Calculates ddG of binding. More...

#include <InterfaceDdGMover.hh>

Inheritance diagram for protocols::features::InterfaceDdGMover:

[legend]

Public Member Functions
	InterfaceDdGMover ()

	~InterfaceDdGMover () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	const_pose_apply (core::pose::Pose const &pose)

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in 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	unbind (core::pose::Pose &pose) const
	"unbinds" a pose based on degrees of freedom previously defined More...

std::set< core::Size >	get_movable_jumps (core::pose::Pose const &pose) const

void	add_chain_id (core::Size chain_id, core::pose::Pose const &pose)
	appends chain_id More...

void	add_chain_id (core::Size chain_id)

void	add_chain_name (std::string const &chain_name, core::pose::Pose const &pose)
	converts chain_name to a chain_id, and then appends More...

void	add_chain_name (std::string const &chain_name)

void	add_jump_id (core::Size jump, core::pose::Pose const &pose)
	gets chain_id from jump id, and then appends More...

void	add_jump_id (core::Size jump)

void	set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
	Sets the scorefunction. More...

void	set_wt_pose (core::pose::Pose const &pose)
	Stores the wildtype pose. More...

void	set_mut_pose (core::pose::Pose const &pose)
	Stores the mutant pose. More...

void	set_wt_pose (core::pose::PoseOP pose)
	Stores the wildtype pose. More...

void	set_mut_pose (core::pose::PoseOP pose)
	Stores the mutant pose. More...

void	set_db_reporter (protocols::features::ReportToDBOP db_reporter)
	Clones db_reporter into all member variable database reporters, and sets batch names accordingly. More...

core::pose::PoseCOP	get_unbound_wt_pose () const

core::pose::PoseCOP	get_bound_wt_pose () const

core::pose::PoseCOP	get_unbound_mut_pose () const

core::pose::PoseCOP	get_bound_mut_pose () const

utility::vector1< std::pair< std::string, core::Real > >	get_all_scores () const

utility::vector1< std::tuple< std::string, core::Size, std::string > >	mutation_list () const
	Determines which residues, if any, are different between bound_wt_pose_ and bound_mut_pose_. 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 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 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
core::Real	compute ()
	Scores the cached poses, caches the scores. More...

Private Attributes
utility::vector1< core::Size >	chain_ids_

utility::vector1< std::string >	chain_names_

utility::vector1< core::Size >	jump_ids_

core::scoring::ScoreFunctionOP	scorefxn_

core::Real	translate_by_
	distance in angstroms to separate moledules More...

core::pose::PoseOP	unbound_wt_pose_
	unbound wildtype pose state; stored for later use More...

core::pose::PoseOP	bound_wt_pose_
	bound wildtype pose state; stored for later use More...

core::pose::PoseOP	unbound_mut_pose_
	unbound mutant pose state; stored for later use More...

core::pose::PoseOP	bound_mut_pose_
	bound mutant pose state; stored for later use More...

core::Real	unbound_wt_score_

core::Real	bound_wt_score_

core::Real	unbound_mut_score_

core::Real	bound_mut_score_

core::Real	ddG_score_

bool	apply_pose_is_mutant_
	Keeps track of whether the pose passed to the apply function will be considered to be the wildtype of mutant structure. More...

protocols::rosetta_scripts::SavePoseMoverOP	wt_save_pose_mover_
	Used in Rosetta scripts context to save a reference pose of the wildtype pose state. More...

protocols::rosetta_scripts::SavePoseMoverOP	mut_save_pose_mover_
	Used in Rosetta scripts context to save a reference pose of the mutant pose state. More...

protocols::features::ReportToDBOP	bound_wt_db_reporter_

protocols::features::ReportToDBOP	unbound_wt_db_reporter_

protocols::features::ReportToDBOP	bound_mut_db_reporter_

protocols::features::ReportToDBOP	unbound_mut_db_reporter_

bool	report_to_db_

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

Calculates ddG of binding.

Constructor & Destructor Documentation

◆ InterfaceDdGMover()

protocols::features::InterfaceDdGMover::InterfaceDdGMover ( )

◆ ~InterfaceDdGMover()

protocols::features::InterfaceDdGMover::~InterfaceDdGMover ( )

overridedefault

Member Function Documentation

◆ add_chain_id() [1/2]

void protocols::features::InterfaceDdGMover::add_chain_id ( core::Size chain_id )

References chain_ids_.

◆ add_chain_id() [2/2]

void protocols::features::InterfaceDdGMover::add_chain_id	(	core::Size	chain_id,
		core::pose::Pose const &	pose
	)

appends chain_id

appends chain_id to chain_ids_

takes pose in as an argument for input checking

References chain_ids_, core::pose::has_chain(), and core::id::to_string().

