protocols::enzdes::EnzRepackMinimize Class Reference

#include <EnzRepackMinimize.hh>

Inheritance diagram for protocols::enzdes::EnzRepackMinimize:

Collaboration diagram for protocols::enzdes::EnzRepackMinimize:

Public Member Functions
	EnzRepackMinimize ()
	EnzRepackMinimize (std::string const name)
virtual	~EnzRepackMinimize ()
void	ensure_scofx_cstfication (core::pose::Pose const &pose)
	turns on constraint score terms in case the pose has an enzdes cst cache More...
void	minimize_in_stages (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool const &cstopt, bool const &min_sc, bool const &min_rb, bool const &min_lig)
void	apply (core::pose::Pose &pose)
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...
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	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
void	set_min_rb (bool const min_rb)
bool	get_min_rb () const
void	set_min_sc (bool const min_sc)
bool	get_min_sc () const
void	set_min_lig (bool const min_lig)
bool	get_min_lig () const
void	set_min_bb (bool const min_bb)
bool	get_min_bb () const
bool	get_design () const
void	set_design (bool const des)
void	set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn)
void	set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn)
core::scoring::ScoreFunctionOP	scorefxn_repack () const
core::scoring::ScoreFunctionOP	scorefxn_minimize () const
core::pack::task::PackerTaskOP	create_ptask (core::pose::Pose &pose)
void	task_factory (core::pack::task::TaskFactoryOP p)
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 ()
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)
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

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_repack_
core::scoring::ScoreFunctionOP	scorefxn_minimize_
bool	cst_opt_
bool	design_
bool	repack_
bool	fix_catalytic_
bool	minimize_in_stages_
bool	min_rb_
bool	min_sc_
bool	min_bb_
bool	min_lig_
bool	minimize_prot_jumps_
bool	backrub_
core::pack::task::PackerTaskOP	task_
core::pack::task::TaskFactoryOP	task_factory_
core::Size	n_cycles_

Additional Inherited Members
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
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 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

Definition at line 43 of file EnzRepackMinimize.hh.

Constructor & Destructor Documentation

protocols::enzdes::EnzRepackMinimize::EnzRepackMinimize

(

)

Definition at line 80 of file EnzRepackMinimize.cc.

Referenced by clone(), and fresh_instance().

protocols::enzdes::EnzRepackMinimize::EnzRepackMinimize

(

std::string const

name)

Definition at line 90 of file EnzRepackMinimize.cc.

protocols::enzdes::EnzRepackMinimize::~EnzRepackMinimize ( )

virtual

Definition at line 100 of file EnzRepackMinimize.cc.

Member Function Documentation

void protocols::enzdes::EnzRepackMinimize::apply ( core::pose::Pose &  pose)

virtual

Implements protocols::moves::Mover.

Definition at line 115 of file EnzRepackMinimize.cc.

References protocols::protein_interface_design::movers::BackrubDDMover::apply(), backrub_, core::pose::Pose::constraint_set(), create_ptask(), cst_opt_, design_, ensure_scofx_cstfication(), fix_catalytic_, core::pose::Pose::fold_tree(), min_bb_, min_lig_, min_rb_, min_sc_, minimize_in_stages(), minimize_in_stages_, minimize_prot_jumps_, n_cycles_, repack_, scorefxn_minimize_, scorefxn_repack_, task_, task_factory_, core::pose::Pose::total_residue(), protocols::enzdes::TR(), and core::pose::Pose::update_residue_neighbors().

protocols::moves::MoverOP protocols::enzdes::EnzRepackMinimize::clone ( ) const

virtual

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 103 of file EnzRepackMinimize.cc.

References EnzRepackMinimize().

core::pack::task::PackerTaskOP protocols::enzdes::EnzRepackMinimize::create_ptask

(

core::pose::Pose &

pose)

Definition at line 177 of file EnzRepackMinimize.cc.

References task_factory_, and protocols::enzdes::TR().

Referenced by apply().

void protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication

(

core::pose::Pose const &

pose)

turns on constraint score terms in case the pose has an enzdes cst cache

Definition at line 213 of file EnzRepackMinimize.cc.

References protocols::enzdes::enzutil::enable_constraint_scoreterms(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::enzdes::enzutil::is_scofx_cstfied(), scorefxn_minimize_, scorefxn_repack_, protocols::enzdes::enzutil::scorefxn_update_from_options(), and protocols::enzdes::TR().

Referenced by apply().

protocols::moves::MoverOP protocols::enzdes::EnzRepackMinimize::fresh_instance ( ) const

virtual

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 109 of file EnzRepackMinimize.cc.

References EnzRepackMinimize().

bool protocols::enzdes::EnzRepackMinimize::get_design ( ) const

inline

Definition at line 80 of file EnzRepackMinimize.hh.

References design_.

bool protocols::enzdes::EnzRepackMinimize::get_min_bb ( ) const

inline

Definition at line 77 of file EnzRepackMinimize.hh.

References min_bb_.

bool protocols::enzdes::EnzRepackMinimize::get_min_lig ( ) const

inline

Definition at line 75 of file EnzRepackMinimize.hh.

References min_lig_.

bool protocols::enzdes::EnzRepackMinimize::get_min_rb ( ) const

inline

Definition at line 71 of file EnzRepackMinimize.hh.

References min_rb_.

bool protocols::enzdes::EnzRepackMinimize::get_min_sc ( ) const

inline

Definition at line 73 of file EnzRepackMinimize.hh.

References min_sc_.

std::string protocols::enzdes::EnzRepackMinimize::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 172 of file EnzRepackMinimize.cc.

