Special Mover designed to send Pose information into PyMOL instance running. More...

#include <PyMOLMover.hh>

Inheritance diagram for protocols::moves::PyMOLMover:

[legend]

Public Member Functions
	PyMOLMover (std::string const &address=default_address(), unsigned int port=default_port(), unsigned int max_packet_size=0)
	ctor More...

void	apply (Pose &) override
	Main Method. More...

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 already implemented. More...

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

void	send_any (std::string ptype, core::pose::Pose const &pose, utility::vector1< std::string > data, core::Size size=6)
	Xiyao's Code. More...

void	label_energy (Pose const &input_pose, std::string energy_type)
	Xiyao's Code. More...

void	send_hbonds (Pose const &pose)

void	send_ss (Pose &pose, std::string ss)

void	send_polars (Pose const &pose)

void	send_movemap (Pose const &pose, core::kinematics::MoveMap const &movemap)

void	send_foldtree (Pose const &pose, core::kinematics::FoldTree const &foldtree)

virtual void	send_colors (Pose const &, std::map< int, int > const &colors, X11Colors default_color=protocols::moves::XC_blue)
	End Xiyao's Code. 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 override
	Outputs details about the Mover, including current settings. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Parses tag for rosetta scripts. More...

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

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

void	set_PyMOL_model_name (std::string name)
	Set the pymol model name. More...

void	set_link (UDPSocketClient const &link)

UDPSocketClient const &	get_link () const

std::string	get_PyMOL_model_name (Pose const &pose) const

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

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 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 Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Member Functions
utility::vector1< core::Real >	get_energies (Pose const &pose, core::scoring::ScoreType energy_type)
	return vector of energy_type energy for each residue More...

std::string	get_pose_name (Pose const &pose)
	return name, stripped of path and ".pdb" More...

bool	is_it_time ()
	End Xiyao's code. More...

Static Private Member Functions
static std::string	default_address ()

static unsigned int	default_port ()

static unsigned int	default_max_packet_size (std::string const &address)

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 std::list< std::string >	Strings

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

Special Mover designed to send Pose information into PyMOL instance running.

Constructor & Destructor Documentation

◆ PyMOLMover()

protocols::moves::PyMOLMover::PyMOLMover	(	std::string const &	address = `default_address()`,
		unsigned int	port = `default_port()`,
		unsigned int	max_packet_size = `0`
	)

ctor

Member Function Documentation

◆ apply() [1/2]

void protocols::moves::PyMOLMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

Referenced by protocols::carbohydrates::GlycanSampler::apply(), protocols::moves::PyMOLObserver::conformationEvent(), protocols::moves::PyMOLObserver::energyEvent(), and protocols::moves::PyMOLObserver::generalEvent().

◆ apply() [2/2]

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_, protocols::moves::Mover::name(), send_energy(), send_membrane_planes(), protocols::moves::UDPSocketClient::sendMessage(), protocols::moves::TR(), update_energy_, and update_membrane_.

◆ clone()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ default_address()

std::string protocols::moves::PyMOLMover::default_address ( )

staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

◆ default_max_packet_size()

unsigned int protocols::moves::PyMOLMover::default_max_packet_size ( std::string const & address )

staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

◆ default_port()

unsigned int protocols::moves::PyMOLMover::default_port ( )

staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

◆ energy_type() [1/2]

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

inline

References energy_type_, and protocols::hybridization::t.

◆ energy_type() [2/2]

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

inline

References energy_type_.

Referenced by protocols::moves::get_energies().

◆ fresh_instance()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_energies()

utility::vector1< core::Real > protocols::moves::PyMOLMover::get_energies	(	Pose const &	pose,
		core::scoring::ScoreType	energy_type
	)

private

return vector of energy_type energy for each residue

Xiyao's code

◆ get_link()

UDPSocketClient const& protocols::moves::PyMOLMover::get_link ( ) const

inline

References link_.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_pose_name()

std::string protocols::moves::PyMOLMover::get_pose_name ( Pose const & pose )

private

return name, stripped of path and ".pdb"

◆ get_PyMOL_model_name()

std::string protocols::moves::PyMOLMover::get_PyMOL_model_name ( Pose const & pose ) const

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

Referenced by protocols::carbohydrates::GlycanSampler::apply(), apply(), send_any(), send_energy(), send_hbonds(), send_membrane_planes(), and send_RAW_Energies().

◆ is_it_time()

bool protocols::moves::PyMOLMover::is_it_time ( )

private

End Xiyao's code.

References last_packet_sent_time_, protocols::hybridization::t, and update_interval_.

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

◆ keep_history() [1/2]

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_.

Referenced by protocols::carbohydrates::GlycanSampler::apply().

◆ keep_history() [2/2]

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

inline

Return current keep_history flag.

References keep_history_.

Referenced by parse_my_tag().

◆ label_energy()

void protocols::moves::PyMOLMover::label_energy	(	Pose const &	input_pose,
		std::string	energy_type = `"total_score"`
	)

Xiyao's Code.

References core::pose::Pose::energies(), protocols::buns::energy, and send_energy().

◆ mover_name()

std::string protocols::moves::PyMOLMover::mover_name ( )

static

Referenced by get_name(), protocols::moves::PyMOLMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::moves::PyMOLMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

Parses tag for rosetta scripts.

PyMOLMoverCreator interface, name of the mover.

PyMOLMoverCreator interface, returns a unique key name to be used in xml file

PyMOLMoverCreator interface, return a new instance

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

Reimplemented from protocols::moves::Mover.

References default_address(), default_max_packet_size(), default_port(), keep_history(), keep_history_, and link_.

◆ print()

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().

◆ provide_xml_schema()

void protocols::moves::PyMOLMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References default_address(), default_max_packet_size(), default_port(), protocols::moves::lowest_max_packet_size, mover_name(), core::id::to_string(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::moves::PyMOLMoverCreator::provide_xml_schema().

◆ pymol_name() [1/2]

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

inline

Specify PyMOL model name.

References pymol_name_.

◆ pymol_name() [2/2]

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

inline

References pymol_name_.

◆ send_any()

void protocols::moves::PyMOLMover::send_any	(	std::string	ptype,
		core::pose::Pose const &	pose,
		utility::vector1< std::string >	data,
		core::Size	size = `6`
	)

Xiyao's Code.

References get_PyMOL_model_name(), protocols::moves::Mover::info(), keep_history_, link_, protocols::moves::Mover::name(), core::pose::Pose::pdb_info(), protocols::moves::UDPSocketClient::sendMessage(), core::pose::Pose::size(), and core::id::to_string().

Referenced by send_foldtree(), send_movemap(), send_polars(), and send_ss().

◆ send_colors()

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

virtual

End Xiyao's Code.

Tell PyMOL to color protein with supplied custom colors

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

◆ send_energy() [1/2]

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

◆ send_energy() [2/2]

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().

◆ send_foldtree()

void protocols::moves::PyMOLMover::send_foldtree	(	Pose const &	pose,
		core::kinematics::FoldTree const &	foldtree
	)

References core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_jump_point(), core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::num_jump(), send_any(), core::pose::Pose::size(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and core::id::to_string().

◆ send_hbonds()

void protocols::moves::PyMOLMover::send_hbonds ( Pose const & pose )

◆ send_membrane_planes()

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

Send Membrane Planes to PyMOL.

If pose is a membrane pose pymol viewer will build CGO planes from points specified

References core::energy_methods::RG_Energy_Fast::calculate_rg_score(), core::conformation::membrane::center, 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(), core::conformation::membrane::normal, core::scoring::rg, protocols::moves::UDPSocketClient::sendMessage(), core::pose::Pose::size(), core::conformation::membrane::thickness, and core::id::to_string().

Referenced by apply().

◆ send_movemap()

void protocols::moves::PyMOLMover::send_movemap	(	Pose const &	pose,
		core::kinematics::MoveMap const &	movemap
	)

References core::kinematics::MoveMap::get_bb(), core::kinematics::MoveMap::get_chi(), send_any(), core::pose::Pose::size(), and core::id::to_string().

◆ send_polars()

void protocols::moves::PyMOLMover::send_polars ( Pose const & pose )

References core::chemical::ResidueType::is_polar(), core::pose::Pose::residue_type(), send_any(), core::pose::Pose::size(), and core::id::to_string().