Referenced by parse_my_tag().

◆ add_chain_name() [1/2]

void protocols::features::InterfaceDdGMover::add_chain_name ( std::string const & chain_name )

References chain_names_.

◆ add_chain_name() [2/2]

void protocols::features::InterfaceDdGMover::add_chain_name	(	std::string const &	chain_name,
		core::pose::Pose const &	pose
	)

converts chain_name to a chain_id, and then appends

converts chain_name to a chain_id and then appends

takes pose in as an argument for input checking

References chain_names_, and core::pose::has_chain().

Referenced by parse_my_tag().

◆ add_jump_id() [1/2]

void protocols::features::InterfaceDdGMover::add_jump_id ( core::Size jump )

References jump_ids_.

◆ add_jump_id() [2/2]

void protocols::features::InterfaceDdGMover::add_jump_id	(	core::Size	jump,
		core::pose::Pose const &	pose
	)

gets chain_id from jump id, and then appends

converts jump to a chain_id and then appends

takes pose in as an argument for input checking

References jump_ids_, core::pose::Pose::num_jump(), and core::id::to_string().

Referenced by parse_my_tag().

◆ apply()

void protocols::features::InterfaceDdGMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References const_pose_apply().

◆ clone()

protocols::moves::MoverOP protocols::features::InterfaceDdGMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ compute()

core::Real protocols::features::InterfaceDdGMover::compute ( )

private

Scores the cached poses, caches the scores.

References bound_mut_pose_, bound_mut_score_, bound_wt_pose_, bound_wt_score_, ddG_score_, mut_save_pose_mover_, mutation_list(), set_mut_pose(), set_wt_pose(), core::id::to_string(), protocols::features::TR(), unbound_mut_pose_, unbound_mut_score_, unbound_wt_pose_, unbound_wt_score_, and wt_save_pose_mover_.

Referenced by const_pose_apply().

◆ const_pose_apply()

void protocols::features::InterfaceDdGMover::const_pose_apply ( core::pose::Pose const & pose )

References apply_pose_is_mutant_, bound_mut_db_reporter_, bound_mut_pose_, bound_wt_db_reporter_, bound_wt_pose_, compute(), report_to_db_, set_mut_pose(), set_wt_pose(), unbound_mut_db_reporter_, unbound_mut_pose_, unbound_wt_db_reporter_, and unbound_wt_pose_.

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::features::InterfaceDdGMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_all_scores()

utility::vector1< std::pair< std::string, core::Real > > protocols::features::InterfaceDdGMover::get_all_scores ( ) const

References bound_mut_score_, bound_wt_score_, ddG_score_, unbound_mut_score_, and unbound_wt_score_.

◆ get_bound_mut_pose()

core::pose::PoseCOP protocols::features::InterfaceDdGMover::get_bound_mut_pose ( ) const

References bound_mut_pose_.

◆ get_bound_wt_pose()

core::pose::PoseCOP protocols::features::InterfaceDdGMover::get_bound_wt_pose ( ) const

References bound_wt_pose_.

◆ get_movable_jumps()

std::set< core::Size > protocols::features::InterfaceDdGMover::get_movable_jumps ( core::pose::Pose const & pose ) const

References chain_ids_, chain_names_, core::pose::Pose::conformation(), core::pose::get_chain_ids_from_chain(), core::pose::get_jump_id_from_chain_id(), jump_ids_, core::conformation::Conformation::num_chains(), and protocols::features::TR().

Referenced by unbind().

◆ get_name()

std::string protocols::features::InterfaceDdGMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References protocols::features::InterfaceDdGMoverCreator::mover_name().

◆ get_unbound_mut_pose()

core::pose::PoseCOP protocols::features::InterfaceDdGMover::get_unbound_mut_pose ( ) const

References unbound_mut_pose_.

◆ get_unbound_wt_pose()

core::pose::PoseCOP protocols::features::InterfaceDdGMover::get_unbound_wt_pose ( ) const

References unbound_wt_pose_.

◆ mover_name()

std::string protocols::features::InterfaceDdGMover::mover_name ( )

static

Referenced by protocols::features::InterfaceDdGMoverCreator::mover_name(), and provide_xml_schema().

◆ mutation_list()

utility::vector1< std::tuple< std::string, core::Size, std::string > > protocols::features::InterfaceDdGMover::mutation_list ( ) const

Determines which residues, if any, are different between bound_wt_pose_ and bound_mut_pose_.

References bound_mut_pose_, bound_wt_pose_, and protocols::features::TR().

Referenced by compute().