References protocols::enzdes::EnzRepackMinimizeCreator::mover_name().

void protocols::enzdes::EnzRepackMinimize::minimize_in_stages	(	core::pose::Pose &	pose,
		core::pack::task::PackerTaskCOP	task,
		bool const &	cstopt,
		bool const &	min_sc,
		bool const &	min_rb,
		bool const &	min_lig
	)

Definition at line 188 of file EnzRepackMinimize.cc.

References min_rb_, scorefxn_minimize(), and protocols::enzdes::TR().

Referenced by apply().

void protocols::enzdes::EnzRepackMinimize::parse_my_tag ( utility::tag::TagPtr const  tag, protocols::moves::DataMap &  data, protocols::filters::Filters_map const &  filters, protocols::moves::Movers_map const &  movers, core::pose::Pose const &  pose  )

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

Definition at line 230 of file EnzRepackMinimize.cc.

References backrub_, cst_opt_, design_, fix_catalytic_, protocols::moves::DataMap::get(), min_bb_, minimize_in_stages_, minimize_prot_jumps_, n_cycles_, protocols::rosetta_scripts::parse_task_operations(), repack_, scorefxn_minimize(), scorefxn_minimize_, scorefxn_repack(), scorefxn_repack_, set_min_bb(), set_min_lig(), set_min_rb(), set_min_sc(), task_factory(), task_factory_, and protocols::enzdes::TR().

core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_minimize

(

)

const

Definition at line 286 of file EnzRepackMinimize.cc.

References scorefxn_minimize_.

Referenced by minimize_in_stages(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_repack

(

)

const

Definition at line 281 of file EnzRepackMinimize.cc.

References scorefxn_repack_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_design ( bool const  des)

inline

Definition at line 81 of file EnzRepackMinimize.hh.

References design_.

void protocols::enzdes::EnzRepackMinimize::set_min_bb ( bool const  min_bb)

inline

Definition at line 76 of file EnzRepackMinimize.hh.

References min_bb_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_min_lig ( bool const  min_lig)

inline

Definition at line 74 of file EnzRepackMinimize.hh.

References min_lig_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_min_rb ( bool const  min_rb)

inline

Definition at line 70 of file EnzRepackMinimize.hh.

References min_rb_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_min_sc ( bool const  min_sc)

inline

Definition at line 72 of file EnzRepackMinimize.hh.

References min_sc_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_scorefxn_minimize

(

core::scoring::ScoreFunctionCOP

scorefxn)

Definition at line 276 of file EnzRepackMinimize.cc.

References scorefxn_minimize_.

void protocols::enzdes::EnzRepackMinimize::set_scorefxn_repack

(

core::scoring::ScoreFunctionCOP

scorefxn)

Definition at line 271 of file EnzRepackMinimize.cc.

References scorefxn_repack_.

void protocols::enzdes::EnzRepackMinimize::task_factory

(

core::pack::task::TaskFactoryOP

p)

Definition at line 291 of file EnzRepackMinimize.cc.

References task_factory_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::enzdes::EnzRepackMinimize::backrub_

private

Definition at line 99 of file EnzRepackMinimize.hh.

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::cst_opt_

private

Definition at line 96 of file EnzRepackMinimize.hh.

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::design_

private

Definition at line 97 of file EnzRepackMinimize.hh.

Referenced by apply(), get_design(), parse_my_tag(), and set_design().

bool protocols::enzdes::EnzRepackMinimize::fix_catalytic_

private

Definition at line 97 of file EnzRepackMinimize.hh.

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::min_bb_

private

Definition at line 99 of file EnzRepackMinimize.hh.

Referenced by apply(), get_min_bb(), parse_my_tag(), and set_min_bb().

bool protocols::enzdes::EnzRepackMinimize::min_lig_

private

Definition at line 99 of file EnzRepackMinimize.hh.

Referenced by apply(), get_min_lig(), and set_min_lig().

bool protocols::enzdes::EnzRepackMinimize::min_rb_

private

Definition at line 99 of file EnzRepackMinimize.hh.

Referenced by apply(), get_min_rb(), minimize_in_stages(), and set_min_rb().

bool protocols::enzdes::EnzRepackMinimize::min_sc_

private

Definition at line 99 of file EnzRepackMinimize.hh.

Referenced by apply(), get_min_sc(), and set_min_sc().

bool protocols::enzdes::EnzRepackMinimize::minimize_in_stages_

private

Definition at line 98 of file EnzRepackMinimize.hh.

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::minimize_prot_jumps_

private

Definition at line 99 of file EnzRepackMinimize.hh.

Referenced by apply(), and parse_my_tag().

core::Size protocols::enzdes::EnzRepackMinimize::n_cycles_

private

Definition at line 102 of file EnzRepackMinimize.hh.

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::repack_

private

Definition at line 97 of file EnzRepackMinimize.hh.

Referenced by apply(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_minimize_

private

Definition at line 95 of file EnzRepackMinimize.hh.

Referenced by apply(), ensure_scofx_cstfication(), parse_my_tag(), scorefxn_minimize(), and set_scorefxn_minimize().

core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_repack_

private

Definition at line 94 of file EnzRepackMinimize.hh.

Referenced by apply(), ensure_scofx_cstfication(), parse_my_tag(), scorefxn_repack(), and set_scorefxn_repack().

core::pack::task::PackerTaskOP protocols::enzdes::EnzRepackMinimize::task_

private

Definition at line 100 of file EnzRepackMinimize.hh.

Referenced by apply().

core::pack::task::TaskFactoryOP protocols::enzdes::EnzRepackMinimize::task_factory_

private

Definition at line 101 of file EnzRepackMinimize.hh.

Referenced by apply(), create_ptask(), parse_my_tag(), and task_factory().

---

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

• src/protocols/enzdes/EnzRepackMinimize.hh
• src/protocols/enzdes/EnzRepackMinimize.cc