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Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::scoring::electron_density_atomwise::ElectronDensityAtomwise Class Reference

#include <ElectronDensityAtomwise.hh>

Public Member Functions

 ElectronDensityAtomwise ()
 constructor More...
 
bool isMapLoaded ()
 Is a map loaded? More...
 
void readMRCandResize ()
 Load an MRC (="new-CCP4") density map. More...
 
void compute_normalization (pose::Pose const &pose)
 
void precompute_unweighted_score ()
 
void is_score_precomputed (bool const &setting)
 
core::Real residue_score (core::conformation::Residue const &rsd)
 
numeric::xyzVector< core::Realatom_gradient (core::pose::Pose const &pose, core::Size const &rsd_id, core::Size const &atm_id)
 

Private Member Functions

void computeCrystParams ()
 
void expandToUnitCell ()
 
void initializeSymmOps (utility::vector1< std::string > const &symList)
 
void resize (core::Real approxGridSpacing)
 
void calculate_index2cart ()
 
void generate_gaussian_1d (core::Real const &sigma)
 
core::Real gaussian_1d (core::Real const &dist)
 
core::Size get_atom_weight (std::string const &elt)
 
core::Real spline_interpolation (ObjexxFCL::FArray3D< core::Real > &coeffs, numeric::xyzVector< core::Real > const &idxX) const
 
void spline_coeffs (ObjexxFCL::FArray3D< core::Real > &data, ObjexxFCL::FArray3D< core::Real > &coeffs)
 
core::Real trilinear_interpolation (ObjexxFCL::FArray3D< core::Real > &score, numeric::xyzVector< core::Real > const &index)
 
numeric::xyzVector< core::Realtrilinear_gradient (ObjexxFCL::FArray3D< core::Real > &score, numeric::xyzVector< core::Real > const &index)
 
numeric::xyzVector< core::Realxyz2index_in_cell (numeric::xyzVector< core::Real > const &xyz_vector)
 
numeric::xyzVector< core::Realfrac2index (numeric::xyzVector< core::Real > const &frac_vector)
 
numeric::xyzVector< core::Realindex2frac (numeric::xyzVector< core::Real > const &frac_vector)
 
numeric::xyzVector< core::Realindex2frac (numeric::xyzVector< int > const &frac_vector)
 

Private Attributes

numeric::xyzMatrix< core::Realf2c
 
numeric::xyzMatrix< core::Realc2f
 
numeric::xyzMatrix< core::Reali2c
 
numeric::xyzMatrix< core::Realc2i
 
bool is_map_loaded_
 
bool is_score_precomputed_
 
core::Real map_reso_
 
core::Real cell_volume
 
core::Real r_cell_volume
 
core::Real max_del_grid
 
core::Real grid_spacing
 
core::Real gaussian_max_d
 
core::Real normalization
 
core::Real avg_rho_obs
 
utility::vector1< core::Realatom_gaussian_value
 
ObjexxFCL::FArray3D< float > density
 
ObjexxFCL::FArray3D< core::Realunweighted_score_coeff
 
utility::vector1
< utility::vector1< core::Size > > 
atom_weight_stored
 
numeric::xyzVector< int > grid
 
numeric::xyzVector< core::Realorig
 
numeric::xyzVector< float > cell_angles
 
numeric::xyzVector< float > cell_dimensions
 
numeric::xyzVector< float > r_cell_angles
 
numeric::xyzVector< float > cos_r_cell_angles
 
numeric::xyzVector< float > r_cell_dimensions
 
utility::vector1
< core::kinematics::RT
symmOps
 

Constructor & Destructor Documentation

core::scoring::electron_density_atomwise::ElectronDensityAtomwise::ElectronDensityAtomwise ( )

constructor

null constructor

Member Function Documentation

numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_gradient ( core::pose::Pose const &  pose,
core::Size const &  rsd_id,
core::Size const &  atm_id 
)
void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::calculate_index2cart ( )
private
void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization ( pose::Pose const &  pose)
void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::computeCrystParams ( )
private
void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::expandToUnitCell ( )
private
numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::frac2index ( numeric::xyzVector< core::Real > const &  frac_vector)
private
core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::gaussian_1d ( core::Real const &  dist)
private
void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::generate_gaussian_1d ( core::Real const &  sigma)
private

References PI.

core::Size core::scoring::electron_density_atomwise::ElectronDensityAtomwise::get_atom_weight ( std::string const &  elt)
private
numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::index2frac ( numeric::xyzVector< core::Real > const &  frac_vector)
private
numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::index2frac ( numeric::xyzVector< int > const &  frac_vector)
private
void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::initializeSymmOps ( utility::vector1< std::string > const &  symList)
private
void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::is_score_precomputed ( bool const &  setting)
inline
bool core::scoring::electron_density_atomwise::ElectronDensityAtomwise::isMapLoaded ( )
inline
void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::precompute_unweighted_score ( )
void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::readMRCandResize ( )
core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score ( core::conformation::Residue const &  rsd)
void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::resize ( core::Real  approxGridSpacing)
private
void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::spline_coeffs ( ObjexxFCL::FArray3D< core::Real > &  data,
ObjexxFCL::FArray3D< core::Real > &  coeffs 
)
private
core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::spline_interpolation ( ObjexxFCL::FArray3D< core::Real > &  coeffs,
numeric::xyzVector< core::Real > const &  idxX 
) const
private
numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::trilinear_gradient ( ObjexxFCL::FArray3D< core::Real > &  score,
numeric::xyzVector< core::Real > const &  index 
)
private
core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::trilinear_interpolation ( ObjexxFCL::FArray3D< core::Real > &  score,
numeric::xyzVector< core::Real > const &  index 
)
private
numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::xyz2index_in_cell ( numeric::xyzVector< core::Real > const &  xyz_vector)
private

Member Data Documentation

utility::vector1< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_gaussian_value
private
utility::vector1< utility::vector1 < core::Size > > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_weight_stored
private
core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::avg_rho_obs
private
numeric::xyzMatrix<core::Real> core::scoring::electron_density_atomwise::ElectronDensityAtomwise::c2f
private
numeric::xyzMatrix<core::Real> core::scoring::electron_density_atomwise::ElectronDensityAtomwise::c2i
private
numeric::xyzVector< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::cell_angles
private
numeric::xyzVector< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::cell_dimensions
private
core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::cell_volume
private
numeric::xyzVector< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::cos_r_cell_angles
private
ObjexxFCL::FArray3D< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::density
private
numeric::xyzMatrix<core::Real> core::scoring::electron_density_atomwise::ElectronDensityAtomwise::f2c
private
core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::gaussian_max_d
private
numeric::xyzVector< int > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::grid
private
core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::grid_spacing
private
numeric::xyzMatrix<core::Real> core::scoring::electron_density_atomwise::ElectronDensityAtomwise::i2c
private
bool core::scoring::electron_density_atomwise::ElectronDensityAtomwise::is_map_loaded_
private

Referenced by isMapLoaded().

bool core::scoring::electron_density_atomwise::ElectronDensityAtomwise::is_score_precomputed_
private

Referenced by is_score_precomputed().

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::map_reso_
private
core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::max_del_grid
private
core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::normalization
private
numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::orig
private
numeric::xyzVector< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::r_cell_angles
private
numeric::xyzVector< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::r_cell_dimensions
private
core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::r_cell_volume
private
utility::vector1< core::kinematics::RT > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::symmOps
private
ObjexxFCL::FArray3D< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::unweighted_score_coeff
private

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