#include <PyMolMover.hh>

Inheritance diagram for protocols::moves::PyMolMover:

Collaboration diagram for protocols::moves::PyMolMover:

Public Member Functions
	PyMolMover ()

virtual	~PyMolMover ()

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

virtual void	apply (Pose &)

virtual void	apply (Pose const &)
	Actually our mover does not change the Pose object, so we have additional const version... More...

void	print (std::string const &message)
	Send message for PyMol to print. More...

void	send_energy (Pose const &, core::scoring::ScoreType stype=core::scoring::total_score)
	Send specified energy to PyMOL. More...

void	send_energy (Pose const &, std::string const &stype)
	Send specified energy to PyMOL. More...

void	send_RAW_Energies (Pose const &, std::string energyType, utility::vector1< int > const &energies)
	Send RAW energy array for coloring by PyMOL. More...

virtual void	send_colors (Pose const &, std::map< int, int > const &colors, X11Colors default_color=protocols::moves::XC_blue)
	Tell PyMOL to color protein with supplied custom colors. More...

bool	update_energy ()

void	update_energy (bool f)

core::scoring::ScoreType	energy_type (void)

void	energy_type (core::scoring::ScoreType t)

void	keep_history (bool kh)
	Set the keep history flag. If set to True - PyMol will keep track of all frames that was sent. More...

bool	keep_history (void)
	Return current keep_history flag. More...

void	update_interval (core::Real t)
	Set current minimum update interval 't' in seconds. Mover will not send anyinformation to PyMOL before atleast 't' secons has passes since last packet was sent. default value is 0, - no packets are skipped. More...

core::Real	update_interval ()
	Return current update interval. More...

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)

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...

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...

virtual 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_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
std::string	get_PyMol_model_name (Pose const &pose) const

bool	is_it_time ()

Private Attributes
UDPSocketClient	link_
	Actual link object. More...

bool	update_energy_

core::scoring::ScoreType	energy_type_

bool	keep_history_
	Should PyMol keep history of all models that was sent? - Default is false. More...

core::Real	update_interval_
	Update interval in seconds. More...

core::Real	last_packet_sent_time_
	Time stamp from where last packet was sent. More...

std::string	name_
	Name of model in pymol. More...

Friends
std::ostream &	operator<< (std::ostream &os, PyMolMover const &mover)

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 272 of file PyMolMover.hh.

Constructor & Destructor Documentation

protocols::moves::PyMolMover::PyMolMover ( )

inline

Definition at line 275 of file PyMolMover.hh.

protocols::moves::PyMolMover::~PyMolMover ( )

virtual

Definition at line 165 of file PyMolMover.cc.

Member Function Documentation

void protocols::moves::PyMolMover::apply ( Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 234 of file PyMolMover.cc.

Referenced by protocols::moves::PyMolObserver::generalEvent().

void protocols::moves::PyMolMover::apply ( Pose const & pose)

virtual

Actually our mover does not change the Pose object, so we have additional const version...

Definition at line 200 of file PyMolMover.cc.

References core::pose::Pose::dump_pdb(), energy_type_, get_PyMol_model_name(), is_it_time(), keep_history_, link_, protocols::moves::Mover::name(), send_energy(), protocols::moves::UDPSocketClient::sendMessage(), and update_energy_.

core::scoring::ScoreType protocols::moves::PyMolMover::energy_type ( void )

inline

Definition at line 308 of file PyMolMover.hh.

References energy_type_.

void protocols::moves::PyMolMover::energy_type ( core::scoring::ScoreType t)

inline

Definition at line 309 of file PyMolMover.hh.

References energy_type_, and core::scoring::hbonds::t().

std::string protocols::moves::PyMolMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 167 of file PyMolMover.cc.

std::string protocols::moves::PyMolMover::get_PyMol_model_name ( Pose const & pose) const

private

Definition at line 172 of file PyMolMover.cc.

References protocols::moves::Mover::info(), name_, and core::pose::Pose::pdb_info().

Referenced by apply(), send_energy(), and send_RAW_Energies().

bool protocols::moves::PyMolMover::is_it_time ( )

private

Definition at line 188 of file PyMolMover.cc.

References last_packet_sent_time_, core::scoring::hbonds::t(), and update_interval_.

Referenced by apply(), print(), send_energy(), and send_RAW_Energies().

void protocols::moves::PyMolMover::keep_history ( bool kh)

inline

Set the keep history flag. If set to True - PyMol will keep track of all frames that was sent.

Definition at line 313 of file PyMolMover.hh.

References keep_history_.

bool protocols::moves::PyMolMover::keep_history ( void )

inline

Return current keep_history flag.

Definition at line 317 of file PyMolMover.hh.

