Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::relax::RelaxProtocolBase Class Reference

#include <RelaxProtocolBase.hh>

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

Public Types

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

 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)
void provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
 Provide the citation. 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 apply (Pose &)=0
 Main Method. 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
virtual std::string get_name () const =0
 Each derived class must specify its name. The class name. 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::moves::Mover
static std::string name ()
static void register_options ()
 Overload this static method if you access options within the mover. More...

Protected Member Functions

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...

Private Attributes

bool fix_omega_
bool minimize_bond_lengths_
bool minimize_bond_angles_
int minimize_bondangle_subset_
int minimize_bondlength_subset_
bool constrain_relax_to_native_coords_
bool constrain_relax_to_start_coords_
bool constrain_coords_
bool coord_constrain_sidechains_
bool ramp_down_constraints_
bool constrain_relax_segments_
utility::vector1< std::string > cst_files_
std::string min_type_
bool cartesian_
 Do cartesian-space minimization? More...
core::Size max_iter_
 maximum minimizer iterations More...
bool limit_aroma_chi2_
core::kinematics::MoveMapOP movemap_
core::select::movemap::MoveMapFactoryOP movemap_factory_
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

◆ parent

Constructor & Destructor Documentation

◆ RelaxProtocolBase() [1/3]

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

References set_defaults().

◆ RelaxProtocolBase() [2/3]

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

References set_defaults().

◆ RelaxProtocolBase() [3/3]

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

References set_defaults().

◆ ~RelaxProtocolBase()

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

Member Function Documentation

◆ add_cst_files()

void protocols::relax::RelaxProtocolBase::add_cst_files ( std::string const &  cstfile)

◆ apply_disulfides()

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

◆ cartesian() [1/2]

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

◆ cartesian() [2/2]

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

Use cartesian (minimization step)

Sets to use the lbfgs_armijo_nonmonotone if true or FR default if false Recommended to set max_iter to 200. Requires scorefunction setup for non-ideal minimization.

References cartesian_.

◆ constrain_coords() [1/2]

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

◆ constrain_coords() [2/2]

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

◆ constrain_relax_segments() [1/2]

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

◆ constrain_relax_segments() [2/2]

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

◆ constrain_relax_to_native_coords() [1/2]

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

◆ constrain_relax_to_native_coords() [2/2]

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

◆ constrain_relax_to_start_coords() [1/2]

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

◆ constrain_relax_to_start_coords() [2/2]

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

◆ coord_constrain_sidechains() [1/2]

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

◆ coord_constrain_sidechains() [2/2]

void protocols::relax::RelaxProtocolBase::coord_constrain_sidechains ( bool  coord_constrain_sidechains)

◆ cst_files()

std::string protocols::relax::RelaxProtocolBase::cst_files ( core::Size const  i) const

References cst_files_.

Referenced by set_up_constraints().

◆ dry_run() [1/2]

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

◆ dry_run() [2/2]

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

References dry_run_.

◆ fix_omega() [1/2]

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

References fix_omega_.

◆ fix_omega() [2/2]

void protocols::relax::RelaxProtocolBase::fix_omega ( bool  fix_omega)

References fix_omega(), and fix_omega_.

Referenced by fix_omega().

◆ fresh_instance()

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

Generates a new Mover object freshly created with the default ctor.

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().

◆ get_movemap() [1/2]

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

References movemap_.

◆ get_movemap() [2/2]

core::kinematics::MoveMapCOP protocols::relax::RelaxProtocolBase::get_movemap ( ) const

◆ get_scorefxn() [1/2]

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

References scorefxn_.

◆ get_scorefxn() [2/2]

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

◆ get_task_factory()

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

◆ initialize_movemap()

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

◆ limit_aroma_chi2()

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

◆ max_iter() [1/2]

core::Size protocols::relax::RelaxProtocolBase::max_iter ( ) const

◆ max_iter() [2/2]

void protocols::relax::RelaxProtocolBase::max_iter ( core::Size  max_iter)

References max_iter(), and max_iter_.

◆ min_type() [1/2]

std::string protocols::relax::RelaxProtocolBase::min_type ( ) const

◆ min_type() [2/2]

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

References min_type(), and min_type_.

◆ minimize_bond_angles() [1/2]

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

◆ minimize_bond_angles() [2/2]

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

◆ minimize_bond_lengths() [1/2]

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

◆ minimize_bond_lengths() [2/2]

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

◆ minimize_bondangle_subset() [1/2]

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

◆ minimize_bondangle_subset() [2/2]

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

◆ minimize_bondlength_subset() [1/2]

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

◆ minimize_bondlength_subset() [2/2]

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

◆ output_debug_structure()

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

◆ provide_citation_info()

void protocols::relax::RelaxProtocolBase::provide_citation_info ( basic::citation_manager::CitationCollectionList &  citations) const

Provide the citation.

Reimplemented from protocols::moves::Mover.

References scorefxn_, and task_factory_.

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

◆ ramp_down_constraints() [1/2]

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

◆ ramp_down_constraints() [2/2]

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

◆ register_options()

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

◆ set_default_coordinate_settings()

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

◆ set_default_minimization_settings()

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

◆ set_default_movemap()

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

◆ set_defaults()

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

◆ set_movemap()

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

◆ set_movemap_factory()

void protocols::relax::RelaxProtocolBase::set_movemap_factory ( core::select::movemap::MoveMapFactoryOP  mm_factory)

◆ set_scorefxn()

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

◆ set_task_factory()

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

◆ set_up_constraints()

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

Member Data Documentation

◆ cartesian_

bool protocols::relax::RelaxProtocolBase::cartesian_

Do cartesian-space minimization?

Referenced by cartesian(), and set_default_minimization_settings().

◆ constrain_coords_

bool protocols::relax::RelaxProtocolBase::constrain_coords_

◆ constrain_relax_segments_

bool protocols::relax::RelaxProtocolBase::constrain_relax_segments_

◆ constrain_relax_to_native_coords_

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords_

◆ constrain_relax_to_start_coords_

bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords_

◆ coord_constrain_sidechains_

bool protocols::relax::RelaxProtocolBase::coord_constrain_sidechains_

◆ cst_files_

utility::vector1< std::string > protocols::relax::RelaxProtocolBase::cst_files_

◆ dry_run_

bool protocols::relax::RelaxProtocolBase::dry_run_

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

Referenced by dry_run(), and set_defaults().

◆ fix_omega_

bool protocols::relax::RelaxProtocolBase::fix_omega_

◆ limit_aroma_chi2_

bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2_

◆ max_iter_

core::Size protocols::relax::RelaxProtocolBase::max_iter_

maximum minimizer iterations

Referenced by max_iter(), and set_default_minimization_settings().

◆ min_type_

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

◆ minimize_bond_angles_

bool protocols::relax::RelaxProtocolBase::minimize_bond_angles_

◆ minimize_bond_lengths_

bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths_

◆ minimize_bondangle_subset_

int protocols::relax::RelaxProtocolBase::minimize_bondangle_subset_

◆ minimize_bondlength_subset_

int protocols::relax::RelaxProtocolBase::minimize_bondlength_subset_

◆ movemap_

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

◆ movemap_factory_

core::select::movemap::MoveMapFactoryOP protocols::relax::RelaxProtocolBase::movemap_factory_

◆ ramp_down_constraints_

bool protocols::relax::RelaxProtocolBase::ramp_down_constraints_

◆ scorefxn_

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

◆ task_factory_

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(), provide_citation_info(), and set_task_factory().

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