::relax::FastRelax::batch_apply().

bool protocols::relax::RelaxProtocolBase::explicit_ramp_constraints ( ) const
inline

Definition at line 84 of file RelaxProtocolBase.hh.

References explicit_ramp_constraints_.

Referenced by protocols::relax::FastRelax::FastRelax().

virtual protocols::moves::MoverOP protocols::relax::RelaxProtocolBase::fresh_instance ( ) const
inlinevirtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

Definition at line 54 of file RelaxProtocolBase.hh.

References protocols::moves::Mover::clone().

core::kinematics::MoveMapOP protocols::relax::RelaxProtocolBase::get_movemap ( )

Definition at line 324 of file RelaxProtocolBase.cc.

References movemap_.

Referenced by protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::ClassicRelax::set_default_minimizer(), protocols::relax::ClassicRelax::set_default_moveset_phase1(), protocols::relax::ClassicRelax::set_default_moveset_phase2(), protocols::relax::ClassicRelax::set_default_moveset_phase3(), and protocols::relax::CentroidRelax::setup_class_movemap_and_constraints().

const core::scoring::ScoreFunctionCOP protocols::relax::RelaxProtocolBase::get_scorefxn ( ) const

Definition at line 225 of file RelaxProtocolBase.cc.

References scorefxn_.

Referenced by protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::ClassicRelax::check_default_full_repacker(), protocols::relax::ClassicRelax::check_default_mc(), protocols::relax::ClassicRelax::check_default_rottrial(), protocols::relax::ClassicRelax::set_default_minimizer(), protocols::relax::CentroidRelax::set_score_function(), and set_up_constraints().

core::scoring::ScoreFunctionOP protocols::relax::RelaxProtocolBase::get_scorefxn ( )
protected

Definition at line 221 of file RelaxProtocolBase.cc.

References scorefxn_.

core::pack::task::TaskFactoryOP const & protocols::relax::RelaxProtocolBase::get_task_factory ( ) const

Definition at line 330 of file RelaxProtocolBase.cc.

References task_factory_.

Referenced by protocols::relax::FastRelax::apply(), and protocols::relax::FastRelax::batch_apply().

void protocols::relax::RelaxProtocolBase::initialize_movemap ( core::pose::Pose const &  pose,
core::kinematics::MoveMap &  movemap 
)
protected

Definition at line 121 of file RelaxProtocolBase.cc.

References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_is_backbone(), core::id::D, core::chemical::ResidueType::has_atom_name(), core::conformation::Residue::mainchain_atoms(), minimize_bond_angles_, minimize_bond_lengths_, minimize_bondangle_subset_, minimize_bondlength_subset_, core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::kinematics::MoveMap::set(), core::id::THETA, core::pose::Pose::total_residue(), and core::conformation::Residue::type().

Referenced by protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), and protocols::relax::CentroidRelax::setup_class_movemap_and_constraints().

bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2 ( ) const
inline

Definition at line 88 of file RelaxProtocolBase.hh.

References limit_aroma_chi2_.

Referenced by protocols::relax::FastRelax::apply().

void protocols::relax::RelaxProtocolBase::minimize_bond_angles ( bool  setting)

Definition at line 297 of file RelaxProtocolBase.cc.

References minimize_bond_angles_.

bool protocols::relax::RelaxProtocolBase::minimize_bond_angles ( ) const

Definition at line 302 of file RelaxProtocolBase.cc.

References minimize_bond_angles_.

void protocols::relax::RelaxProtocolBase::minimize_bond_lengths ( bool  setting)

Definition at line 296 of file RelaxProtocolBase.cc.

References minimize_bond_lengths_.

bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths ( ) const

Definition at line 301 of file RelaxProtocolBase.cc.

References minimize_bond_lengths_.

void protocols::relax::RelaxProtocolBase::minimize_bondangle_subset ( int  setting)

Definition at line 298 of file RelaxProtocolBase.cc.

References minimize_bondangle_subset_.

int protocols::relax::RelaxProtocolBase::minimize_bondangle_subset ( ) const

Definition at line 304 of file RelaxProtocolBase.cc.

References minimize_bondangle_subset_.

void protocols::relax::RelaxProtocolBase::minimize_bondlength_subset ( int  setting)

Definition at line 299 of file RelaxProtocolBase.cc.

References minimize_bondlength_subset_.

int protocols::relax::RelaxProtocolBase::minimize_bondlength_subset ( ) const

Definition at line 303 of file RelaxProtocolBase.cc.

References minimize_bondlength_subset_.

void protocols::relax::RelaxProtocolBase::output_debug_structure ( core::pose::Pose &  pose,
std::string  prefix 
)
protected

Definition at line 529 of file RelaxProtocolBase.cc.

