Adds and removes ambiguous site constraints for the Antibody Paratope to antigen, defined for simplicity as the CDRs, however a set of paratope residues can be given to the class to use instead. More...

#include <ParatopeSiteConstraintMover.hh>

Inheritance diagram for protocols::antibody::constraints::ParatopeSiteConstraintMover:

[legend]

Public Member Functions
	ParatopeSiteConstraintMover ()

	ParatopeSiteConstraintMover (AntibodyInfoCOP ab_info)

	~ParatopeSiteConstraintMover () override

	ParatopeSiteConstraintMover (ParatopeSiteConstraintMover 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
	Add AmbiguousSiteConstraints to specified paratope residues, or each CDR set. Default is all of them. If there are already exits AmbiguousSiteConstraints from the antigen to the residue, add them. If they are missing, such as after a graft, add them. More...

void	remove (core::pose::Pose &pose, bool reset_paratope_residues=false)
	Remove constraints from each paratope residue and antigen chain set. If reset_paratope_residues is true, then it will update the set of paratope residues it has. This is used after pose length changes such as CDR insertion or deletion. More...

void	constrain_to_paratope_cdrs (utility::vector1< CDRNameEnum > const &paratope_cdrs)
	Optionally use only these CDRs as the paratope. Useful for constraining to Light or Heavy chain CDRs. More...

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

void	constrain_to_paratope_residues (utility::vector1< bool > const &paratope_residues)
	Optionally constrain to a set of pre-determined paratope residues. More...

void	constrain_to_antigen_chains (utility::vector1< std::string > const &antigen_chains)
	Optionally constrain to a set of antigen chains instead of all of them. More...

void	set_constraint_func (core::scoring::func::FuncOP constraint_func)
	Optionally set the Func that will be used for the constraint. Default is the Flat_Harmonic at 0, 1, 5. More...

void	set_interface_distance (core::Real interface_distance)
	Set the interface distance that will be only be used as the tolerance for the linear harmonic constraint if no constraint func is set. More...

void	set_defaults ()

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

core::scoring::constraints::SiteConstraintOP	setup_constraints (core::pose::Pose const &pose, core::Size resnum, std::string chain)

Private Attributes
AntibodyInfoCOP	ab_info_

utility::vector1< bool >	cdrs_to_apply_

core::select::residue_selector::ResidueSelectorOP	paratope_residues_

utility::vector1< std::string >	antigen_chains_

core::Real	interface_distance_

core::scoring::func::FuncOP	current_func_

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

Adds and removes ambiguous site constraints for the Antibody Paratope to antigen, defined for simplicity as the CDRs, however a set of paratope residues can be given to the class to use instead.

Constructor & Destructor Documentation

◆ ParatopeSiteConstraintMover() [1/3]

protocols::antibody::constraints::ParatopeSiteConstraintMover::ParatopeSiteConstraintMover ( )

References set_defaults().

◆ ParatopeSiteConstraintMover() [2/3]

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

References ab_info_, and set_defaults().

◆ ~ParatopeSiteConstraintMover()

protocols::antibody::constraints::ParatopeSiteConstraintMover::~ParatopeSiteConstraintMover ( )

overridedefault

◆ ParatopeSiteConstraintMover() [3/3]

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

References ab_info_, and current_func_.

Member Function Documentation

◆ apply()

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

overridevirtual

Add AmbiguousSiteConstraints to specified paratope residues, or each CDR set. Default is all of them. If there are already exits AmbiguousSiteConstraints from the antigen to the residue, add them. If they are missing, such as after a graft, add them.

Implements protocols::moves::Mover.

References ab_info_, core::pose::Pose::add_constraint(), antigen_chains_, cdrs_to_apply_, core::pose::Pose::constraint_set(), current_func_, protocols::moves::FAIL_BAD_INPUT, interface_distance_, protocols::antibody::l1, protocols::antibody::l2, protocols::antibody::l3, paratope_residues_, paratope_residues_from_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::ParatopeSiteConstraintMover::clone ( ) const

overridevirtual

Copy this object and return a pointer to the copy.

Reimplemented from protocols::moves::Mover.

◆ constrain_to_antigen_chains()

void protocols::antibody::constraints::ParatopeSiteConstraintMover::constrain_to_antigen_chains ( utility::vector1< std::string > const & antigen_chains )

Optionally constrain to a set of antigen chains instead of all of them.

References antigen_chains_.

