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protocols::relax::RelaxProtocolBase Class Reference

#include <RelaxProtocolBase.hh>

Inheritance diagram for protocols::relax::RelaxProtocolBase:
Inheritance graph
Collaboration diagram for protocols::relax::RelaxProtocolBase:
Collaboration graph

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 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)
get_scorefxn () const
void set_task_factory (core::pack::task::TaskFactoryOP taskf)
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)
Moveroperator= (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 Stringsinfo ()
 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...

Member Typedef Documentation

Constructor & Destructor Documentation

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

References set_defaults().

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

References set_defaults().

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

References set_defaults().

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

Member Function Documentation

void protocols::relax::RelaxProtocolBase::apply_disulfides ( core::pose::Pose pose)
void protocols::relax::RelaxProtocolBase::cartesian ( bool  newval)

References cartesian_.

bool protocols::relax::RelaxProtocolBase::cartesian ( ) const
bool protocols::relax::RelaxProtocolBase::constrain_coords ( ) const
void protocols::relax::RelaxProtocolBase::constrain_coords ( bool  constrain_coords)
bool protocols::relax::RelaxProtocolBase::constrain_relax_segments ( ) const
void protocols::relax::RelaxProtocolBase::constrain_relax_segments ( bool  constrain_relax_segments)
bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords ( ) const
void protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords ( bool  constrain_relax_to_native_coords)
bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords ( ) const
void protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords ( bool  constrain_relax_to_start_coords)
bool protocols::relax::RelaxProtocolBase::dry_run ( ) const
bool protocols::relax::RelaxProtocolBase::explicit_ramp_constraints ( ) const
virtual protocols::moves::MoverOP protocols::relax::RelaxProtocolBase::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).

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.

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

core::kinematics::MoveMapOP protocols::relax::RelaxProtocolBase::get_movemap ( )
const core::scoring::ScoreFunctionCOP protocols::relax::RelaxProtocolBase::get_scorefxn ( ) const
core::scoring::ScoreFunctionOP protocols::relax::RelaxProtocolBase::get_scorefxn ( )

References scorefxn_.

core::pack::task::TaskFactoryOP const & protocols::relax::RelaxProtocolBase::get_task_factory ( ) const
void protocols::relax::RelaxProtocolBase::initialize_movemap ( core::pose::Pose const &  pose,
core::kinematics::MoveMap movemap 
bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2 ( ) const
void protocols::relax::RelaxProtocolBase::minimize_bond_angles ( bool  setting)

References minimize_bond_angles_.

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

References minimize_bond_angles_.

void protocols::relax::RelaxProtocolBase::minimize_bond_lengths ( bool  setting)
bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths ( ) const
void protocols::relax::RelaxProtocolBase::minimize_bondangle_subset ( int  setting)
int protocols::relax::RelaxProtocolBase::minimize_bondangle_subset ( ) const
void protocols::relax::RelaxProtocolBase::minimize_bondlength_subset ( int  setting)
int protocols::relax::RelaxProtocolBase::minimize_bondlength_subset ( ) const
void protocols::relax::RelaxProtocolBase::output_debug_structure ( core::pose::Pose pose,
std::string  prefix 
bool protocols::relax::RelaxProtocolBase::ramp_down_constraints ( ) const
void protocols::relax::RelaxProtocolBase::ramp_down_constraints ( bool  ramp_down_constraints)
void protocols::relax::RelaxProtocolBase::register_options ( )
void protocols::relax::RelaxProtocolBase::set_default_coordinate_settings ( )
void protocols::relax::RelaxProtocolBase::set_default_minimization_settings ( )
void protocols::relax::RelaxProtocolBase::set_default_movemap ( )
void protocols::relax::RelaxProtocolBase::set_defaults ( )
void protocols::relax::RelaxProtocolBase::set_dry_run ( bool  setting)

References dry_run_.

void protocols::relax::RelaxProtocolBase::set_min_type ( std::string  min_type)
void protocols::relax::RelaxProtocolBase::set_movemap ( core::kinematics::MoveMapOP  movemap)
void protocols::relax::RelaxProtocolBase::set_scorefxn ( core::scoring::ScoreFunctionOP  score)
void protocols::relax::RelaxProtocolBase::set_task_factory ( core::pack::task::TaskFactoryOP  taskf)
void protocols::relax::RelaxProtocolBase::set_up_constraints ( core::pose::Pose pose,
core::kinematics::MoveMap local_movemap 

Member Data Documentation

bool protocols::relax::RelaxProtocolBase::cartesian_
bool protocols::relax::RelaxProtocolBase::constrain_coords_
bool protocols::relax::RelaxProtocolBase::constrain_relax_segments_
bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords_
bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords_
bool protocols::relax::RelaxProtocolBase::coord_constrain_sidechains_
bool protocols::relax::RelaxProtocolBase::dry_run_

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

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

bool protocols::relax::RelaxProtocolBase::explicit_ramp_constraints_
bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2_
std::string protocols::relax::RelaxProtocolBase::min_type_
bool protocols::relax::RelaxProtocolBase::minimize_bond_angles_
bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths_
int protocols::relax::RelaxProtocolBase::minimize_bondangle_subset_
int protocols::relax::RelaxProtocolBase::minimize_bondlength_subset_
core::kinematics::MoveMapOP protocols::relax::RelaxProtocolBase::movemap_
bool protocols::relax::RelaxProtocolBase::ramp_down_constraints_
core::scoring::ScoreFunctionOP protocols::relax::RelaxProtocolBase::scorefxn_

Referenced by get_scorefxn(), and set_scorefxn().

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

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

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

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