References keep_history_.

void protocols::moves::PyMolMover::print ( std::string const & message)

Send message for PyMol to print.

Definition at line 240 of file PyMolMover.cc.

References is_it_time(), keep_history_, link_, and protocols::moves::UDPSocketClient::sendMessage().

void protocols::moves::PyMolMover::send_colors	(	Pose const &	pose,
		std::map< int, int > const &	colors,
		X11Colors	default_color = `protocols::moves::XC_blue`
	)

virtual

Tell PyMOL to color protein with supplied custom colors.

Definition at line 346 of file PyMolMover.cc.

References send_RAW_Energies(), core::pose::Pose::total_residue(), protocols::moves::XC_first_color, and protocols::moves::XC_last_color.

void protocols::moves::PyMolMover::send_energy	(	Pose const &	pose,
		core::scoring::ScoreType	stype = `core::scoring::total_score`
	)

Send specified energy to PyMOL.

Definition at line 287 of file PyMolMover.cc.

References core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), get_PyMol_model_name(), protocols::moves::Mover::info(), is_it_time(), keep_history_, link_, protocols::moves::Mover::name(), core::scoring::name_from_score_type(), core::pose::Pose::pdb_info(), core::scoring::Energies::residue_total_energies(), core::scoring::Energies::residue_total_energy(), protocols::moves::UDPSocketClient::sendMessage(), core::pose::Pose::total_residue(), and core::scoring::total_score.

Referenced by apply(), and send_energy().

void protocols::moves::PyMolMover::send_energy	(	Pose const &	pose,
		std::string const &	stype
	)

Send specified energy to PyMOL.

Definition at line 340 of file PyMolMover.cc.

References core::scoring::ScoreTypeManager::score_type_from_name(), and send_energy().

void protocols::moves::PyMolMover::send_RAW_Energies	(	Pose const &	pose,
		std::string	energyType,
		utility::vector1< int > const &	energies
	)

Send RAW energy array for coloring by PyMOL.

Definition at line 249 of file PyMolMover.cc.

References get_PyMol_model_name(), protocols::moves::Mover::info(), is_it_time(), keep_history_, link_, protocols::moves::Mover::name(), core::pose::Pose::pdb_info(), and protocols::moves::UDPSocketClient::sendMessage().

Referenced by send_colors().

bool protocols::moves::PyMolMover::update_energy ( )

inline

Definition at line 304 of file PyMolMover.hh.

References update_energy_.

void protocols::moves::PyMolMover::update_energy ( bool f)

inline

Definition at line 305 of file PyMolMover.hh.

References update_energy_.

void protocols::moves::PyMolMover::update_interval ( core::Real t)

inline

Set current minimum update interval 't' in seconds. Mover will not send anyinformation to PyMOL before atleast 't' secons has passes since last packet was sent. default value is 0, - no packets are skipped.

Definition at line 323 of file PyMolMover.hh.

References core::scoring::hbonds::t(), and update_interval_.

core::Real protocols::moves::PyMolMover::update_interval ( )

inline

Return current update interval.

Definition at line 327 of file PyMolMover.hh.

References update_interval_.

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		PyMolMover const &	mover
	)

friend

Definition at line 329 of file PyMolMover.hh.

Member Data Documentation

core::scoring::ScoreType protocols::moves::PyMolMover::energy_type_

private

Definition at line 352 of file PyMolMover.hh.

Referenced by apply(), and energy_type().

bool protocols::moves::PyMolMover::keep_history_

private

Should PyMol keep history of all models that was sent? - Default is false.

Definition at line 355 of file PyMolMover.hh.

Referenced by apply(), keep_history(), print(), send_energy(), and send_RAW_Energies().

core::Real protocols::moves::PyMolMover::last_packet_sent_time_

private

Time stamp from where last packet was sent.

Definition at line 361 of file PyMolMover.hh.

Referenced by is_it_time().

UDPSocketClient protocols::moves::PyMolMover::link_

private

Actual link object.

Definition at line 348 of file PyMolMover.hh.

Referenced by apply(), print(), send_energy(), and send_RAW_Energies().

std::string protocols::moves::PyMolMover::name_

private

Name of model in pymol.

Definition at line 364 of file PyMolMover.hh.

Referenced by get_PyMol_model_name().

bool protocols::moves::PyMolMover::update_energy_

private

Definition at line 350 of file PyMolMover.hh.

Referenced by apply(), and update_energy().

core::Real protocols::moves::PyMolMover::update_interval_

private

Update interval in seconds.

Definition at line 358 of file PyMolMover.hh.

Referenced by is_it_time(), and update_interval().

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

src/protocols/moves/PyMolMover.hh
src/protocols/moves/PyMolMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation