#include <NMRSpinlabel.hh>

Inheritance diagram for core::scoring::nmr::NMRSpinlabel:

Public Types
enum	CONFORMER_FILTER { DISTANCE = 1, BUMP_ENERGY = 2 }
	type of spinlabel conformer filtering DISTANCE = measure the distance of spinlabel side chain heavy atoms to the NBR_ATOM in every neighborhood residue in the spinlabel environment and count how many atoms are within the NBR_RADIUS BUMP_ENERGY = filter based on packer energy of a spinlabel conformer with all neighboring residues and keep conformers with energy lower than bump energy threshold More...

typedef core::chemical::ResidueTypeOP	ResidueTypeOP

typedef core::chemical::ResidueTypeCOP	ResidueTypeCOP

typedef utility::vector1 < std::pair< Real, Vector > >	WeightCoordVector

Public Member Functions
	NMRSpinlabel (std::string const &residue_type_set, std::string const &residue_type)
	construct from strings of residue type set and residue type; the other properties (e.g. radical atom) are looked up in the database More...

	NMRSpinlabel (ResidueTypeCOP residue_type, std::string const &radical_atom, NMRDummySpinlabelEnsembleCOP dummy_ensemble)
	construct from ResidueType, radical atom name and NMRDummySpinlabelEnsemble More...

	NMRSpinlabel (NMRSpinlabel const &other)
	copy constructor More...

NMRSpinlabel &	operator= (NMRSpinlabel const &rhs)
	assignment operator More...

	~NMRSpinlabel () override
	destructor More...

std::string	get_name () const
	Getters. More...

std::string	get_code () const

ResidueTypeCOP	get_residue_type () const

std::string	get_radical_atom () const

std::string	get_distance_potential_histogram_file () const

NMRDummySpinlabelEnsembleCOP	get_dummy_ensemble () const

NMRDummySpinlabelEnsembleOP	get_dummy_ensemble ()

WeightCoordVector const &	get_radical_atom_coordinates () const

Size	get_max_ensemble_size () const

Size	get_current_ensemble_size () const

void	set_highres_conformer_filter_type (std::string const &filter_type)

CONFORMER_FILTER	get_highres_conformer_filter_type () const

Real	get_boltzman_factor () const

void	set_boltzmann_factor (Real const kt)

void	set_path_to_distance_potential_histogram_file (std::string const &filename)

WeightCoordVector	filter_spinlabel_ensemble_by_distance_check (pose::Pose const &pose, Size const &target_resid)
	filter dummy spinlabel ensemble given the neighborhood of a particular target residue in the pose. Return a vector of each spinlabel conformer's weight and radical atom coordinates. Performs also clustering of coordinates internally such that the vector size does not exceed the maximal number of spinlabel conformers. More...

WeightCoordVector	filter_spinlabel_ensemble_by_mask (pose::Pose const &pose, Size const &target_resid, utility::vector1< bool > const &mask, utility::vector1< Real > const &scores)
	filter dummy ensemble and keep those spinlabels provided in boolean mask More...

void	show (std::ostream &TR)

Private Member Functions
	NMRSpinlabel ()
	default constructor More...

void	init_spinlabel_name ()

void	convert_string_to_conformer_filter_type (std::string const &filter_type)
	utility function to convert string to class specific enum More...

void	cluster_conformers_and_set_weights_and_coordinates (WeightCoordVector &weights_coords, utility::vector1< utility::vector1< Real >> &rmsd_mat)
	Performs clustering of the spinlabel coordinates vector before setting the class member. The input vector doesn't store all spinlabel atoms but only the coordinates of the radical atom. Clustering is done based on input RMSD matrix. More...

void	set_weights_and_coordinates (WeightCoordVector const &weights_coords)

void	init_radical_atom_weights_and_coordinates ()

void	register_options ()
	register command line options More...

void	init_from_cml ()

