#include <PREMover.hh>

Inheritance diagram for protocols::nmr::pre::PREMover:

[legend]

Public Types
typedef core::Real	Real

typedef core::Size	Size

typedef core::scoring::nmr::pre::PREData	PREData

typedef core::scoring::nmr::pre::PREDataOP	PREDataOP

typedef core::scoring::nmr::pre::PREDataOP	PREDataCOP

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::pose::Pose	Pose

typedef protocols::moves::MoverOP	MoverOP

typedef std::map< std::string, std::pair< std::string, core::Real > >	SpinlabelHistogramMap

typedef utility::vector1< PREDistanceRecord >	PREDistances

typedef std::map< core::Size, PREDistances >	SpinlabelToPREDistances

typedef utility::fixedsizearray1< Real, 8 >	Vec8

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

Public Member Functions
	PREMover ()
	Default constructor. More...

	PREMover (std::string const &pre_data_file, Pose const &pose)
	Construct PREMover from PRE data input file. More...

	PREMover (PREMover const &other)
	Copy constructor. More...

PREMover &	operator= (PREMover const &rhs)
	Copy assignment. More...

	~PREMover () override
	destructor More...

std::string	get_name () const override
	Get the name of this mover. More...

MoverOP	clone () const override
	Make a deep copy of this mover. More...

MoverOP	fresh_instance () const override
	Create a fresh instance of this mover. More...

void	apply (Pose &pose) override
	Calculate CB-CB distances from PRE rates and append them as atom pair distance constraints to the pose. More...

void	show (std::ostream &TR) const override
	Outputs details about the Mover, including current settings. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
	Parse tags of XML script. More...

PREDataCOP	get_pre_data ()

std::string const &	get_pre_data_file ()

ScoreFunctionCOP	get_scorefunction () const

bool	weighted_average () const

bool	minimize_w_pre_csts () const

void	set_pre_data (PREDataCOP pre_data)

void	set_scorefunction (ScoreFunctionCOP sfxn)

void	set_weighted_average (bool av)

void	set_minimize_w_pre_csts (bool min)

void	add_histogram_file (std::string const &spinlabel_name, std::string const &histogram_file, Real bin_size=0.5)

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 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)
	Create XML schema definition for PREMover. More...

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
Real	R2_to_dist_dd_curie (Vec8 const &params, Real const R2)
	Calculate distance from R2 relaxation rate. More...

Real	R1_to_dist_dd_curie (Vec8 const &params, Real const R1)
	Calculate distance from R1 relaxation rate. More...

void	pre_data_to_distances (core::scoring::nmr::pre::PREData const &pre_data, SpinlabelToPREDistances &all_sl_distances)
	Calculate distances from relaxation rates and map them to their respective spinlabel and protein residue(s) More...

Private Attributes
SpinlabelHistogramMap	histogram_files_
	Map of histogram files for very spinlabel type that is used in pre_data_. The histogram is used for instantiation of a SplineFunc potential for conversion of the measured PRE distance (e.g. for HN) into a CB-CB atom pair constraint. More...

PREDataCOP	pre_data_
	collection of all PRE datasets for multiple spinlabel sites More...

std::string	pre_data_file_
	The file to read the PRE data from at apply time. More...

ScoreFunctionCOP	sfxn_
	scorefunction object More...

bool	weighted_average_
	use PRESingleSet weights to calculate an average distance in case that the same PRE distance was measured multiple times (e.g. at different field strengths) for the same spinlabel site More...

bool	minimize_
	Do one round of minimization of input pose after PRE distances constraints are added to the pose. More...

Additional Inherited Members
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...