References protocols::jd2::current_output_name(), protocols::moves::Mover::get_current_tag(), and core::io::silent::SilentFileData::write_silent_struct().

bool protocols::relax::RelaxProtocolBase::ramp_down_constraints ( ) const
inline

Definition at line 85 of file RelaxProtocolBase.hh.

References ramp_down_constraints_.

Referenced by protocols::relax::FastRelax::FastRelax(), and ramp_down_constraints().

void protocols::relax::RelaxProtocolBase::ramp_down_constraints ( bool  ramp_down_constraints)
inline

Definition at line 99 of file RelaxProtocolBase.hh.

References explicit_ramp_constraints_, ramp_down_constraints(), and ramp_down_constraints_.

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

Definition at line 306 of file RelaxProtocolBase.cc.

Referenced by protocols::relax::ClassicRelax::register_options().

void protocols::relax::RelaxProtocolBase::set_default_coordinate_settings ( )

Definition at line 256 of file RelaxProtocolBase.cc.

References constrain_coords_, constrain_relax_segments_, constrain_relax_to_native_coords_, constrain_relax_to_start_coords_, coord_constrain_sidechains_, explicit_ramp_constraints_, limit_aroma_chi2_, and ramp_down_constraints_.

Referenced by set_defaults().

void protocols::relax::RelaxProtocolBase::set_default_minimization_settings ( )

Definition at line 240 of file RelaxProtocolBase.cc.

References cartesian_, min_type_, minimize_bond_angles_, minimize_bond_lengths_, minimize_bondangle_subset_, and minimize_bondlength_subset_.

Referenced by set_defaults().

void protocols::relax::RelaxProtocolBase::set_default_movemap ( )

Definition at line 272 of file RelaxProtocolBase.cc.

References movemap_.

Referenced by protocols::relax::ClassicRelax::set_default(), and set_defaults().

void protocols::relax::RelaxProtocolBase::set_defaults ( )

Definition at line 229 of file RelaxProtocolBase.cc.

References dry_run_, set_default_coordinate_settings(), set_default_minimization_settings(), set_default_movemap(), and task_factory_.

Referenced by RelaxProtocolBase().

void protocols::relax::RelaxProtocolBase::set_dry_run ( bool  setting)
inline

Definition at line 123 of file RelaxProtocolBase.hh.

References dry_run_.

void protocols::relax::RelaxProtocolBase::set_min_type ( std::string  min_type)

Definition at line 288 of file RelaxProtocolBase.cc.

References min_type_.

Referenced by protocols::hybridization::HybridizeProtocol::apply().

void protocols::relax::RelaxProtocolBase::set_movemap ( core::kinematics::MoveMapOP  movemap)

Definition at line 284 of file RelaxProtocolBase.cc.

References movemap_.

Referenced by protocols::relax::FastRelax::apply(), protocols::relax::CentroidRelax::CentroidRelax(), protocols::relax::ClassicRelax::ClassicRelax(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::relax::FastRelax::parse_def(), protocols::relax::FastRelax::parse_my_tag(), and protocols::relax::CentroidRelax::setup_class_movemap_and_constraints().

void protocols::relax::RelaxProtocolBase::set_scorefxn ( core::scoring::ScoreFunctionOP  score)

Definition at line 217 of file RelaxProtocolBase.cc.

References scorefxn_.

Referenced by protocols::relax::FastRelax::parse_def(), protocols::relax::FastRelax::parse_my_tag(), protocols::relax::ClassicRelax::set_default(), and protocols::relax::CentroidRelax::set_score_function().

void protocols::relax::RelaxProtocolBase::set_task_factory ( core::pack::task::TaskFactoryOP  taskf)

Definition at line 292 of file RelaxProtocolBase.cc.

References task_factory_.

Referenced by protocols::hybridization::HybridizeProtocol::apply(), protocols::relax::FastRelax::parse_def(), and protocols::relax::FastRelax::parse_my_tag().

void protocols::relax::RelaxProtocolBase::set_up_constraints ( core::pose::Pose &  pose,
core::kinematics::MoveMap &  local_movemap 
)
protected

Definition at line 390 of file RelaxProtocolBase.cc.

References core::chemical::aa_vrt, core::pose::Pose::add_constraint(), core::pose::addVirtualResAsRoot(), core::scoring::atom_pair_constraint, core::sequence::calpha_superimpose_with_mapping(), constrain_coords_, constrain_relax_segments_, constrain_relax_to_native_coords_, coord_constrain_sidechains_, core::scoring::coordinate_constraint, protocols::relax::derive_sc_sc_restraints(), core::pose::Pose::fold_tree(), protocols::moves::Mover::get_native_pose(), get_scorefxn(), core::id::SequenceMapping::identity(), core::kinematics::FoldTree::is_root(), core::pose::Pose::num_jump(), ramp_down_constraints_, core::pose::Pose::residue(), core::id::SequenceMapping::reverse(), core::kinematics::FoldTree::root(), core::pose::Pose::sequence(), core::pose::sequence_map_from_pdbinfo(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::total_residue(), and protocols::relax::TR().