◆ send_RAW_Energies()

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 already implemented.

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().

◆ send_ss()

void protocols::moves::PyMOLMover::send_ss	(	Pose &	pose,
		std::string	ss = `""`
	)

References protocols::simple_filters::dssp(), and send_any().

◆ set_link()

void protocols::moves::PyMOLMover::set_link ( UDPSocketClient const & link )

inline

References link_.

◆ set_PyMOL_model_name()

void protocols::moves::PyMOLMover::set_PyMOL_model_name ( std::string name )

Set the pymol model name.

References protocols::moves::Mover::name(), and pymol_name_.

Referenced by protocols::carbohydrates::GlycanSampler::apply().

◆ show()

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

overridevirtual

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<<().

◆ update_energy() [1/2]

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_.

◆ update_energy() [2/2]

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

inline

References update_energy_.

◆ update_interval() [1/2]

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

inline

Return current update interval.

References update_interval_.

◆ update_interval() [2/2]

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 protocols::hybridization::t, and update_interval_.

Member Data Documentation

◆ energy_type_

core::scoring::ScoreType protocols::moves::PyMOLMover::energy_type_

private

Referenced by apply(), and energy_type().

◆ keep_history_

bool protocols::moves::PyMOLMover::keep_history_

private

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

Referenced by apply(), keep_history(), parse_my_tag(), print(), send_any(), send_energy(), send_hbonds(), send_membrane_planes(), send_RAW_Energies(), and show().

◆ last_packet_sent_time_

core::Real protocols::moves::PyMOLMover::last_packet_sent_time_

private

Time stamp from where last packet was sent.

Referenced by is_it_time(), and show().

◆ link_

UDPSocketClient protocols::moves::PyMOLMover::link_

private

Actual link object.

Referenced by apply(), get_link(), parse_my_tag(), print(), send_any(), send_energy(), send_hbonds(), send_membrane_planes(), send_RAW_Energies(), set_link(), and show().

◆ pymol_name_

std::string protocols::moves::PyMOLMover::pymol_name_

private

Name of model in pymol.

Referenced by get_PyMOL_model_name(), pymol_name(), and set_PyMOL_model_name().

◆ update_energy_

bool protocols::moves::PyMOLMover::update_energy_

private

Referenced by apply(), show(), and update_energy().

◆ update_interval_

core::Real protocols::moves::PyMOLMover::update_interval_

private

Update interval in seconds.

Referenced by is_it_time(), show(), and update_interval().

◆ update_membrane_

bool protocols::moves::PyMOLMover::update_membrane_

private

If pose is a membrane pose, send planes.

Referenced by apply().

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

src/protocols/moves/PyMOLMover.hh
src/protocols/moves/PyMOLMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PyMOLMover()

Member Function Documentation

◆ apply() [1/2]

◆ apply() [2/2]

◆ clone()

◆ default_address()

◆ default_max_packet_size()

◆ default_port()

◆ energy_type() [1/2]

◆ energy_type() [2/2]

◆ fresh_instance()

◆ get_energies()

◆ get_link()

◆ get_name()

◆ get_pose_name()

◆ get_PyMOL_model_name()

◆ is_it_time()

◆ keep_history() [1/2]

◆ keep_history() [2/2]

◆ label_energy()

◆ mover_name()

◆ parse_my_tag()

◆ print()

◆ provide_xml_schema()

◆ pymol_name() [1/2]

◆ pymol_name() [2/2]

◆ send_any()

◆ send_colors()

◆ send_energy() [1/2]

◆ send_energy() [2/2]

◆ send_foldtree()

◆ send_hbonds()

◆ send_membrane_planes()

◆ send_movemap()

◆ send_polars()

◆ send_RAW_Energies()

◆ send_ss()

◆ set_link()

◆ set_PyMOL_model_name()

◆ show()

◆ update_energy() [1/2]

◆ update_energy() [2/2]

◆ update_interval() [1/2]

◆ update_interval() [2/2]

Member Data Documentation

◆ energy_type_

◆ keep_history_

◆ last_packet_sent_time_

◆ link_

◆ pymol_name_

◆ update_energy_

◆ update_interval_

◆ update_membrane_