Member Typedef Documentation

◆ MoverOP

typedef protocols::moves::MoverOP protocols::nmr::pre::PREMover::MoverOP

◆ Pose

typedef core::pose::Pose protocols::nmr::pre::PREMover::Pose

◆ PREData

typedef core::scoring::nmr::pre::PREData protocols::nmr::pre::PREMover::PREData

◆ PREDataCOP

typedef core::scoring::nmr::pre::PREDataOP protocols::nmr::pre::PREMover::PREDataCOP

◆ PREDataOP

typedef core::scoring::nmr::pre::PREDataOP protocols::nmr::pre::PREMover::PREDataOP

◆ PREDistances

typedef utility::vector1< PREDistanceRecord > protocols::nmr::pre::PREMover::PREDistances

◆ Real

typedef core::Real protocols::nmr::pre::PREMover::Real

◆ ScoreFunctionCOP

typedef core::scoring::ScoreFunctionCOP protocols::nmr::pre::PREMover::ScoreFunctionCOP

◆ ScoreFunctionOP

typedef core::scoring::ScoreFunctionOP protocols::nmr::pre::PREMover::ScoreFunctionOP

◆ Size

typedef core::Size protocols::nmr::pre::PREMover::Size

◆ SpinlabelHistogramMap

typedef std::map< std::string, std::pair< std::string, core::Real > > protocols::nmr::pre::PREMover::SpinlabelHistogramMap

◆ SpinlabelToPREDistances

typedef std::map< core::Size, PREDistances > protocols::nmr::pre::PREMover::SpinlabelToPREDistances

◆ Vec8

typedef utility::fixedsizearray1< Real, 8 > protocols::nmr::pre::PREMover::Vec8

Constructor & Destructor Documentation

◆ PREMover() [1/3]

protocols::nmr::pre::PREMover::PREMover ( )

Default constructor.

References core::scoring::get_score_function(), and sfxn_.

Referenced by clone().

◆ PREMover() [2/3]

protocols::nmr::pre::PREMover::PREMover	(	std::string const &	pre_data_file,
		Pose const &	pose
	)

Construct PREMover from PRE data input file.

References histogram_files_, pre_data_, and protocols::nmr::pre::TR().

◆ PREMover() [3/3]

protocols::nmr::pre::PREMover::PREMover ( PREMover const & other )

default

Copy constructor.

◆ ~PREMover()

protocols::nmr::pre::PREMover::~PREMover ( )

override

destructor

Member Function Documentation

◆ add_histogram_file()

void protocols::nmr::pre::PREMover::add_histogram_file	(	std::string const &	spinlabel_name,
		std::string const &	histogram_file,
		Real	bin_size = `0.5`
	)

References histogram_files_.

Referenced by parse_my_tag().

◆ apply()

void protocols::nmr::pre::PREMover::apply ( Pose & pose )

overridevirtual

Calculate CB-CB distances from PRE rates and append them as atom pair distance constraints to the pose.

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::chemical::ResidueType::atom_index(), core::scoring::atom_pair_constraint, core::pose::Pose::constraint_set(), core::sequence::end, core::conformation::Residue::has(), histogram_files_, core::chemical::is_canonical_L_aa_or_gly(), minimize_, pre_data_, pre_data_file_, pre_data_to_distances(), core::pose::Pose::residue(), sfxn_, core::id::to_string(), core::pose::Pose::total_residue(), protocols::nmr::pre::TR(), and core::conformation::Residue::type().

◆ clone()

protocols::moves::MoverOP protocols::nmr::pre::PREMover::clone ( ) const

overridevirtual

Make a deep copy of this mover.

Reimplemented from protocols::moves::Mover.

References PREMover().

◆ fresh_instance()

protocols::moves::MoverOP protocols::nmr::pre::PREMover::fresh_instance ( ) const

overridevirtual

Create a fresh instance of this mover.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::nmr::pre::PREMover::get_name ( ) const

overridevirtual

Get the name of this mover.

Implements protocols::moves::Mover.

References mover_name().

◆ get_pre_data()

PREDataCOP protocols::nmr::pre::PREMover::get_pre_data ( )

inline

Getter and Setters

Can be null

References pre_data_.

◆ get_pre_data_file()

std::string const& protocols::nmr::pre::PREMover::get_pre_data_file ( )

inline

References pre_data_file_.