Referenced by protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::apply(), and protocols::relax::CentroidRelax::setup_class_movemap_and_constraints().

Member Data Documentation

bool protocols::relax::RelaxProtocolBase::cartesian_
protected

Do cartesian-space minimization?

Definition at line 169 of file RelaxProtocolBase.hh.

Referenced by protocols::relax::CentroidRelax::apply(), cartesian(), protocols::relax::FastRelax::do_minimize(), protocols::relax::CentroidRelax::set_cartesian(), and set_default_minimization_settings().

bool protocols::relax::RelaxProtocolBase::constrain_coords_
protected

Definition at line 159 of file RelaxProtocolBase.hh.

Referenced by constrain_coords(), set_default_coordinate_settings(), and set_up_constraints().

bool protocols::relax::RelaxProtocolBase::constrain_relax_segments_
protected

Definition at line 163 of file RelaxProtocolBase.hh.

Referenced by constrain_relax_segments(), set_default_coordinate_settings(), and set_up_constraints().

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords_
protected

Definition at line 157 of file RelaxProtocolBase.hh.

Referenced by constrain_relax_to_native_coords(), set_default_coordinate_settings(), and set_up_constraints().

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords_
protected

Definition at line 158 of file RelaxProtocolBase.hh.

Referenced by constrain_relax_to_start_coords(), and set_default_coordinate_settings().

bool protocols::relax::RelaxProtocolBase::coord_constrain_sidechains_
protected

Definition at line 160 of file RelaxProtocolBase.hh.

Referenced by set_default_coordinate_settings(), and set_up_constraints().

bool protocols::relax::RelaxProtocolBase::dry_run_
private

Is this a dry run (i.e. do no cycles)

Definition at line 188 of file RelaxProtocolBase.hh.

Referenced by dry_run(), set_defaults(), and set_dry_run().

bool protocols::relax::RelaxProtocolBase::explicit_ramp_constraints_
protected

Definition at line 161 of file RelaxProtocolBase.hh.

Referenced by explicit_ramp_constraints(), ramp_down_constraints(), and set_default_coordinate_settings().

bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2_
protected

Definition at line 174 of file RelaxProtocolBase.hh.

Referenced by limit_aroma_chi2(), and set_default_coordinate_settings().

std::string protocols::relax::RelaxProtocolBase::min_type_
protected

Definition at line 166 of file RelaxProtocolBase.hh.

Referenced by protocols::relax::CentroidRelax::apply(), protocols::relax::FastRelax::do_minimize(), protocols::relax::ClassicRelax::set_default(), set_default_minimization_settings(), protocols::relax::CentroidRelax::set_min_type(), and set_min_type().

bool protocols::relax::RelaxProtocolBase::minimize_bond_angles_
private

Definition at line 151 of file RelaxProtocolBase.hh.

Referenced by initialize_movemap(), minimize_bond_angles(), and set_default_minimization_settings().

bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths_
private

Definition at line 150 of file RelaxProtocolBase.hh.

Referenced by initialize_movemap(), minimize_bond_lengths(), and set_default_minimization_settings().

int protocols::relax::RelaxProtocolBase::minimize_bondangle_subset_
private

Definition at line 152 of file RelaxProtocolBase.hh.

Referenced by initialize_movemap(), minimize_bondangle_subset(), and set_default_minimization_settings().

int protocols::relax::RelaxProtocolBase::minimize_bondlength_subset_
private

Definition at line 153 of file RelaxProtocolBase.hh.

Referenced by initialize_movemap(), minimize_bondlength_subset(), and set_default_minimization_settings().

core::kinematics::MoveMapOP protocols::relax::RelaxProtocolBase::movemap_
private

Definition at line 179 of file RelaxProtocolBase.hh.

Referenced by apply_disulfides(), get_movemap(), set_default_movemap(), and set_movemap().

bool protocols::relax::RelaxProtocolBase::ramp_down_constraints_
protected

Definition at line 162 of file RelaxProtocolBase.hh.

Referenced by protocols::relax::ClassicRelax::apply(), ramp_down_constraints(), set_default_coordinate_settings(), and set_up_constraints().

core::scoring::ScoreFunctionOP protocols::relax::RelaxProtocolBase::scorefxn_
private

Definition at line 182 of file RelaxProtocolBase.hh.

Referenced by get_scorefxn(), and set_scorefxn().

core::pack::task::TaskFactoryOP protocols::relax::RelaxProtocolBase::task_factory_
private

task factory for packer ( used only FastRelax as of 11/05/2010 )

Definition at line 185 of file RelaxProtocolBase.hh.

Referenced by get_task_factory(), set_defaults(), and set_task_factory().

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:49:35 for Rosetta 3.5 by   doxygen 1.8.4