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protocols::relax::RelaxProtocolBase Class Reference

#include <RelaxProtocolBase.hh>

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

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)
 
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 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

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 ( )
overridedefault

Member Function Documentation

void protocols::relax::RelaxProtocolBase::add_cst_files ( std::string const &  cstfile)
inlineprotected
void protocols::relax::RelaxProtocolBase::apply_disulfides ( core::pose::Pose pose)
bool protocols::relax::RelaxProtocolBase::cartesian ( ) const
inline
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_.

bool protocols::relax::RelaxProtocolBase::constrain_coords ( ) const
inline
void protocols::relax::RelaxProtocolBase::constrain_coords ( bool  constrain_coords)
bool protocols::relax::RelaxProtocolBase::constrain_relax_segments ( ) const
inline
void protocols::relax::RelaxProtocolBase::constrain_relax_segments ( bool  constrain_relax_segments)
bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords ( ) const
inline
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
inline
void protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords ( bool  constrain_relax_to_start_coords)
bool protocols::relax::RelaxProtocolBase::coord_constrain_sidechains ( ) const
inline
void protocols::relax::RelaxProtocolBase::coord_constrain_sidechains ( bool  coord_constrain_sidechains)
std::string protocols::relax::RelaxProtocolBase::cst_files ( core::Size const  i) const
inlineprotected

References cst_files_.

Referenced by set_up_constraints().

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

References dry_run_.

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

References fix_omega_.

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

References fix_omega(), and fix_omega_.

Referenced by fix_omega().

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

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().

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

References movemap_.

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

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 
)
protected
bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2 ( ) const
inlineprotected
core::Size protocols::relax::RelaxProtocolBase::max_iter ( ) const
inline
void protocols::relax::RelaxProtocolBase::max_iter ( core::Size  max_iter)

References max_iter(), and max_iter_.

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

References min_type(), and min_type_.

bool protocols::relax::RelaxProtocolBase::minimize_bond_angles ( ) const
inline
void protocols::relax::RelaxProtocolBase::minimize_bond_angles ( bool  minimize_bond_angles)
bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths ( ) const
inline
void protocols::relax::RelaxProtocolBase::minimize_bond_lengths ( bool  minimize_bond_lengths)
int protocols::relax::RelaxProtocolBase::minimize_bondangle_subset ( ) const
inlineprotected
void protocols::relax::RelaxProtocolBase::minimize_bondangle_subset ( int  minimize_bondangle_subset)
inlineprotected
int protocols::relax::RelaxProtocolBase::minimize_bondlength_subset ( ) const
inlineprotected
void protocols::relax::RelaxProtocolBase::minimize_bondlength_subset ( int  minimize_bondlength_subset)
inlineprotected
bool protocols::relax::RelaxProtocolBase::mover_is_unpublished ( ) const
overridevirtual

Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?

Defaults to false. Derived relax protocols may override this to provide authorship info. If set to true, the provide_authorship_info_for_unpublished() override should also be provided.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

bool protocols::relax::RelaxProtocolBase::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Defaults to false. Derived relax protocols may override this to provide citation info. If set to true, the provide_citation_info() override should also be provided.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

void protocols::relax::RelaxProtocolBase::output_debug_structure ( core::pose::Pose pose,
std::string  prefix 
)
protected
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::relax::RelaxProtocolBase::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provide a list of authors and their e-mail addresses, as strings.

Returns
A list of pairs of (author, e-mail address). The default version only provides authorship information for gthe task operations in the task factory. Empty list if not unpublished.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

References scorefxn_, and task_factory_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::relax::RelaxProtocolBase::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

The default implementation of this function provides citations only for the task operations in the task factory.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

References scorefxn_, and task_factory_.

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

bool protocols::relax::RelaxProtocolBase::ramp_down_constraints ( ) const
inline
void protocols::relax::RelaxProtocolBase::ramp_down_constraints ( bool  ramp_down_constraints)
void protocols::relax::RelaxProtocolBase::register_options ( )
static
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_movemap ( core::kinematics::MoveMapOP  movemap)
void protocols::relax::RelaxProtocolBase::set_movemap_factory ( core::select::movemap::MoveMapFactoryOP  mm_factory)
void protocols::relax::RelaxProtocolBase::set_scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)
void protocols::relax::RelaxProtocolBase::set_task_factory ( core::pack::task::TaskFactoryOP  task_factory)
void protocols::relax::RelaxProtocolBase::set_up_constraints ( core::pose::Pose pose,
core::kinematics::MoveMap local_movemap 
)
protected

Member Data Documentation

bool protocols::relax::RelaxProtocolBase::cartesian_
private

Do cartesian-space minimization?

Referenced by cartesian(), and set_default_minimization_settings().

bool protocols::relax::RelaxProtocolBase::constrain_coords_
private
bool protocols::relax::RelaxProtocolBase::constrain_relax_segments_
private
bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords_
private
bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords_
private
bool protocols::relax::RelaxProtocolBase::coord_constrain_sidechains_
private
utility::vector1< std::string > protocols::relax::RelaxProtocolBase::cst_files_
private
bool protocols::relax::RelaxProtocolBase::dry_run_
private

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

Referenced by dry_run(), and set_defaults().

bool protocols::relax::RelaxProtocolBase::fix_omega_
private
bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2_
private
core::Size protocols::relax::RelaxProtocolBase::max_iter_
private

maximum minimizer iterations

Referenced by max_iter(), and set_default_minimization_settings().

std::string protocols::relax::RelaxProtocolBase::min_type_
private
bool protocols::relax::RelaxProtocolBase::minimize_bond_angles_
private
bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths_
private
int protocols::relax::RelaxProtocolBase::minimize_bondangle_subset_
private
int protocols::relax::RelaxProtocolBase::minimize_bondlength_subset_
private
core::kinematics::MoveMapOP protocols::relax::RelaxProtocolBase::movemap_
private
core::select::movemap::MoveMapFactoryOP protocols::relax::RelaxProtocolBase::movemap_factory_
private
bool protocols::relax::RelaxProtocolBase::ramp_down_constraints_
private
core::scoring::ScoreFunctionOP protocols::relax::RelaxProtocolBase::scorefxn_
private
core::pack::task::TaskFactoryOP protocols::relax::RelaxProtocolBase::task_factory_
private

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

Referenced by get_task_factory(), provide_authorship_info_for_unpublished(), provide_citation_info(), and set_task_factory().


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