Class that represents a "dummy" spinlabel ensemble. It holds information about each individual conformer member (atom coordinates, number of observations) and data to score those based on atom clashes with the neighborhood of the ensemble. To speed up the clash score calculation, this class holds also an object of type NMRDummySpinlabelVoxelGrid which gets filled with constant pointers to NMRDummySpinlabelAtoms. More...

#include <NMRDummySpinlabelEnsemble.hh>

Inheritance diagram for core::scoring::nmr::NMRDummySpinlabelEnsemble:

[legend]

Public Types
typedef utility::vector1 < NMRDummySpinlabelConformerOP > ::iterator	NMRDummySpinlabelConformerTableIter

typedef utility::vector1 < NMRDummySpinlabelConformerOP > ::const_iterator	NMRDummySpinlabelConformerTableCOIter

Public Member Functions
	NMRDummySpinlabelEnsemble (std::string const &database_file, chemical::ResidueType const &restype)
	Construct from database file and residue type. More...

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

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

	~NMRDummySpinlabelEnsemble () override
	destructor More...

void	clash_check (pose::Pose const &pose, Size const target_resid, Real const radius)
	Perform a clash score calculation for every spinlabel conformer in the ensemble by calculating pairwise distances to neighborhood residues which are within a given radius. Specifically, the distance between every side-chain heavy atom in the spinlabel conformer and the neighbor atom of a pose residue is calculated. If the distance is smaller than the pose residue's neighbor radius, is is assumed that the spinlabel conformer will fall within the side-chain radius of the neighborhood residue and thus it will be labeled as clashing otherwise it will not. More...

HT	coordinate_transform_onto_target_site (pose::Pose const &pose, Size const resid) const
	returns the transformation matrix which transforms a xyz coordinate from the frame of the spinlabel ensemble into the frame of the target site residue. More...

utility::vector1 < NMRDummySpinlabelConformerOP > &	get_conformer_table ()
	Getters. More...

Size	get_ensemble_size () const

utility::vector1 < utility::vector1< Real > > const &	get_rmsd_mat ()

NMRDummySpinlabelVoxelGridOP	get_voxel_grid ()

NMRDummySpinlabelVoxelGridCOP	get_voxel_grid () const

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

void	init_from_database_file (std::string const &database_file, chemical::ResidueType const &restype)
	utility function used for initialization from database files More...

void	define_ensemble_frame ()
	define the origin of the xyz coordinate frame of the ensemble. this needs to be done only once when we initialize the object. More...

HT	coordinate_transform_from_target_site (pose::Pose const &pose, Size const resid) const
	calculate the homogeneous transform that relates the target residue (i.e. in our case the residue that represents the spinlabel site) with the coordinate frame of the dummy spinlabel ensemble. In this way we don't need to move the spinlabel ensemble which contains many more coordinates but can leave it static. More...

void	register_options ()

void	init_from_cml ()

Private Attributes
Size	ensemble_size_

utility::vector1 < NMRDummySpinlabelConformerOP >	conformer_table_

HT	ensemble_origin_

utility::vector1 < utility::vector1< Real > >	rmsd_mat_

NMRDummySpinlabelVoxelGridOP	grid_

bool	elaborate_clash_check_

Detailed Description

Class that represents a "dummy" spinlabel ensemble. It holds information about each individual conformer member (atom coordinates, number of observations) and data to score those based on atom clashes with the neighborhood of the ensemble. To speed up the clash score calculation, this class holds also an object of type NMRDummySpinlabelVoxelGrid which gets filled with constant pointers to NMRDummySpinlabelAtoms.

Member Typedef Documentation

typedef utility::vector1< NMRDummySpinlabelConformerOP >::const_iterator core::scoring::nmr::NMRDummySpinlabelEnsemble::NMRDummySpinlabelConformerTableCOIter

typedef utility::vector1< NMRDummySpinlabelConformerOP >::iterator core::scoring::nmr::NMRDummySpinlabelEnsemble::NMRDummySpinlabelConformerTableIter

Constructor & Destructor Documentation

core::scoring::nmr::NMRDummySpinlabelEnsemble::NMRDummySpinlabelEnsemble ( )

private

default constructor

core::scoring::nmr::NMRDummySpinlabelEnsemble::NMRDummySpinlabelEnsemble	(	std::string const &	database_file,
		chemical::ResidueType const &	restype
	)

Construct from database file and residue type.

