![]() |
Rosetta
2020.50
|
#include <UltraLightResidue.hh>
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_ |
core::conformation::UltraLightResidue::UltraLightResidue | ( | ResidueCOP | residue | ) |
References atom_ids_, center_, core::pose::center_of_mass(), coords_, heavy_coords_, residue(), and residue_.
|
private |
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().
|
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().
|
inline |
|
inline |
get const ref to residue heavy atom coords
References heavy_coords_.
core::Real core::conformation::UltraLightResidue::max_dist_to_center | ( | ) | 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().
|
inline |
References coords_.
|
inline |
References coords_.
|
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().
|
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().
|
private |
Referenced by UltraLightResidue(), and update_conformation().
|
private |
Referenced by align_to_residue(), center(), max_dist_to_center(), slide(), transform(), and UltraLightResidue().
|
private |
Referenced by align_to_residue(), coords_vector(), max_dist_to_center(), natoms(), operator[](), set_coords(), slide(), transform(), UltraLightResidue(), and update_conformation().
|
private |
Referenced by align_to_residue(), heavy_coords_vector(), slide(), transform(), and UltraLightResidue().
|
private |
Referenced by residue(), and UltraLightResidue().