◆ constrain_to_paratope_cdrs() [1/2]

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

◆ constrain_to_paratope_cdrs() [2/2]

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

Optionally use only these CDRs as the paratope. Useful for constraining to Light or Heavy chain CDRs.

◆ constrain_to_paratope_residues()

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

Optionally constrain to a set of pre-determined paratope residues.

References paratope_residues_.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

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

static

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

◆ paratope_residues_from_cdrs()

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

private

References ab_info_, protocols::antibody::CDRNameEnum_total, cdrs_to_apply_, and core::pose::Pose::size().

Referenced by apply(), and remove().

◆ parse_my_tag()

void protocols::antibody::constraints::ParatopeSiteConstraintMover::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 antigen_chains_, cdrs_to_apply_, protocols::antibody::get_cdr_bool_from_tag(), interface_distance_, paratope_residues_, and protocols::antibody::TR().

◆ provide_citation_info()

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

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References paratope_residues_.

◆ provide_xml_schema()

void protocols::antibody::constraints::ParatopeSiteConstraintMover::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::ParatopeSiteConstraintMoverCreator::provide_xml_schema().

◆ remove()

void protocols::antibody::constraints::ParatopeSiteConstraintMover::remove	(	core::pose::Pose &	pose,
		bool	reset_paratope_residues = `false`
	)

Remove constraints from each paratope residue and antigen chain set. If reset_paratope_residues is true, then it will update the set of paratope residues it has. This is used after pose length changes such as CDR insertion or deletion.

References ab_info_, antigen_chains_, paratope_residues_, paratope_residues_from_cdrs(), core::pose::Pose::remove_constraints(), setup_constraints(), and core::pose::Pose::size().

◆ set_constraint_func()

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

Optionally set the Func that will be used for the constraint. Default is the Flat_Harmonic at 0, 1, 5.

References current_func_.

◆ set_defaults()

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

References antigen_chains_, cdrs_to_apply_, interface_distance_, and paratope_residues_.

Referenced by ParatopeSiteConstraintMover().

◆ set_interface_distance()

void protocols::antibody::constraints::ParatopeSiteConstraintMover::set_interface_distance ( core::Real interface_distance )

Set the interface distance that will be only be used as the tolerance for the linear harmonic constraint if no constraint func is set.

References interface_distance_.

◆ setup_constraints()

core::scoring::constraints::SiteConstraintOP protocols::antibody::constraints::ParatopeSiteConstraintMover::setup_constraints	(	core::pose::Pose const &	pose,
		core::Size	resnum,
		std::string	chain
	)

private

References current_func_.

Referenced by apply(), and remove().

Member Data Documentation

◆ ab_info_

AntibodyInfoCOP protocols::antibody::constraints::ParatopeSiteConstraintMover::ab_info_

private

Referenced by apply(), paratope_residues_from_cdrs(), ParatopeSiteConstraintMover(), and remove().

◆ antigen_chains_

utility::vector1<std::string> protocols::antibody::constraints::ParatopeSiteConstraintMover::antigen_chains_

private

Referenced by apply(), constrain_to_antigen_chains(), parse_my_tag(), remove(), and set_defaults().

◆ cdrs_to_apply_

utility::vector1<bool> protocols::antibody::constraints::ParatopeSiteConstraintMover::cdrs_to_apply_

private

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

◆ current_func_

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

private

Referenced by apply(), ParatopeSiteConstraintMover(), set_constraint_func(), and setup_constraints().

◆ interface_distance_

core::Real protocols::antibody::constraints::ParatopeSiteConstraintMover::interface_distance_

private

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

◆ paratope_residues_

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

private

Referenced by apply(), constrain_to_paratope_residues(), parse_my_tag(), provide_citation_info(), remove(), and set_defaults().

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

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

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ParatopeSiteConstraintMover() [1/3]

◆ ParatopeSiteConstraintMover() [2/3]

◆ ~ParatopeSiteConstraintMover()

◆ ParatopeSiteConstraintMover() [3/3]

Member Function Documentation

◆ apply()

◆ clone()

◆ constrain_to_antigen_chains()

◆ constrain_to_paratope_cdrs() [1/2]

◆ constrain_to_paratope_cdrs() [2/2]

◆ constrain_to_paratope_residues()

◆ get_name()

◆ 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_

◆ antigen_chains_

◆ cdrs_to_apply_

◆ current_func_

◆ interface_distance_

◆ paratope_residues_