◆ get_scorefunction()

ScoreFunctionCOP protocols::nmr::pre::PREMover::get_scorefunction ( ) const

inline

References sfxn_.

◆ minimize_w_pre_csts()

bool protocols::nmr::pre::PREMover::minimize_w_pre_csts ( ) const

inline

References minimize_.

◆ mover_name()

std::string protocols::nmr::pre::PREMover::mover_name ( )

static

Referenced by get_name(), protocols::nmr::pre::PREMoverCreator::keyname(), and provide_xml_schema().

◆ operator=()

PREMover & protocols::nmr::pre::PREMover::operator= ( PREMover const & rhs )

default

Copy assignment.

◆ parse_my_tag()

void protocols::nmr::pre::PREMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

Parse tags of XML script.

Reimplemented from protocols::moves::Mover.

References add_histogram_file(), protocols::abinitio::filename(), minimize_, core::scoring::parse_score_function(), pre_data_file_, sfxn_, protocols::nmr::pre::TR(), and weighted_average_.

◆ pre_data_to_distances()

void protocols::nmr::pre::PREMover::pre_data_to_distances	(	core::scoring::nmr::pre::PREData const &	pre_data,
		SpinlabelToPREDistances &	all_sl_distances
	)

private

Calculate distances from relaxation rates and map them to their respective spinlabel and protein residue(s)

References core::scoring::nmr::pre::PREData::get_number_spinlabel_sites(), core::scoring::nmr::pre::PREData::get_pre_multiset_vec(), core::scoring::nmr::R1_PARA, R1_to_dist_dd_curie(), core::scoring::nmr::R2_PARA, R2_to_dist_dd_curie(), protocols::nmr::pre::TR(), and weighted_average_.

Referenced by apply().

◆ provide_xml_schema()

void protocols::nmr::pre::PREMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Create XML schema definition for PREMover.

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::nmr::pre::PREMoverCreator::provide_xml_schema().

◆ R1_to_dist_dd_curie()

core::Real protocols::nmr::pre::PREMover::R1_to_dist_dd_curie	(	Vec8 const &	params,
		Real const	R1
	)

private

Calculate distance from R1 relaxation rate.

Considers dipolar and Curie relaxation @params params[1] = gamma_I: gyromagnetic ratio of the nuclear spin (must be provided in rad/(s*T), dimension is 10^6) params[2] = gJ: electron Lande factor params[3] = S: total spin quantum number params[4] = omega_I: nuclear spin resonance frequency (must be provided in rad/s, dimension is 10^6) params[5] = tau_c: total correlation time (must be provided in s, typical dimension is 10^-9) params[6] = tau_r: rotational correlation time (must be provided in s, typical dimension is 10^-9) params[7] = B0: magnetic field strength (in Tesla) params[8] = T: temperature (in K) R1: R1 relaxation rate (in Hz)

Referenced by pre_data_to_distances().

◆ R2_to_dist_dd_curie()

core::Real protocols::nmr::pre::PREMover::R2_to_dist_dd_curie	(	Vec8 const &	params,
		Real const	R2
	)

private

Calculate distance from R2 relaxation rate.

Considers dipolar and Curie relaxation @params params[1] = gamma_I: gyromagnetic ratio of the nuclear spin (must be provided in rad/(s*T), dimension is 10^6) params[2] = gJ: electron Lande factor params[3] = S: total spin quantum number params[4] = omega_I: nuclear spin resonance frequency (must be provided in rad/s, dimension is 10^6) params[5] = tau_c: total correlation time (must be provided in s, typical dimension is 10^-9) params[6] = tau_r: rotational correlation time (must be provided in s, typical dimension is 10^-9) params[7] = B0: magnetic field strength (in Tesla) params[8] = T: temperature (in K) R2: R2 relaxation rate (in Hz)

Referenced by pre_data_to_distances().

◆ set_minimize_w_pre_csts()

void protocols::nmr::pre::PREMover::set_minimize_w_pre_csts ( bool min )

inline

References protocols::mean_field::min(), and minimize_.

