Add SiteConstraints from the Epitope to the Paratope and from the Paratope to the Epitope. Will only add the constraint if not already present. More...

#include <ParatopeEpitopeSiteConstraintMover.hh>

Inheritance diagram for protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover:

[legend]

Public Member Functions
	ParatopeEpitopeSiteConstraintMover ()

	ParatopeEpitopeSiteConstraintMover (AntibodyInfoCOP ab_info)

	ParatopeEpitopeSiteConstraintMover (AntibodyInfoCOP ab_info, utility::vector1< CDRNameEnum > paratope_cdrs)

	ParatopeEpitopeSiteConstraintMover (AntibodyInfoCOP ab_info, utility::vector1< CDRNameEnum > paratope_cdrs, utility::vector1< bool > const &epitope_residues)

	~ParatopeEpitopeSiteConstraintMover () override

	ParatopeEpitopeSiteConstraintMover (ParatopeEpitopeSiteConstraintMover const &src)

protocols::moves::MoverOP	clone () const override
	Copy this object and return a pointer to the copy. More...

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

void	remove (core::pose::Pose &pose)

void	constrain_to_paratope_cdrs (utility::vector1< CDRNameEnum > const &paratope_cdrs)

void	constrain_to_paratope_cdrs (utility::vector1< bool > const &paratope_cdrs)

void	constrain_to_paratope_residues (utility::vector1< bool > const &paratope_residues)

void	constrain_to_epitope_residues (utility::vector1< design::PDBNumbering > const &epitope_residues, core::pose::Pose const &pose)
	@Brief Manually set the epitope residues via PDB Numbering More...

void	constrain_to_epitope_residues (utility::vector1< bool > const &epitope_residues)
	@Brief Manually set the epitope residues via pose Numbering More...

void	set_constraint_func (core::scoring::func::FuncOP constraint_func)

void	set_interface_distance (core::Real const distance)
	The interface distance for antigen epitope auto-detection and the distance at which the default at which the default flat-harmonic constraint will give a penalty. 10A default. More...

void	set_defaults ()

core::select::residue_selector::ResidueSelectorOP	get_epitope_residues () const

utility::vector1< bool >	get_epitope_residues (core::pose::Pose const &pose) const

utility::vector1< bool >	get_paratope_residues (core::pose::Pose const &pose) const

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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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...

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::scoring::constraints::SiteConstraintOP	setup_constraints (core::pose::Pose const &pose, core::Size residue, utility::vector1< bool > const &residues) const

utility::vector1< bool >	paratope_residues_from_cdrs (core::pose::Pose const &pose, utility::vector1< bool > const &paratope_cdrs) const

Private Attributes
AntibodyInfoCOP	ab_info_

core::select::residue_selector::ResidueSelectorOP	paratope_residues_

core::select::residue_selector::ResidueSelectorOP	epitope_residues_

utility::vector1< bool >	paratope_cdrs_

core::scoring::func::FuncOP	current_func_

core::Real	interface_distance_

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

Add SiteConstraints from the Epitope to the Paratope and from the Paratope to the Epitope. Will only add the constraint if not already present.

If no paratope interface residues are given, detects the epitope at 10 A from antibody chain(s). Optionally constrain to paratope CDRs or a specific set of paratope residues. Uses a Linear Harmonic at 0, 1, 10 by default. Which means epitope will have penalty at greater than 10 A. Linear Harmonic distance tolerance (last number) is set at the interface distance.

Constructor & Destructor Documentation

◆ ParatopeEpitopeSiteConstraintMover() [1/5]

protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::ParatopeEpitopeSiteConstraintMover ( )

References set_defaults().

◆ ParatopeEpitopeSiteConstraintMover() [2/5]

protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::ParatopeEpitopeSiteConstraintMover ( AntibodyInfoCOP ab_info )

References ab_info_, and set_defaults().

