#include <PyMolMover.hh>

Public Member Functions
	PyMolMover ()
	ctor More...

	PyMolMover (PyMolMover const &other)
	cctor More...

virtual	~PyMolMover ()
	dtor More...

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...

void	send_membrane_planes (Pose const &)
	Send Membrane Planes to 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...

std::string	pymol_name ()
	Specify PyMOL model name. More...

void	pymol_name (std::string new_pymol_name)

bool	update_energy ()
	Flag that specify if PyMOL mover should send current Pose energy on every apply. If name set to empty string (default) then name derived from pdb_info will be used. More...

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...

void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Parses tag for rosetta scripts. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	required in the context of the parser/scripting scheme More...

virtual protocols::moves::MoverOP	clone () const
	required in the context of the parser/scripting scheme 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

void	set_type (std::string const &setting)

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
	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...

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	update_membrane_
	If pose is a membrane pose, send planes. More...

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	pymol_name_
	Name of model in pymol. More...

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

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. 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...

Constructor & Destructor Documentation

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

ctor

References scoring, and total_score.

Referenced by fresh_instance().

protocols::moves::PyMolMover::PyMolMover ( PyMolMover const & other )

cctor

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

virtual

dtor

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

Referenced by protocols::moves::PyMolObserver::conformationEvent(), protocols::moves::PyMolObserver::energyEvent(), and 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...

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

protocols::moves::MoverOP protocols::moves::PyMolMover::clone ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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

inline

References energy_type_.

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

inline

References energy_type_.

protocols::moves::MoverOP protocols::moves::PyMolMover::fresh_instance ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

References PyMolMover().

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

virtual

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

Implements protocols::moves::Mover.

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

private

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

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

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

private

References last_packet_sent_time_, t, and update_interval_.

Referenced by apply(), print(), send_energy(), send_membrane_planes(), 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.

References keep_history_.

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

inline

Return current keep_history flag.

References keep_history_.

Referenced by parse_my_tag().

void protocols::moves::PyMolMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &
	)

virtual

Parses tag for rosetta scripts.

allows for the setting of certain variabel from the rosetta scripts interface, only keep history

Reimplemented from protocols::moves::Mover.

References keep_history(), and keep_history_.

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

Send message for PyMol to print.

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

std::string protocols::moves::PyMolMover::pymol_name ( )

inline

Specify PyMOL model name.

References pymol_name_.

void protocols::moves::PyMolMover::pymol_name ( std::string new_pymol_name )

inline

References pymol_name_.

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.

References PyAssert, 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`
	)

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

Send specified energy to PyMOL.

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

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

Send Membrane Planes to PyMol.

If pose is a membrane pose and view_in_pymol flag is set to true pymol viewer will build CGO planes from points specified

References core::pose::Pose::conformation(), get_PyMol_model_name(), is_it_time(), core::conformation::Conformation::is_membrane(), keep_history_, link_, core::conformation::Conformation::membrane_info(), protocols::moves::Mover::name(), normal, protocols::moves::UDPSocketClient::sendMessage(), utility::to_string(), and utility_exit_with_message.

Referenced by apply().

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.

References chain, 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().

void protocols::moves::PyMolMover::show ( std::ostream & output = std::cout ) const

virtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References keep_history_, last_packet_sent_time_, link_, protocols::moves::Mover::show(), update_energy_, and update_interval_.

Referenced by protocols::moves::operator<<().

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

inline

Flag that specify if PyMOL mover should send current Pose energy on every apply. If name set to empty string (default) then name derived from pdb_info will be used.

References update_energy_.

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

inline

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.

References update_interval_.

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

inline

Return current update interval.

References update_interval_.