◆ parse_my_tag()

void protocols::features::InterfaceDdGMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References add_chain_id(), add_chain_name(), add_jump_id(), apply_pose_is_mutant_, chain_ids_, chain_names_, jump_ids_, mut_save_pose_mover_, protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), set_db_reporter(), set_scorefxn(), protocols::features::TR(), and wt_save_pose_mover_.

◆ provide_xml_schema()

void protocols::features::InterfaceDdGMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::features::InterfaceDdGMoverCreator::provide_xml_schema().

◆ set_db_reporter()

void protocols::features::InterfaceDdGMover::set_db_reporter ( protocols::features::ReportToDBOP db_reporter )

Clones db_reporter into all member variable database reporters, and sets batch names accordingly.

References bound_mut_db_reporter_, bound_wt_db_reporter_, report_to_db_, unbound_mut_db_reporter_, and unbound_wt_db_reporter_.

Referenced by parse_my_tag().

◆ set_mut_pose() [1/2]

void protocols::features::InterfaceDdGMover::set_mut_pose ( core::pose::Pose const & pose )

Stores the mutant pose.

References bound_mut_pose_, core::pose::Pose::clone(), unbind(), and unbound_mut_pose_.

Referenced by compute(), and const_pose_apply().

◆ set_mut_pose() [2/2]

void protocols::features::InterfaceDdGMover::set_mut_pose ( core::pose::PoseOP pose )

Stores the mutant pose.

References bound_mut_pose_, unbind(), and unbound_mut_pose_.

◆ set_scorefxn()

void protocols::features::InterfaceDdGMover::set_scorefxn ( core::scoring::ScoreFunctionCOP sfxn_in )

Sets the scorefunction.

References scorefxn_.

Referenced by parse_my_tag().

◆ set_wt_pose() [1/2]

void protocols::features::InterfaceDdGMover::set_wt_pose ( core::pose::Pose const & pose )

Stores the wildtype pose.

References bound_wt_pose_, core::pose::Pose::clone(), unbind(), and unbound_wt_pose_.

Referenced by compute(), and const_pose_apply().

◆ set_wt_pose() [2/2]

void protocols::features::InterfaceDdGMover::set_wt_pose ( core::pose::PoseOP pose )

Stores the wildtype pose.

References bound_wt_pose_, unbind(), and unbound_wt_pose_.

◆ unbind()

void protocols::features::InterfaceDdGMover::unbind ( core::pose::Pose & pose ) const

"unbinds" a pose based on degrees of freedom previously defined

References chain_ids_, chain_names_, core::pose::Pose::conformation(), get_movable_jumps(), core::pose::symmetry::is_symmetric(), jump_ids_, protocols::toolbox::rigid_body::translate(), and translate_by_.

Referenced by set_mut_pose(), and set_wt_pose().

Member Data Documentation

◆ apply_pose_is_mutant_

bool protocols::features::InterfaceDdGMover::apply_pose_is_mutant_

private

Keeps track of whether the pose passed to the apply function will be considered to be the wildtype of mutant structure.

Referenced by const_pose_apply(), and parse_my_tag().

◆ bound_mut_db_reporter_

protocols::features::ReportToDBOP protocols::features::InterfaceDdGMover::bound_mut_db_reporter_

private

Referenced by const_pose_apply(), and set_db_reporter().

◆ bound_mut_pose_

core::pose::PoseOP protocols::features::InterfaceDdGMover::bound_mut_pose_

private

bound mutant pose state; stored for later use

Referenced by compute(), const_pose_apply(), get_bound_mut_pose(), mutation_list(), and set_mut_pose().

◆ bound_mut_score_

core::Real protocols::features::InterfaceDdGMover::bound_mut_score_

private

Referenced by compute(), and get_all_scores().

◆ bound_wt_db_reporter_

protocols::features::ReportToDBOP protocols::features::InterfaceDdGMover::bound_wt_db_reporter_

private

Referenced by const_pose_apply(), and set_db_reporter().

◆ bound_wt_pose_

core::pose::PoseOP protocols::features::InterfaceDdGMover::bound_wt_pose_

private

bound wildtype pose state; stored for later use

Referenced by compute(), const_pose_apply(), get_bound_wt_pose(), mutation_list(), and set_wt_pose().

◆ bound_wt_score_

core::Real protocols::features::InterfaceDdGMover::bound_wt_score_

private

Referenced by compute(), and get_all_scores().

◆ chain_ids_

utility::vector1<core::Size> protocols::features::InterfaceDdGMover::chain_ids_

private

Referenced by add_chain_id(), get_movable_jumps(), parse_my_tag(), and unbind().

