Mutates framework positions to what is needed for a particular cluster if that cluster has needed mutations. More...

#include <MutateFrameworkForCluster.hh>

Inheritance diagram for protocols::antibody::design::MutateFrameworkForCluster:

[legend]

Public Member Functions
	MutateFrameworkForCluster ()
	Constructor for RosettaScripts only. More...

	MutateFrameworkForCluster (AntibodyInfoCOP ab_info)

	MutateFrameworkForCluster (MutateFrameworkForCluster const &src)

	~MutateFrameworkForCluster () override

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

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

void	set_cdrs (utility::vector1< bool > const &cdrs)

void	set_pack_shell (core::Real const pack_shell)
	Set the distance for the packing shell. More...

void	set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)

void	set_custom_data (std::map< clusters::CDRClusterEnum, utility::vector1< MutantPosition > > const &mutant_info)
	Set custom data instead of loading it from the database. More...

std::map< clusters::CDRClusterEnum, utility::vector1< MutantPosition > >	get_data ()
	Get data used to do the design. More...

bool	has_framework_dependant_clusters (core::pose::Pose const &pose)

bool	has_framework_dependant_cluster (core::pose::Pose const &pose, CDRNameEnum const cdr)

utility::vector1< clusters::CDRClusterEnum >	framework_dependant_clusters ()
	Get all framework dependant clusters in list. More...

utility::vector1< bool >	framework_dependant_positions (core::pose::Pose const &pose)
	Get all framework positions that would be required by clusters regardless of whether that cluster is in the pose. More...

utility::vector1< bool >	framework_dependant_positions (core::pose::Pose const &pose, clusters::CDRClusterEnum const cluster)
	Get all framework positions that would be required by a cluster regardless of whether that cluster is in the pose. More...

utility::vector1< bool >	framework_dependant_mutations (core::pose::Pose const &pose, clusters::CDRClusterEnum const cluster, core::Size const resnum)
	Get all framework mutations for a particular framework dependent position, regardless of whether that cluster is in the pose. 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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

Private Member Functions
void	set_defaults ()

void	load_data ()

Private Attributes
AntibodyInfoCOP	ab_info_

bool	regenerate_abinfo_ = false

core::scoring::ScoreFunctionCOP	scorefxn_

std::map< clusters::CDRClusterEnum, utility::vector1< MutantPosition > >	mutant_info_

utility::vector1< bool >	cdrs_

core::Real	pack_shell_

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

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...

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

Mutates framework positions to what is needed for a particular cluster if that cluster has needed mutations.

Will use clusters from pose data cache if there, otherwise, will use clusters set from AntibodyInfo.

Use set_cdr or set_cdrs to limit to a particular CDR or set of CDRs.

Constructor & Destructor Documentation

◆ MutateFrameworkForCluster() [1/3]

protocols::antibody::design::MutateFrameworkForCluster::MutateFrameworkForCluster ( )

Constructor for RosettaScripts only.

References load_data(), and set_defaults().

◆ MutateFrameworkForCluster() [2/3]

protocols::antibody::design::MutateFrameworkForCluster::MutateFrameworkForCluster ( AntibodyInfoCOP ab_info )

References load_data(), and set_defaults().

◆ MutateFrameworkForCluster() [3/3]

protocols::antibody::design::MutateFrameworkForCluster::MutateFrameworkForCluster ( MutateFrameworkForCluster const & src )

default

◆ ~MutateFrameworkForCluster()

