core::conformation::UltraLightResidue Class Reference

#include <UltraLightResidue.hh>

Inheritance diagram for core::conformation::UltraLightResidue:

Public Member Functions
	UltraLightResidue (ResidueCOP residue)
void	update_conformation (Conformation &conformation) const
	update conformation with current coords. Slow. More...
void	transform (numeric::xyzMatrix< core::Real > const &rotation_matrix, core::Vector const &translation_vector)
void	transform (numeric::xyzMatrix< core::Real > const &rotation_matrix, core::Vector const &translation_vector, core::Vector group_center)
void	align_to_residue (UltraLightResidue const &other_residue)
void	slide (core::Vector const &translation_vector)
PointPosition &	operator[] (core::Size index)
PointPosition const &	operator[] (core::Size index) const
ResidueCOP	residue () const
	return a constant pointer to the base residue More...
core::Size	natoms () const
	return number of atoms in ultralight residue More...
PointPosition	center () const
	get centerpoint of residue More...
core::Real	max_dist_to_center () const
	Return the maximum distance from any atom to the center. More...
void	set_coords (utility::vector1< PointPosition > const &input_coords)
	get const ref to residue coords More...
utility::vector1 < PointPosition > const &	coords_vector () const
	get const ref to residue coords More...
utility::vector1 < PointPosition > const &	heavy_coords_vector () const
	get const ref to residue heavy atom coords More...

Private Member Functions
	UltraLightResidue ()

Private Attributes
utility::vector1< id::AtomID >	atom_ids_
utility::vector1< PointPosition >	coords_
utility::vector1< PointPosition >	heavy_coords_
ResidueCOP	residue_
PointPosition	center_

Constructor & Destructor Documentation

core::conformation::UltraLightResidue::UltraLightResidue

(

ResidueCOP

residue

)

References atom_ids_, center_, core::pose::center_of_mass(), coords_, heavy_coords_, residue(), and residue_.

core::conformation::UltraLightResidue::UltraLightResidue ( )

private

Member Function Documentation

void core::conformation::UltraLightResidue::align_to_residue

(

UltraLightResidue const &

other_residue

)

References core::simple_metrics::metrics::bogus, center(), center_, core::pose::center_of_mass(), protocols::simple_filters::coords(), coords_, coords_vector(), and heavy_coords_.

Referenced by protocols::ligand_docking::TransformEnsemble::change_conformer(), protocols::ligand_docking::Transform::change_conformer(), and protocols::ligand_docking::Transform::check_conformers().

PointPosition core::conformation::UltraLightResidue::center ( ) const

inline

get centerpoint of residue

References center_.

Referenced by align_to_residue(), protocols::ligand_docking::Transform::randomize_ligand(), and protocols::ligand_docking::Transform::transform_ligand().

utility::vector1<PointPosition> const& core::conformation::UltraLightResidue::coords_vector ( ) const

inline

get const ref to residue coords

References coords_.

Referenced by align_to_residue().

utility::vector1<PointPosition> const& core::conformation::UltraLightResidue::heavy_coords_vector ( ) const

inline

get const ref to residue heavy atom coords

References heavy_coords_.

core::Real core::conformation::UltraLightResidue::max_dist_to_center

(

)

const

Return the maximum distance from any atom to the center.

References center_, and coords_.

core::Size core::conformation::UltraLightResidue::natoms ( ) const

inline

return number of atoms in ultralight residue

References coords_.

Referenced by protocols::ligand_docking::Transform::check_rmsd(), protocols::ligand_docking::TransformEnsemble::dump_conformer(), protocols::ligand_docking::Transform::dump_conformer(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::qsar::scoring_grid::SolvationMetaGrid::score(), protocols::qsar::scoring_grid::ShapeGrid::score(), protocols::qsar::scoring_grid::ChargeGrid::score(), and protocols::qsar::scoring_grid::SingleGrid::score().

PointPosition& core::conformation::UltraLightResidue::operator[] ( core::Size  index )

inline

References coords_.

PointPosition const& core::conformation::UltraLightResidue::operator[] ( core::Size  index ) const

inline

References coords_.

ResidueCOP core::conformation::UltraLightResidue::residue ( ) const

inline

return a constant pointer to the base residue

References residue_.

Referenced by protocols::qsar::scoring_grid::HbaGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::atom_score(), protocols::qsar::scoring_grid::VdwGrid::atom_score(), protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score(), protocols::qsar::scoring_grid::ChargeGrid::atom_score(), protocols::qsar::scoring_grid::PCSSingleGrid::atom_score(), protocols::qsar::scoring_grid::LigandPropertyScore::score(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::qsar::scoring_grid::SolvationMetaGrid::score(), protocols::qsar::scoring_grid::ChargeGrid::score(), protocols::qsar::scoring_grid::PCSSingleGrid::score(), and UltraLightResidue().

void core::conformation::UltraLightResidue::set_coords ( utility::vector1< PointPosition > const &  input_coords )

inline

get const ref to residue coords

References coords_.

void core::conformation::UltraLightResidue::slide

(

core::Vector const &

translation_vector

)

References center_, core::pose::center_of_mass(), coords_, heavy_coords_, and rot().

void core::conformation::UltraLightResidue::transform	(	numeric::xyzMatrix< core::Real > const &	rotation_matrix,
		core::Vector const &	translation_vector
	)

References center_, core::pose::center_of_mass(), coords_, heavy_coords_, and rot().

Referenced by protocols::ligand_docking::Transform::randomize_ligand(), and protocols::ligand_docking::Transform::transform_ligand().

void core::conformation::UltraLightResidue::transform	(	numeric::xyzMatrix< core::Real > const &	rotation_matrix,
		core::Vector const &	translation_vector,
		core::Vector	group_center
	)

References center_, core::pose::center_of_mass(), coords_, heavy_coords_, and rot().

void core::conformation::UltraLightResidue::update_conformation

(

Conformation &

conformation

)

const

update conformation with current coords. Slow.

References atom_ids_, core::conformation::Conformation::batch_set_xyz(), and coords_.

Referenced by protocols::ligand_docking::Transform::convert_to_full_pose(), and protocols::ligand_docking::Transform::score_constraints().

Member Data Documentation

utility::vector1<id::AtomID> core::conformation::UltraLightResidue::atom_ids_

private

Referenced by UltraLightResidue(), and update_conformation().

PointPosition core::conformation::UltraLightResidue::center_

private

Referenced by align_to_residue(), center(), max_dist_to_center(), slide(), transform(), and UltraLightResidue().

utility::vector1<PointPosition > core::conformation::UltraLightResidue::coords_

private

Referenced by align_to_residue(), coords_vector(), max_dist_to_center(), natoms(), operator[](), set_coords(), slide(), transform(), UltraLightResidue(), and update_conformation().

utility::vector1<PointPosition > core::conformation::UltraLightResidue::heavy_coords_

private

Referenced by align_to_residue(), heavy_coords_vector(), slide(), transform(), and UltraLightResidue().

ResidueCOP core::conformation::UltraLightResidue::residue_

private

Referenced by residue(), and UltraLightResidue().

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

• src/core/conformation/UltraLightResidue.hh
• src/core/conformation/UltraLightResidue.cc