◆ set_pre_data()

void protocols::nmr::pre::PREMover::set_pre_data ( PREDataCOP pre_data )

inline

References pre_data_.

◆ set_scorefunction()

void protocols::nmr::pre::PREMover::set_scorefunction ( ScoreFunctionCOP sfxn )

inline

References sfxn_.

◆ set_weighted_average()

void protocols::nmr::pre::PREMover::set_weighted_average ( bool av )

inline

References weighted_average_.

◆ show()

void protocols::nmr::pre::PREMover::show ( std::ostream & output ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References histogram_files_, pre_data_, pre_data_file_, and protocols::frag_picker::tracer().

◆ weighted_average()

bool protocols::nmr::pre::PREMover::weighted_average ( ) const

inline

References weighted_average_.

Member Data Documentation

◆ histogram_files_

SpinlabelHistogramMap protocols::nmr::pre::PREMover::histogram_files_

private

Map of histogram files for very spinlabel type that is used in pre_data_. The histogram is used for instantiation of a SplineFunc potential for conversion of the measured PRE distance (e.g. for HN) into a CB-CB atom pair constraint.

Referenced by add_histogram_file(), apply(), PREMover(), and show().

◆ minimize_

bool protocols::nmr::pre::PREMover::minimize_

private

Do one round of minimization of input pose after PRE distances constraints are added to the pose.

Referenced by apply(), minimize_w_pre_csts(), parse_my_tag(), and set_minimize_w_pre_csts().

◆ pre_data_

PREDataCOP protocols::nmr::pre::PREMover::pre_data_

private

collection of all PRE datasets for multiple spinlabel sites

Referenced by apply(), get_pre_data(), PREMover(), set_pre_data(), and show().

◆ pre_data_file_

std::string protocols::nmr::pre::PREMover::pre_data_file_

private

The file to read the PRE data from at apply time.

Referenced by apply(), get_pre_data_file(), parse_my_tag(), and show().

◆ sfxn_

ScoreFunctionCOP protocols::nmr::pre::PREMover::sfxn_

private

scorefunction object

Referenced by apply(), get_scorefunction(), parse_my_tag(), PREMover(), and set_scorefunction().

◆ weighted_average_

bool protocols::nmr::pre::PREMover::weighted_average_

private

use PRESingleSet weights to calculate an average distance in case that the same PRE distance was measured multiple times (e.g. at different field strengths) for the same spinlabel site

Referenced by parse_my_tag(), pre_data_to_distances(), set_weighted_average(), and weighted_average().

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

src/protocols/nmr/pre/PREMover.hh
src/protocols/nmr/pre/PREMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ MoverOP

◆ Pose

◆ PREData

◆ PREDataCOP

◆ PREDataOP

◆ PREDistances

◆ Real

◆ ScoreFunctionCOP

◆ ScoreFunctionOP

◆ Size

◆ SpinlabelHistogramMap

◆ SpinlabelToPREDistances

◆ Vec8

Constructor & Destructor Documentation

◆ PREMover() [1/3]

◆ PREMover() [2/3]

◆ PREMover() [3/3]

◆ ~PREMover()

Member Function Documentation

◆ add_histogram_file()

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ get_pre_data()

◆ get_pre_data_file()

◆ get_scorefunction()

◆ minimize_w_pre_csts()

◆ mover_name()

◆ operator=()

◆ parse_my_tag()

◆ pre_data_to_distances()

◆ provide_xml_schema()

◆ R1_to_dist_dd_curie()

◆ R2_to_dist_dd_curie()

◆ set_minimize_w_pre_csts()

◆ set_pre_data()

◆ set_scorefunction()

◆ set_weighted_average()

◆ show()

◆ weighted_average()

Member Data Documentation

◆ histogram_files_

◆ minimize_

◆ pre_data_

◆ pre_data_file_

◆ sfxn_

◆ weighted_average_