protocols::antibody::design::MutateFrameworkForCluster::~MutateFrameworkForCluster ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::antibody::design::MutateFrameworkForCluster::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References ab_info_, core::select::residue_selector::NeighborhoodResidueSelector::apply(), protocols::minimization_packing::PackRotamersMover::apply(), core::pack::task::operation::RestrictResidueToRepacking::apply(), core::pack::task::operation::PreventRepacking::apply(), core::pose::datacache::CacheableDataType::CDR_CLUSTER_INFO, cdrs_, core::pose::Pose::data(), framework_dependant_clusters(), protocols::antibody::clusters::BasicCDRClusterSet::get_cluster(), protocols::antibody::design::get_resnum_from_single_string_w_landmark(), core::pack::task::operation::RestrictResidueToRepacking::include_residue(), core::pack::task::operation::PreventRepacking::include_residue(), mutant_info_, protocols::antibody::design::MutantPosition::mutants_allowed_, core::enzymes::NA, protocols::antibody::design::MutantPosition::numbering_scheme_, pack_shell_, protocols::antibody::design::MutantPosition::pdb_position_, regenerate_abinfo_, scorefxn_, core::pose::Pose::size(), and protocols::antibody::TR().

◆ framework_dependant_clusters()

utility::vector1< CDRClusterEnum > protocols::antibody::design::MutateFrameworkForCluster::framework_dependant_clusters ( )

Get all framework dependant clusters in list.

References mutant_info_.

Referenced by apply().

◆ framework_dependant_mutations()

utility::vector1< bool > protocols::antibody::design::MutateFrameworkForCluster::framework_dependant_mutations	(	core::pose::Pose const &	pose,
		clusters::CDRClusterEnum const	cluster,
		core::Size const	resnum
	)

Get all framework mutations for a particular framework dependent position, regardless of whether that cluster is in the pose.

References ab_info_, protocols::antibody::design::get_resnum_from_single_string_w_landmark(), and mutant_info_.

◆ framework_dependant_positions() [1/2]

utility::vector1< bool > protocols::antibody::design::MutateFrameworkForCluster::framework_dependant_positions ( core::pose::Pose const & pose )

Get all framework positions that would be required by clusters regardless of whether that cluster is in the pose.

References ab_info_, protocols::antibody::design::get_resnum_from_single_string_w_landmark(), mutant_info_, and core::pose::Pose::size().

◆ framework_dependant_positions() [2/2]

utility::vector1< bool > protocols::antibody::design::MutateFrameworkForCluster::framework_dependant_positions	(	core::pose::Pose const &	pose,
		clusters::CDRClusterEnum const	cluster
	)

Get all framework positions that would be required by a cluster regardless of whether that cluster is in the pose.

References ab_info_, protocols::antibody::design::get_resnum_from_single_string_w_landmark(), mutant_info_, and core::pose::Pose::size().

◆ fresh_instance()

protocols::moves::MoverOP protocols::antibody::design::MutateFrameworkForCluster::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_data()

std::map< clusters::CDRClusterEnum, utility::vector1< MutantPosition > > protocols::antibody::design::MutateFrameworkForCluster::get_data ( )

Get data used to do the design.

References mutant_info_.

◆ get_name()

std::string protocols::antibody::design::MutateFrameworkForCluster::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

Referenced by provide_citation_info().

◆ has_framework_dependant_cluster()

bool protocols::antibody::design::MutateFrameworkForCluster::has_framework_dependant_cluster	(	core::pose::Pose const &	pose,
		CDRNameEnum const	cdr
	)

References ab_info_, protocols::antibody::clusters::get_cluster_from_cache_or_ab_info(), and mutant_info_.

Referenced by has_framework_dependant_clusters().

◆ has_framework_dependant_clusters()

bool protocols::antibody::design::MutateFrameworkForCluster::has_framework_dependant_clusters ( core::pose::Pose const & pose )

References ab_info_, and has_framework_dependant_cluster().

◆ load_data()

void protocols::antibody::design::MutateFrameworkForCluster::load_data ( )

private

References core::chemical::aa_from_oneletter_code(), ab_info_, protocols::abinitio::filename(), core::conformation::membrane::in, mutant_info_, protocols::antibody::design::MutantPosition::mutants_allowed_, protocols::antibody::design::MutantPosition::numbering_scheme_, protocols::antibody::AntibodyEnumManager::numbering_scheme_string_to_enum(), and protocols::antibody::design::MutantPosition::pdb_position_.

Referenced by MutateFrameworkForCluster().