Class NMRDummySpinlabelEnsemble.

Construct from database file

References define_ensemble_frame(), init_from_cml(), init_from_database_file(), and register_options().

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

copy constructor

References conformer_table_, and grid_.

core::scoring::nmr::NMRDummySpinlabelEnsemble::~NMRDummySpinlabelEnsemble ( )

override

destructor

Member Function Documentation

void core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check	(	pose::Pose const &	pose,
		Size const	target_resid,
		Real const	radius
	)

Perform a clash score calculation for every spinlabel conformer in the ensemble by calculating pairwise distances to neighborhood residues which are within a given radius. Specifically, the distance between every side-chain heavy atom in the spinlabel conformer and the neighbor atom of a pose residue is calculated. If the distance is smaller than the pose residue's neighbor radius, is is assumed that the spinlabel conformer will fall within the side-chain radius of the neighborhood residue and thus it will be labeled as clashing otherwise it will not.

References core::pose::motif::a(), core::conformation::Residue::atom_name(), protocols::match::upstream::b, core::scoring::nmr::NMRDummySpinlabelConformer::clash_on(), core::scoring::nmr::NMRDummySpinlabelConformer::clash_score(), conformer_table_, coordinate_transform_from_target_site(), core::kinematics::distance(), elaborate_clash_check_, ensemble_size_, grid_, core::scoring::nmr::NMRDummySpinlabelConformer::has_clash(), core::conformation::Residue::is_virtual_residue(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::name3(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Residue::nbr_radius(), core::pose::Pose::residue(), core::simple_metrics::metrics::sum, core::pose::Pose::total_residue(), and core::scoring::nmr::TR().

HT core::scoring::nmr::NMRDummySpinlabelEnsemble::coordinate_transform_from_target_site	(	pose::Pose const &	pose,
		Size const	resid
	)		const

private

calculate the homogeneous transform that relates the target residue (i.e. in our case the residue that represents the spinlabel site) with the coordinate frame of the dummy spinlabel ensemble. In this way we don't need to move the spinlabel ensemble which contains many more coordinates but can leave it static.

References core::scoring::nmr::define_local_frame(), ensemble_origin_, core::conformation::Residue::has(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by clash_check(), and coordinate_transform_onto_target_site().

HT core::scoring::nmr::NMRDummySpinlabelEnsemble::coordinate_transform_onto_target_site	(	pose::Pose const &	pose,
		Size const	resid
	)		const

returns the transformation matrix which transforms a xyz coordinate from the frame of the spinlabel ensemble into the frame of the target site residue.

References coordinate_transform_from_target_site().

void core::scoring::nmr::NMRDummySpinlabelEnsemble::define_ensemble_frame ( )

private

define the origin of the xyz coordinate frame of the ensemble. this needs to be done only once when we initialize the object.

References conformer_table_, core::scoring::nmr::define_local_frame(), ensemble_origin_, and ensemble_size_.

Referenced by NMRDummySpinlabelEnsemble().

utility::vector1< NMRDummySpinlabelConformerOP >& core::scoring::nmr::NMRDummySpinlabelEnsemble::get_conformer_table ( )

inline

Getters.

References conformer_table_.

Size core::scoring::nmr::NMRDummySpinlabelEnsemble::get_ensemble_size ( ) const

inline

References ensemble_size_.

utility::vector1<utility::vector1<Real> > const& core::scoring::nmr::NMRDummySpinlabelEnsemble::get_rmsd_mat ( )

inline

References rmsd_mat_.

NMRDummySpinlabelVoxelGridOP core::scoring::nmr::NMRDummySpinlabelEnsemble::get_voxel_grid ( )

inline

References grid_.

NMRDummySpinlabelVoxelGridCOP core::scoring::nmr::NMRDummySpinlabelEnsemble::get_voxel_grid ( ) const

inline

References grid_.

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

private

References elaborate_clash_check_.

Referenced by NMRDummySpinlabelEnsemble().

void core::scoring::nmr::NMRDummySpinlabelEnsemble::init_from_database_file	(	std::string const &	database_file,
		chemical::ResidueType const &	restype
	)