◆ ParatopeEpitopeSiteConstraintMover() [3/5]

protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::ParatopeEpitopeSiteConstraintMover	(	AntibodyInfoCOP	ab_info,
		utility::vector1< CDRNameEnum >	paratope_cdrs
	)

◆ ParatopeEpitopeSiteConstraintMover() [4/5]

protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::ParatopeEpitopeSiteConstraintMover	(	AntibodyInfoCOP	ab_info,
		utility::vector1< CDRNameEnum >	paratope_cdrs,
		utility::vector1< bool > const &	epitope_residues
	)

◆ ~ParatopeEpitopeSiteConstraintMover()

protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::~ParatopeEpitopeSiteConstraintMover ( )

overridedefault

◆ ParatopeEpitopeSiteConstraintMover() [5/5]

protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::ParatopeEpitopeSiteConstraintMover ( ParatopeEpitopeSiteConstraintMover const & src )

References ab_info_, and current_func_.

Member Function Documentation

◆ apply()

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References ab_info_, core::pose::Pose::add_constraint(), core::pose::Pose::constraint_set(), current_func_, protocols::moves::FAIL_BAD_INPUT, get_epitope_residues(), get_paratope_residues(), interface_distance_, protocols::antibody::l1, protocols::antibody::l2, protocols::antibody::l3, paratope_cdrs_, protocols::moves::Mover::set_last_move_status(), setup_constraints(), core::pose::Pose::size(), and protocols::antibody::TR().

◆ clone()

protocols::moves::MoverOP protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::clone ( ) const

overridevirtual

Copy this object and return a pointer to the copy.

Reimplemented from protocols::moves::Mover.

◆ constrain_to_epitope_residues() [1/2]

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::constrain_to_epitope_residues ( utility::vector1< bool > const & epitope_residues )

@Brief Manually set the epitope residues via pose Numbering

◆ constrain_to_epitope_residues() [2/2]

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::constrain_to_epitope_residues	(	utility::vector1< design::PDBNumbering > const &	epitope_residues,
		core::pose::Pose const &	pose
	)

@Brief Manually set the epitope residues via PDB Numbering

◆ constrain_to_paratope_cdrs() [1/2]

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::constrain_to_paratope_cdrs ( utility::vector1< bool > const & paratope_cdrs )

◆ constrain_to_paratope_cdrs() [2/2]

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::constrain_to_paratope_cdrs ( utility::vector1< CDRNameEnum > const & paratope_cdrs )

◆ constrain_to_paratope_residues()

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::constrain_to_paratope_residues ( utility::vector1< bool > const & paratope_residues )

References paratope_residues_.

◆ get_epitope_residues() [1/2]

core::select::residue_selector::ResidueSelectorOP protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::get_epitope_residues ( ) const

inline

References epitope_residues_.

Referenced by apply(), and remove().

◆ get_epitope_residues() [2/2]

utility::vector1< bool > protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::get_epitope_residues ( core::pose::Pose const & pose ) const

References ab_info_, epitope_residues_, interface_distance_, and protocols::antibody::select_epitope_residues().

◆ get_name()

std::string protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_paratope_residues()

utility::vector1< bool > protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::get_paratope_residues ( core::pose::Pose const & pose ) const

References paratope_cdrs_, paratope_residues_, and paratope_residues_from_cdrs().

Referenced by apply(), and remove().

◆ mover_name()

std::string protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::mover_name ( )

static

Referenced by get_name(), protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator::keyname(), and provide_xml_schema().

◆ paratope_residues_from_cdrs()

vector1< bool > protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::paratope_residues_from_cdrs	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	paratope_cdrs
	)		const

private

References ab_info_, protocols::antibody::cdr_end, protocols::antibody::cdr_start, and core::pose::Pose::size().

Referenced by get_paratope_residues().

◆ parse_my_tag()

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References epitope_residues_, protocols::antibody::get_cdr_bool_from_tag(), interface_distance_, paratope_cdrs_, paratope_residues_, and protocols::antibody::TR().

◆ provide_citation_info()

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References epitope_residues_, and paratope_residues_.