◆ parse_my_tag()

void protocols::antibody::design::MutateFrameworkForCluster::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 cdrs_, protocols::antibody::get_cdr_bool_from_tag(), pack_shell_, core::scoring::parse_score_function(), regenerate_abinfo_, and scorefxn_.

◆ provide_citation_info()

void protocols::antibody::design::MutateFrameworkForCluster::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References get_name().

◆ set_cdr_only()

void protocols::antibody::design::MutateFrameworkForCluster::set_cdr_only ( CDRNameEnum const & cdr )

References cdrs_.

◆ set_cdrs()

void protocols::antibody::design::MutateFrameworkForCluster::set_cdrs ( utility::vector1< bool > const & cdrs )

References cdrs_.

◆ set_custom_data()

void protocols::antibody::design::MutateFrameworkForCluster::set_custom_data ( std::map< clusters::CDRClusterEnum, utility::vector1< MutantPosition > > const & mutant_info )

Set custom data instead of loading it from the database.

References mutant_info_.

◆ set_defaults()

void protocols::antibody::design::MutateFrameworkForCluster::set_defaults ( )

private

References cdrs_, core::scoring::get_score_function(), pack_shell_, and scorefxn_.

Referenced by MutateFrameworkForCluster().

◆ set_pack_shell()

void protocols::antibody::design::MutateFrameworkForCluster::set_pack_shell ( core::Real const pack_shell )

Set the distance for the packing shell.

References pack_shell_.

◆ set_scorefxn()

void protocols::antibody::design::MutateFrameworkForCluster::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn )

References scorefxn_.

Member Data Documentation

◆ ab_info_

AntibodyInfoCOP protocols::antibody::design::MutateFrameworkForCluster::ab_info_

private

Referenced by apply(), framework_dependant_mutations(), framework_dependant_positions(), has_framework_dependant_cluster(), has_framework_dependant_clusters(), and load_data().

◆ cdrs_

utility::vector1<bool> protocols::antibody::design::MutateFrameworkForCluster::cdrs_

private

Referenced by apply(), parse_my_tag(), set_cdr_only(), set_cdrs(), and set_defaults().

◆ mutant_info_

std::map<clusters::CDRClusterEnum, utility::vector1<MutantPosition> > protocols::antibody::design::MutateFrameworkForCluster::mutant_info_

private

Referenced by apply(), framework_dependant_clusters(), framework_dependant_mutations(), framework_dependant_positions(), get_data(), has_framework_dependant_cluster(), load_data(), and set_custom_data().

◆ pack_shell_

core::Real protocols::antibody::design::MutateFrameworkForCluster::pack_shell_

private

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

◆ regenerate_abinfo_

bool protocols::antibody::design::MutateFrameworkForCluster::regenerate_abinfo_ = false

private

Referenced by apply(), and parse_my_tag().

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::antibody::design::MutateFrameworkForCluster::scorefxn_

private

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

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

src/protocols/antibody/design/MutateFrameworkForCluster.hh
src/protocols/antibody/design/MutateFrameworkForCluster.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MutateFrameworkForCluster() [1/3]

◆ MutateFrameworkForCluster() [2/3]

◆ MutateFrameworkForCluster() [3/3]

◆ ~MutateFrameworkForCluster()

Member Function Documentation

◆ apply()

◆ framework_dependant_clusters()

◆ framework_dependant_mutations()

◆ framework_dependant_positions() [1/2]

◆ framework_dependant_positions() [2/2]

◆ fresh_instance()

◆ get_data()

◆ get_name()

◆ has_framework_dependant_cluster()

◆ has_framework_dependant_clusters()

◆ load_data()

◆ parse_my_tag()

◆ provide_citation_info()

◆ set_cdr_only()

◆ set_cdrs()

◆ set_custom_data()

◆ set_defaults()

◆ set_pack_shell()

◆ set_scorefxn()

Member Data Documentation

◆ ab_info_

◆ cdrs_

◆ mutant_info_

◆ pack_shell_

◆ regenerate_abinfo_

◆ scorefxn_