Private Attributes
std::string	name_

std::string	three_letter_code_

ResidueTypeCOP	residue_type_

std::string	radical_atom_

std::string	distance_potential_histogram_file_

NMRDummySpinlabelEnsembleOP	dummy_ensemble_

WeightCoordVector	weights_coordinates_table_

Size	max_ensemble_size_

CONFORMER_FILTER	highres_conformer_filter_type_

Real	boltzmann_factor_

Member Typedef Documentation

typedef core::chemical::ResidueTypeCOP core::scoring::nmr::NMRSpinlabel::ResidueTypeCOP

typedef core::chemical::ResidueTypeOP core::scoring::nmr::NMRSpinlabel::ResidueTypeOP

typedef utility::vector1< std::pair< Real, Vector > > core::scoring::nmr::NMRSpinlabel::WeightCoordVector

Member Enumeration Documentation

enum core::scoring::nmr::NMRSpinlabel::CONFORMER_FILTER

type of spinlabel conformer filtering DISTANCE = measure the distance of spinlabel side chain heavy atoms to the NBR_ATOM in every neighborhood residue in the spinlabel environment and count how many atoms are within the NBR_RADIUS BUMP_ENERGY = filter based on packer energy of a spinlabel conformer with all neighboring residues and keep conformers with energy lower than bump energy threshold

Enumerator
DISTANCE
BUMP_ENERGY

Constructor & Destructor Documentation

core::scoring::nmr::NMRSpinlabel::NMRSpinlabel	(	std::string const &	residue_type_set,
		std::string const &	residue_type
	)

construct from strings of residue type set and residue type; the other properties (e.g. radical atom) are looked up in the database

References distance_potential_histogram_file_, dummy_ensemble_, init_from_cml(), init_radical_atom_weights_and_coordinates(), init_spinlabel_name(), radical_atom_, register_options(), and residue_type_.

core::scoring::nmr::NMRSpinlabel::NMRSpinlabel	(	chemical::ResidueTypeCOP	residue_type,
		std::string const &	radical_atom,
		NMRDummySpinlabelEnsembleCOP	dummy_ensemble
	)

construct from ResidueType, radical atom name and NMRDummySpinlabelEnsemble

References init_from_cml(), init_radical_atom_weights_and_coordinates(), init_spinlabel_name(), and register_options().

core::scoring::nmr::NMRSpinlabel::NMRSpinlabel ( NMRSpinlabel const & other )

copy constructor

References init_spinlabel_name().

core::scoring::nmr::NMRSpinlabel::~NMRSpinlabel ( )

override

destructor

core::scoring::nmr::NMRSpinlabel::NMRSpinlabel ( )

private

default constructor

Member Function Documentation

void core::scoring::nmr::NMRSpinlabel::cluster_conformers_and_set_weights_and_coordinates	(	WeightCoordVector &	weights_coords,
		utility::vector1< utility::vector1< Real >> &	rmsd_mat
	)

private

Performs clustering of the spinlabel coordinates vector before setting the class member. The input vector doesn't store all spinlabel atoms but only the coordinates of the radical atom. Clustering is done based on input RMSD matrix.

References core::conformation::membrane::center, protocols::mean_field::max(), max_ensemble_size_, and core::scoring::nmr::TR().

Referenced by filter_spinlabel_ensemble_by_distance_check(), and filter_spinlabel_ensemble_by_mask().

void core::scoring::nmr::NMRSpinlabel::convert_string_to_conformer_filter_type ( std::string const & filter_type )

private

utility function to convert string to class specific enum

References BUMP_ENERGY, DISTANCE, highres_conformer_filter_type_, and protocols::kinmatch::str().

Referenced by init_from_cml(), and set_highres_conformer_filter_type().

NMRSpinlabel::WeightCoordVector core::scoring::nmr::NMRSpinlabel::filter_spinlabel_ensemble_by_distance_check	(	pose::Pose const &	pose,
		Size const &	target_resid
	)

filter dummy spinlabel ensemble given the neighborhood of a particular target residue in the pose. Return a vector of each spinlabel conformer's weight and radical atom coordinates. Performs also clustering of coordinates internally such that the vector size does not exceed the maximal number of spinlabel conformers.

These are the two functions through which the user interfaces with the class to create an ensemble of valid spinlabel conformers (i.e. those that are expected to be seen given the current environment). In the first function, a simple distance check is performed and conformers that have heavy atoms within the NBR_RADIUS of other residues are marked as clashing. In the second function, the user provides a boolean mask for spinlabels which should be kept.

References cluster_conformers_and_set_weights_and_coordinates(), dummy_ensemble_, max_ensemble_size_, radical_atom_, residue_type_, set_weights_and_coordinates(), and core::scoring::nmr::TR().

NMRSpinlabel::WeightCoordVector core::scoring::nmr::NMRSpinlabel::filter_spinlabel_ensemble_by_mask	(	pose::Pose const &	pose,
		Size const &	target_resid,
		utility::vector1< bool > const &	mask,
		utility::vector1< Real > const &	scores
	)

filter dummy ensemble and keep those spinlabels provided in boolean mask

References boltzmann_factor_, cluster_conformers_and_set_weights_and_coordinates(), dummy_ensemble_, max_ensemble_size_, radical_atom_, set_weights_and_coordinates(), and core::scoring::nmr::TR().

Referenced by protocols::nmr::filter_spinlabel_ensemble_by_packerenergy().

Real core::scoring::nmr::NMRSpinlabel::get_boltzman_factor ( ) const

inline

References boltzmann_factor_.

std::string core::scoring::nmr::NMRSpinlabel::get_code ( ) const

inline

References three_letter_code_.

Referenced by protocols::nmr::filter_spinlabel_ensemble_by_packerenergy().

Size core::scoring::nmr::NMRSpinlabel::get_current_ensemble_size ( ) const

inline

References weights_coordinates_table_.

std::string core::scoring::nmr::NMRSpinlabel::get_distance_potential_histogram_file ( ) const

inline

References distance_potential_histogram_file_.

NMRDummySpinlabelEnsembleCOP core::scoring::nmr::NMRSpinlabel::get_dummy_ensemble ( ) const

inline

References dummy_ensemble_.

Referenced by protocols::nmr::filter_spinlabel_ensemble_by_packerenergy().

NMRDummySpinlabelEnsembleOP core::scoring::nmr::NMRSpinlabel::get_dummy_ensemble ( )

inline

References dummy_ensemble_.

CONFORMER_FILTER core::scoring::nmr::NMRSpinlabel::get_highres_conformer_filter_type ( ) const

inline

References highres_conformer_filter_type_.

Size core::scoring::nmr::NMRSpinlabel::get_max_ensemble_size ( ) const

inline

References max_ensemble_size_.

std::string core::scoring::nmr::NMRSpinlabel::get_name ( ) const

inline

Getters.

References name_.

std::string core::scoring::nmr::NMRSpinlabel::get_radical_atom ( ) const

inline

References radical_atom_.

WeightCoordVector const& core::scoring::nmr::NMRSpinlabel::get_radical_atom_coordinates ( ) const

inline

References weights_coordinates_table_.

ResidueTypeCOP core::scoring::nmr::NMRSpinlabel::get_residue_type ( ) const

inline

References residue_type_.

void core::scoring::nmr::NMRSpinlabel::init_from_cml ( )

private

References boltzmann_factor_, convert_string_to_conformer_filter_type(), and max_ensemble_size_.

Referenced by NMRSpinlabel().

void core::scoring::nmr::NMRSpinlabel::init_radical_atom_weights_and_coordinates ( )

private

References dummy_ensemble_, radical_atom_, and weights_coordinates_table_.

Referenced by NMRSpinlabel().

void core::scoring::nmr::NMRSpinlabel::init_spinlabel_name ( )

private

References name_, residue_type_, and three_letter_code_.

Referenced by NMRSpinlabel(), and operator=().