◆ chain_names_

utility::vector1<std::string> protocols::features::InterfaceDdGMover::chain_names_

private

Referenced by add_chain_name(), get_movable_jumps(), parse_my_tag(), and unbind().

◆ ddG_score_

core::Real protocols::features::InterfaceDdGMover::ddG_score_

private

Referenced by compute(), and get_all_scores().

◆ jump_ids_

utility::vector1<core::Size> protocols::features::InterfaceDdGMover::jump_ids_

private

Referenced by add_jump_id(), get_movable_jumps(), parse_my_tag(), and unbind().

◆ mut_save_pose_mover_

protocols::rosetta_scripts::SavePoseMoverOP protocols::features::InterfaceDdGMover::mut_save_pose_mover_

private

Used in Rosetta scripts context to save a reference pose of the mutant pose state.

Referenced by compute(), and parse_my_tag().

◆ report_to_db_

bool protocols::features::InterfaceDdGMover::report_to_db_

private

Referenced by const_pose_apply(), and set_db_reporter().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::features::InterfaceDdGMover::scorefxn_

private

Referenced by set_scorefxn().

◆ translate_by_

core::Real protocols::features::InterfaceDdGMover::translate_by_

private

distance in angstroms to separate moledules

Referenced by unbind().

◆ unbound_mut_db_reporter_

protocols::features::ReportToDBOP protocols::features::InterfaceDdGMover::unbound_mut_db_reporter_

private

Referenced by const_pose_apply(), and set_db_reporter().

◆ unbound_mut_pose_

core::pose::PoseOP protocols::features::InterfaceDdGMover::unbound_mut_pose_

private

unbound mutant pose state; stored for later use

Referenced by compute(), const_pose_apply(), get_unbound_mut_pose(), and set_mut_pose().

◆ unbound_mut_score_

core::Real protocols::features::InterfaceDdGMover::unbound_mut_score_

private

Referenced by compute(), and get_all_scores().

◆ unbound_wt_db_reporter_

protocols::features::ReportToDBOP protocols::features::InterfaceDdGMover::unbound_wt_db_reporter_

private

Referenced by const_pose_apply(), and set_db_reporter().

◆ unbound_wt_pose_

core::pose::PoseOP protocols::features::InterfaceDdGMover::unbound_wt_pose_

private

unbound wildtype pose state; stored for later use

Referenced by compute(), const_pose_apply(), get_unbound_wt_pose(), and set_wt_pose().

◆ unbound_wt_score_

core::Real protocols::features::InterfaceDdGMover::unbound_wt_score_

private

Referenced by compute(), and get_all_scores().

◆ wt_save_pose_mover_

protocols::rosetta_scripts::SavePoseMoverOP protocols::features::InterfaceDdGMover::wt_save_pose_mover_

private

Used in Rosetta scripts context to save a reference pose of the wildtype pose state.

Referenced by compute(), and parse_my_tag().

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

src/protocols/features/InterfaceDdGMover.hh
src/protocols/features/InterfaceDdGMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ InterfaceDdGMover()

◆ ~InterfaceDdGMover()

Member Function Documentation

◆ add_chain_id() [1/2]

◆ add_chain_id() [2/2]

◆ add_chain_name() [1/2]

◆ add_chain_name() [2/2]

◆ add_jump_id() [1/2]

◆ add_jump_id() [2/2]

◆ apply()

◆ clone()

◆ compute()

◆ const_pose_apply()

◆ fresh_instance()

◆ get_all_scores()

◆ get_bound_mut_pose()

◆ get_bound_wt_pose()

◆ get_movable_jumps()

◆ get_name()

◆ get_unbound_mut_pose()

◆ get_unbound_wt_pose()

◆ mover_name()

◆ mutation_list()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_db_reporter()

◆ set_mut_pose() [1/2]

◆ set_mut_pose() [2/2]

◆ set_scorefxn()

◆ set_wt_pose() [1/2]

◆ set_wt_pose() [2/2]

◆ unbind()

Member Data Documentation

◆ apply_pose_is_mutant_

◆ bound_mut_db_reporter_

◆ bound_mut_pose_

◆ bound_mut_score_

◆ bound_wt_db_reporter_

◆ bound_wt_pose_

◆ bound_wt_score_

◆ chain_ids_

◆ chain_names_

◆ ddG_score_

◆ jump_ids_

◆ mut_save_pose_mover_

◆ report_to_db_

◆ scorefxn_

◆ translate_by_

◆ unbound_mut_db_reporter_

◆ unbound_mut_pose_

◆ unbound_mut_score_

◆ unbound_wt_db_reporter_

◆ unbound_wt_pose_

◆ unbound_wt_score_

◆ wt_save_pose_mover_