◆ provide_xml_schema()

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::antibody::attributes_for_get_cdr_bool_from_tag(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator::provide_xml_schema().

◆ remove()

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::remove ( core::pose::Pose & pose )

References get_epitope_residues(), get_paratope_residues(), core::pose::Pose::remove_constraints(), setup_constraints(), and core::pose::Pose::size().

◆ set_constraint_func()

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::set_constraint_func ( core::scoring::func::FuncOP constraint_func )

References current_func_.

◆ set_defaults()

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::set_defaults ( )

References current_func_, epitope_residues_, interface_distance_, paratope_cdrs_, and paratope_residues_.

Referenced by ParatopeEpitopeSiteConstraintMover().

◆ set_interface_distance()

void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::set_interface_distance ( core::Real const distance )

The interface distance for antigen epitope auto-detection and the distance at which the default at which the default flat-harmonic constraint will give a penalty. 10A default.

References core::kinematics::distance(), and interface_distance_.

◆ setup_constraints()

core::scoring::constraints::SiteConstraintOP protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::setup_constraints	(	core::pose::Pose const &	pose,
		core::Size	residue,
		utility::vector1< bool > const &	residues
	)		const

private

References current_func_.

Referenced by apply(), and remove().

Member Data Documentation

◆ ab_info_

AntibodyInfoCOP protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::ab_info_

private

Referenced by apply(), get_epitope_residues(), paratope_residues_from_cdrs(), and ParatopeEpitopeSiteConstraintMover().

◆ current_func_

core::scoring::func::FuncOP protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::current_func_

private

Referenced by apply(), ParatopeEpitopeSiteConstraintMover(), set_constraint_func(), set_defaults(), and setup_constraints().

◆ epitope_residues_

core::select::residue_selector::ResidueSelectorOP protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::epitope_residues_

private

Referenced by get_epitope_residues(), parse_my_tag(), provide_citation_info(), and set_defaults().

◆ interface_distance_

core::Real protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::interface_distance_

private

Referenced by apply(), get_epitope_residues(), parse_my_tag(), set_defaults(), and set_interface_distance().

◆ paratope_cdrs_

utility::vector1<bool> protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::paratope_cdrs_

private

Referenced by apply(), get_paratope_residues(), parse_my_tag(), and set_defaults().

◆ paratope_residues_

core::select::residue_selector::ResidueSelectorOP protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::paratope_residues_

private

Referenced by constrain_to_paratope_residues(), get_paratope_residues(), parse_my_tag(), provide_citation_info(), and set_defaults().

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

src/protocols/antibody/constraints/ParatopeEpitopeSiteConstraintMover.hh
src/protocols/antibody/constraints/ParatopeEpitopeSiteConstraintMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ParatopeEpitopeSiteConstraintMover() [1/5]

◆ ParatopeEpitopeSiteConstraintMover() [2/5]

◆ ParatopeEpitopeSiteConstraintMover() [3/5]

◆ ParatopeEpitopeSiteConstraintMover() [4/5]

◆ ~ParatopeEpitopeSiteConstraintMover()

◆ ParatopeEpitopeSiteConstraintMover() [5/5]

Member Function Documentation

◆ apply()

◆ clone()

◆ constrain_to_epitope_residues() [1/2]

◆ constrain_to_epitope_residues() [2/2]

◆ constrain_to_paratope_cdrs() [1/2]

◆ constrain_to_paratope_cdrs() [2/2]

◆ constrain_to_paratope_residues()

◆ get_epitope_residues() [1/2]

◆ get_epitope_residues() [2/2]

◆ get_name()

◆ get_paratope_residues()

◆ mover_name()

◆ paratope_residues_from_cdrs()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ remove()

◆ set_constraint_func()

◆ set_defaults()

◆ set_interface_distance()

◆ setup_constraints()

Member Data Documentation

◆ ab_info_

◆ current_func_

◆ epitope_residues_

◆ interface_distance_

◆ paratope_cdrs_

◆ paratope_residues_