NMRSpinlabel & core::scoring::nmr::NMRSpinlabel::operator= ( NMRSpinlabel const & rhs )

assignment operator

References boltzmann_factor_, distance_potential_histogram_file_, dummy_ensemble_, highres_conformer_filter_type_, init_spinlabel_name(), max_ensemble_size_, radical_atom_, residue_type_, and weights_coordinates_table_.

void core::scoring::nmr::NMRSpinlabel::register_options ( )

private

register command line options

Referenced by NMRSpinlabel().

void core::scoring::nmr::NMRSpinlabel::set_boltzmann_factor ( Real const kt )

inline

References boltzmann_factor_.

void core::scoring::nmr::NMRSpinlabel::set_highres_conformer_filter_type ( std::string const & filter_type )

References convert_string_to_conformer_filter_type().

void core::scoring::nmr::NMRSpinlabel::set_path_to_distance_potential_histogram_file ( std::string const & filename )

inline

References distance_potential_histogram_file_, and protocols::abinitio::filename().

void core::scoring::nmr::NMRSpinlabel::set_weights_and_coordinates ( WeightCoordVector const & weights_coords )

private

References weights_coordinates_table_.

Referenced by filter_spinlabel_ensemble_by_distance_check(), and filter_spinlabel_ensemble_by_mask().

void core::scoring::nmr::NMRSpinlabel::show ( std::ostream & TR )

References name_, radical_atom_, three_letter_code_, and weights_coordinates_table_.

Member Data Documentation

Real core::scoring::nmr::NMRSpinlabel::boltzmann_factor_

private

Referenced by filter_spinlabel_ensemble_by_mask(), get_boltzman_factor(), init_from_cml(), operator=(), and set_boltzmann_factor().

std::string core::scoring::nmr::NMRSpinlabel::distance_potential_histogram_file_

private

Referenced by get_distance_potential_histogram_file(), NMRSpinlabel(), operator=(), and set_path_to_distance_potential_histogram_file().

NMRDummySpinlabelEnsembleOP core::scoring::nmr::NMRSpinlabel::dummy_ensemble_

private

Referenced by filter_spinlabel_ensemble_by_distance_check(), filter_spinlabel_ensemble_by_mask(), get_dummy_ensemble(), init_radical_atom_weights_and_coordinates(), NMRSpinlabel(), and operator=().

CONFORMER_FILTER core::scoring::nmr::NMRSpinlabel::highres_conformer_filter_type_

private

Referenced by convert_string_to_conformer_filter_type(), get_highres_conformer_filter_type(), and operator=().

Size core::scoring::nmr::NMRSpinlabel::max_ensemble_size_

private

Referenced by cluster_conformers_and_set_weights_and_coordinates(), filter_spinlabel_ensemble_by_distance_check(), filter_spinlabel_ensemble_by_mask(), get_max_ensemble_size(), init_from_cml(), and operator=().

std::string core::scoring::nmr::NMRSpinlabel::name_

private

Referenced by get_name(), init_spinlabel_name(), and show().

std::string core::scoring::nmr::NMRSpinlabel::radical_atom_

private

Referenced by filter_spinlabel_ensemble_by_distance_check(), filter_spinlabel_ensemble_by_mask(), get_radical_atom(), init_radical_atom_weights_and_coordinates(), NMRSpinlabel(), operator=(), and show().

ResidueTypeCOP core::scoring::nmr::NMRSpinlabel::residue_type_

private

Referenced by filter_spinlabel_ensemble_by_distance_check(), get_residue_type(), init_spinlabel_name(), NMRSpinlabel(), and operator=().

std::string core::scoring::nmr::NMRSpinlabel::three_letter_code_

private

Referenced by get_code(), init_spinlabel_name(), and show().

WeightCoordVector core::scoring::nmr::NMRSpinlabel::weights_coordinates_table_

private

Referenced by get_current_ensemble_size(), get_radical_atom_coordinates(), init_radical_atom_weights_and_coordinates(), operator=(), set_weights_and_coordinates(), and show().

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

src/core/scoring/nmr/NMRSpinlabel.hh
src/core/scoring/nmr/NMRSpinlabel.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation