Add Cluster or General Dihedral CircularHarmonic constraints to a CDR. Cluster constraints currently only work for AHO renumbered CDRs. (This will be rafactored to create constraints on-the-fly from cluster Mean/SD instead of from cst files.) More...

#include <CDRDihedralConstraintMover.hh>

Inheritance diagram for protocols::antibody::constraints::CDRDihedralConstraintMover:

[legend]

Public Member Functions
	CDRDihedralConstraintMover ()

	CDRDihedralConstraintMover (AntibodyInfoCOP ab_info)

	CDRDihedralConstraintMover (AntibodyInfoCOP ab_info, CDRNameEnum cdr)

	CDRDihedralConstraintMover (CDRDihedralConstraintMover const &src)

	~CDRDihedralConstraintMover () override

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	set_use_cluster_csts (bool use_cluster_csts)
	Attempt to add cluster-based dihedral constraints. If this is set to false will simply add General Dihedral constraints instead. Default True. More...

void	set_use_general_csts_on_cluster_failure (bool use_general_csts_on_failure)
	If we are set to use cluster csts and: 1) the cluster is NA, 2) there is sparse data for the cluster, or 3) The CDR is H3 and we have chosen not to use cluster data for H3 (default), THEN add general dihedral constraints instead. More...

void	set_cdr (CDRNameEnum cdr)

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

void	set_force_cluster (clusters::CDRClusterEnum cluster)
	Do not use AntibodyInfo to for cluster - use this cluster instead. More...

void	set_remove_any_set_forced_cluster ()
	Remove any forced cluster settings. More...

void	set_cluster_csts_data_cutoff (core::Size cutoff)

void	set_cluster_csts_use_mean_cst_data (bool use_mean_cst_data)
	Use constraints which have the means as the actual cluster means. Setting this to false will use constraints that have the cst means set as cluster center data. More...

void	set_cluster_csts_use_outlier_data (bool use_outlier_data)

void	set_use_cluster_for_H3 (bool use_cluster_for_H3)
	Set to use H3 cluster data for constraints if we are doing cluster-based constraints. Default False - H3 does not cluster well. If use_general_data_on_failure is false, we will skip H3. More...

void	set_general_phi_sd (core::Real phi_sd)

void	set_general_psi_sd (core::Real psi_sd)

void	set_ignore_pose_datacache (bool ignore_pose_datacache)
	By default, if cluster information is present in the datacache, we attempt to use that first. Override this behavior by setting this option to true. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

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...

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
void	set_defaults ()

void	read_command_line_options ()

bool	add_harmonic_cluster_constraint (core::pose::Pose &pose, clusters::CDRClusterEnum const cluster)
	Adds a harmonic constraint to a Pose CDR based on cluster type. More...

core::Size	get_number_of_struct_used_for_csts (clusters::CDRClusterEnum const cluster)

std::string	get_harmonic_cluster_constraint_filename (clusters::CDRClusterEnum const cluster)
	Gets the cluster constraint name. Returns NA if not found. More...

std::string	get_harmonic_cluster_constraint_db_directory ()

Private Attributes
AntibodyInfoCOP	ab_info_

CDRNameEnum	cdr_

std::string	db_base_path_

bool	cdr_is_set_

clusters::CDRClusterEnum	forced_cluster_

bool	force_cluster_

bool	use_cluster_csts_

bool	use_outliers_

bool	use_mean_cst_data_

bool	use_general_csts_on_failure_

bool	use_cluster_for_H3_

bool	ignore_pose_datacache_

core::Size	cluster_data_cutoff_

core::Real	general_phi_sd_

core::Real	general_psi_sd_

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 Cluster or General Dihedral CircularHarmonic constraints to a CDR. Cluster constraints currently only work for AHO renumbered CDRs. (This will be rafactored to create constraints on-the-fly from cluster Mean/SD instead of from cst files.)

Constructor & Destructor Documentation

◆ CDRDihedralConstraintMover() [1/4]

protocols::antibody::constraints::CDRDihedralConstraintMover::CDRDihedralConstraintMover ( )

References read_command_line_options(), and set_defaults().

Referenced by clone().

◆ CDRDihedralConstraintMover() [2/4]

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

References read_command_line_options(), and set_defaults().

◆ CDRDihedralConstraintMover() [3/4]

protocols::antibody::constraints::CDRDihedralConstraintMover::CDRDihedralConstraintMover	(	AntibodyInfoCOP	ab_info,
		CDRNameEnum	cdr
	)

References read_command_line_options(), set_cdr(), and set_defaults().

◆ CDRDihedralConstraintMover() [4/4]

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

References ab_info_.

◆ ~CDRDihedralConstraintMover()

protocols::antibody::constraints::CDRDihedralConstraintMover::~CDRDihedralConstraintMover ( )

overridedefault

Member Function Documentation

◆ add_harmonic_cluster_constraint()

bool protocols::antibody::constraints::CDRDihedralConstraintMover::add_harmonic_cluster_constraint	(	core::pose::Pose &	pose,
		clusters::CDRClusterEnum const	cluster
	)

private

Adds a harmonic constraint to a Pose CDR based on cluster type.

Currently requires North_AHO numbering.

References ab_info_, core::pose::Pose::add_constraints(), get_harmonic_cluster_constraint_filename(), and protocols::antibody::TR().

Referenced by apply().

◆ apply()

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

overridevirtual

◆ clone()

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

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References CDRDihedralConstraintMover().

◆ fresh_instance()

protocols::moves::MoverOP protocols::antibody::constraints::CDRDihedralConstraintMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_harmonic_cluster_constraint_db_directory()

std::string protocols::antibody::constraints::CDRDihedralConstraintMover::get_harmonic_cluster_constraint_db_directory ( )

private

References db_base_path_, use_mean_cst_data_, and use_outliers_.

Referenced by get_harmonic_cluster_constraint_filename(), and get_number_of_struct_used_for_csts().

◆ get_harmonic_cluster_constraint_filename()

std::string protocols::antibody::constraints::CDRDihedralConstraintMover::get_harmonic_cluster_constraint_filename ( clusters::CDRClusterEnum const cluster )

private

Gets the cluster constraint name. Returns NA if not found.

References ab_info_, get_harmonic_cluster_constraint_db_directory(), protocols::hybridization::path, and protocols::antibody::TR().

Referenced by add_harmonic_cluster_constraint().

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_number_of_struct_used_for_csts()

core::Size protocols::antibody::constraints::CDRDihedralConstraintMover::get_number_of_struct_used_for_csts ( clusters::CDRClusterEnum const cluster )

private

References ab_info_, get_harmonic_cluster_constraint_db_directory(), and protocols::hybridization::path.

Referenced by apply().

◆ mover_name()

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

static

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

◆ parse_my_tag()

void protocols::antibody::constraints::CDRDihedralConstraintMover::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 protocols::antibody::clusters::CDRClusterEnumManager::cdr_cluster_string_to_enum(), protocols::antibody::AntibodyEnumManager::cdr_name_string_to_enum(), cluster_data_cutoff_, general_phi_sd_, general_psi_sd_, set_cdr(), set_force_cluster(), use_cluster_csts_, use_general_csts_on_failure_, and use_outliers_.

◆ provide_citation_info()

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

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

◆ provide_xml_schema()

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

static

References protocols::antibody::clusters::CDRClusterEnumManager::get_recognized_cluster_definitions(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

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

◆ read_command_line_options()

void protocols::antibody::constraints::CDRDihedralConstraintMover::read_command_line_options ( )

private

References cluster_data_cutoff_, general_phi_sd_, general_psi_sd_, use_mean_cst_data_, and use_outliers_.

Referenced by CDRDihedralConstraintMover().

◆ set_cdr()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_cdr ( CDRNameEnum cdr )

References cdr_, and cdr_is_set_.

Referenced by protocols::antibody::AntibodyCDRGrafter::apply(), CDRDihedralConstraintMover(), and parse_my_tag().

◆ set_cluster_csts_data_cutoff()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_cluster_csts_data_cutoff ( core::Size cutoff )

References cluster_data_cutoff_.

◆ set_cluster_csts_use_mean_cst_data()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_cluster_csts_use_mean_cst_data ( bool use_mean_cst_data )

Use constraints which have the means as the actual cluster means. Setting this to false will use constraints that have the cst means set as cluster center data.

References use_mean_cst_data_.

◆ set_cluster_csts_use_outlier_data()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_cluster_csts_use_outlier_data ( bool use_outlier_data )

References use_outliers_.

◆ set_defaults()

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

private

References cdr_is_set_, db_base_path_, force_cluster_, ignore_pose_datacache_, use_cluster_csts_, use_cluster_for_H3_, use_general_csts_on_failure_, and use_outliers_.

Referenced by CDRDihedralConstraintMover().

◆ set_force_cluster()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_force_cluster ( clusters::CDRClusterEnum cluster )

Do not use AntibodyInfo to for cluster - use this cluster instead.

References force_cluster_, and forced_cluster_.

Referenced by parse_my_tag().

◆ set_general_phi_sd()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_general_phi_sd ( core::Real phi_sd )

References general_phi_sd_.

◆ set_general_psi_sd()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_general_psi_sd ( core::Real psi_sd )

References general_psi_sd_.

◆ set_ignore_pose_datacache()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_ignore_pose_datacache ( bool ignore_pose_datacache )

By default, if cluster information is present in the datacache, we attempt to use that first. Override this behavior by setting this option to true.

References ignore_pose_datacache_.

◆ set_remove_any_set_forced_cluster()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_remove_any_set_forced_cluster ( )

Remove any forced cluster settings.

References force_cluster_.

◆ set_use_cluster_csts()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_use_cluster_csts ( bool use_cluster_csts )

Attempt to add cluster-based dihedral constraints. If this is set to false will simply add General Dihedral constraints instead. Default True.

References use_cluster_csts_.

Referenced by protocols::antibody::AntibodyCDRGrafter::apply().

◆ set_use_cluster_for_H3()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_use_cluster_for_H3 ( bool use_cluster_for_H3 )

Set to use H3 cluster data for constraints if we are doing cluster-based constraints. Default False - H3 does not cluster well. If use_general_data_on_failure is false, we will skip H3.

References use_cluster_for_H3_.

◆ set_use_general_csts_on_cluster_failure()

void protocols::antibody::constraints::CDRDihedralConstraintMover::set_use_general_csts_on_cluster_failure ( bool use_general_csts_on_failure )

If we are set to use cluster csts and: 1) the cluster is NA, 2) there is sparse data for the cluster, or 3) The CDR is H3 and we have chosen not to use cluster data for H3 (default), THEN add general dihedral constraints instead.

References use_general_csts_on_failure_.

Member Data Documentation

◆ ab_info_

AntibodyInfoCOP protocols::antibody::constraints::CDRDihedralConstraintMover::ab_info_

private

Referenced by add_harmonic_cluster_constraint(), apply(), CDRDihedralConstraintMover(), get_harmonic_cluster_constraint_filename(), and get_number_of_struct_used_for_csts().

◆ cdr_

CDRNameEnum protocols::antibody::constraints::CDRDihedralConstraintMover::cdr_

private

Referenced by apply(), and set_cdr().

◆ cdr_is_set_

bool protocols::antibody::constraints::CDRDihedralConstraintMover::cdr_is_set_

private

Referenced by apply(), set_cdr(), and set_defaults().

◆ cluster_data_cutoff_

core::Size protocols::antibody::constraints::CDRDihedralConstraintMover::cluster_data_cutoff_

private

Referenced by apply(), parse_my_tag(), read_command_line_options(), and set_cluster_csts_data_cutoff().

◆ db_base_path_

std::string protocols::antibody::constraints::CDRDihedralConstraintMover::db_base_path_

private

Referenced by get_harmonic_cluster_constraint_db_directory(), and set_defaults().

◆ force_cluster_

bool protocols::antibody::constraints::CDRDihedralConstraintMover::force_cluster_

private

Referenced by apply(), set_defaults(), set_force_cluster(), and set_remove_any_set_forced_cluster().

◆ forced_cluster_

clusters::CDRClusterEnum protocols::antibody::constraints::CDRDihedralConstraintMover::forced_cluster_

private

Referenced by apply(), and set_force_cluster().

◆ general_phi_sd_

core::Real protocols::antibody::constraints::CDRDihedralConstraintMover::general_phi_sd_

private

Referenced by apply(), parse_my_tag(), read_command_line_options(), and set_general_phi_sd().

◆ general_psi_sd_

core::Real protocols::antibody::constraints::CDRDihedralConstraintMover::general_psi_sd_

private

Referenced by apply(), parse_my_tag(), read_command_line_options(), and set_general_psi_sd().

◆ ignore_pose_datacache_

bool protocols::antibody::constraints::CDRDihedralConstraintMover::ignore_pose_datacache_

private

Referenced by apply(), set_defaults(), and set_ignore_pose_datacache().

◆ use_cluster_csts_

bool protocols::antibody::constraints::CDRDihedralConstraintMover::use_cluster_csts_

private

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

◆ use_cluster_for_H3_

bool protocols::antibody::constraints::CDRDihedralConstraintMover::use_cluster_for_H3_

private

Referenced by apply(), set_defaults(), and set_use_cluster_for_H3().

◆ use_general_csts_on_failure_

bool protocols::antibody::constraints::CDRDihedralConstraintMover::use_general_csts_on_failure_

private

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

◆ use_mean_cst_data_

bool protocols::antibody::constraints::CDRDihedralConstraintMover::use_mean_cst_data_

private

Referenced by get_harmonic_cluster_constraint_db_directory(), read_command_line_options(), and set_cluster_csts_use_mean_cst_data().

◆ use_outliers_

bool protocols::antibody::constraints::CDRDihedralConstraintMover::use_outliers_

private

Referenced by get_harmonic_cluster_constraint_db_directory(), parse_my_tag(), read_command_line_options(), set_cluster_csts_use_outlier_data(), and set_defaults().

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

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

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CDRDihedralConstraintMover() [1/4]

◆ CDRDihedralConstraintMover() [2/4]

◆ CDRDihedralConstraintMover() [3/4]

◆ CDRDihedralConstraintMover() [4/4]

◆ ~CDRDihedralConstraintMover()

Member Function Documentation

◆ add_harmonic_cluster_constraint()

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_harmonic_cluster_constraint_db_directory()

◆ get_harmonic_cluster_constraint_filename()

◆ get_name()

◆ get_number_of_struct_used_for_csts()

◆ mover_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ read_command_line_options()

◆ set_cdr()

◆ set_cluster_csts_data_cutoff()

◆ set_cluster_csts_use_mean_cst_data()

◆ set_cluster_csts_use_outlier_data()

◆ set_defaults()

◆ set_force_cluster()

◆ set_general_phi_sd()

◆ set_general_psi_sd()

◆ set_ignore_pose_datacache()

◆ set_remove_any_set_forced_cluster()

◆ set_use_cluster_csts()

◆ set_use_cluster_for_H3()

◆ set_use_general_csts_on_cluster_failure()

Member Data Documentation

◆ ab_info_

◆ cdr_

◆ cdr_is_set_

◆ cluster_data_cutoff_

◆ db_base_path_

◆ force_cluster_

◆ forced_cluster_

◆ general_phi_sd_

◆ general_psi_sd_

◆ ignore_pose_datacache_

◆ use_cluster_csts_

◆ use_cluster_for_H3_

◆ use_general_csts_on_failure_

◆ use_mean_cst_data_

◆ use_outliers_