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 ()
core::Real	residue_score (core::conformation::Residue const &rsd)
numeric::xyzVector< core::Real >	atom_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< double > &coeffs, numeric::xyzVector< core::Real > const &idxX) const
void	spline_coeffs (ObjexxFCL::FArray3D< double > &data, ObjexxFCL::FArray3D< double > &coeffs)
core::Real	trilinear_interpolation (ObjexxFCL::FArray3D< double > &score, numeric::xyzVector< core::Real > const &index)
numeric::xyzVector< core::Real >	trilinear_gradient (ObjexxFCL::FArray3D< double > &score, numeric::xyzVector< core::Real > const &index)
numeric::xyzVector< core::Real >	xyz2index_in_cell (numeric::xyzVector< core::Real > const &xyz_vector)
numeric::xyzVector< core::Real >	frac2index (numeric::xyzVector< core::Real > const &frac_vector)
numeric::xyzVector< core::Real >	index2frac (numeric::xyzVector< core::Real > const &frac_vector)
numeric::xyzVector< core::Real >	index2frac (numeric::xyzVector< int > const &frac_vector)

Private Attributes
numeric::xyzMatrix< core::Real >	f2c
numeric::xyzMatrix< core::Real >	c2f
numeric::xyzMatrix< core::Real >	i2c
numeric::xyzMatrix< core::Real >	c2i
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::Real >	atom_gaussian_value
ObjexxFCL::FArray3D< float >	density
ObjexxFCL::FArray3D< double >	unweighted_score_coeff
utility::vector1 < utility::vector1< core::Size > >	atom_weight_stored
numeric::xyzVector< int >	grid
numeric::xyzVector< core::Real >	orig
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

References grid.

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
	)

References core::conformation::Residue::is_virtual(), core::pose::Pose::residue(), numeric::xyzMatrix< class >::transpose(), weight, and core::conformation::Residue::xyz().

Referenced by core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::eval_atom_derivative().

void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::calculate_index2cart ( )

private

References grid, and numeric::xyzMatrix< class >::rows().

void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization

(

pose::Pose const &

pose

)

References core::chemical::aa_vrt, density, grid, numeric::xyzVector< class >::length(), basic::options::OptionKeys::edensity::mapreso, core::conformation::Residue::nheavyatoms(), basic::options::option, core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::electron_density_atomwise::TR, and weight.

Referenced by core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::setup_for_scoring().

void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::computeCrystParams ( )

private

References core::id::D, core::scoring::electron_density_atomwise::d2r(), numeric::xyzMatrix< class >::rows(), core::scoring::sa, core::scoring::electron_density_atomwise::square(), and core::scoring::electron_density_atomwise::TR.

void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::expandToUnitCell ( )

private

References density, grid, and core::scoring::electron_density_atomwise::pos_mod().

numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::frac2index ( numeric::xyzVector< core::Real > const &  frac_vector )

private

References grid.

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 numeric::constants::f::pi, and PI.

core::Size core::scoring::electron_density_atomwise::ElectronDensityAtomwise::get_atom_weight ( std::string const &  elt )

private

References core::scoring::electron_density_atomwise::TR.

numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::index2frac ( numeric::xyzVector< core::Real > const &  frac_vector )

private

References grid.

numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::index2frac ( numeric::xyzVector< int > const &  frac_vector )

private

References grid.

void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::initializeSymmOps ( utility::vector1< std::string > const &  symList )

private

References utility::string_split(), and core::scoring::electron_density_atomwise::TR.

bool core::scoring::electron_density_atomwise::ElectronDensityAtomwise::isMapLoaded ( )

inline

Is a map loaded?

References is_map_loaded.

Referenced by core::scoring::electron_density_atomwise::get_density_map().

void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::precompute_unweighted_score

(

)

References density, numeric::fourier::fft3_dynamic(), grid, numeric::fourier::ifft3_dynamic(), numeric::xyzVector< class >::length(), and core::scoring::electron_density::spline_coeffs().

Referenced by core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::setup_for_scoring().

void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::readMRCandResize

(

)

Load an MRC (="new-CCP4") density map.

References core::scoring::electron_density_atomwise::CCP4HDSIZE, density, core::sequence::end, grid, grid_spacing, basic::options::OptionKeys::edensity::grid_spacing, basic::options::OptionKeys::edensity::mapfile, basic::options::OptionKeys::edensity::mapreso, mode, basic::options::option, core::id::swap(), core::scoring::electron_density_atomwise::swap4_aligned(), core::scoring::electron_density_atomwise::TR, user, and utility_exit_with_message.

Referenced by core::scoring::electron_density_atomwise::get_density_map().

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score

(

core::conformation::Residue const &

rsd

)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), score, core::conformation::Residue::seqpos(), core::scoring::total_score, weight, and core::conformation::Residue::xyz().

Referenced by core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::residue_pair_energy().

void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::resize ( core::Real  approxGridSpacing )

private

References density, exit, numeric::fourier::fft3(), grid, numeric::fourier::ifft3(), and core::scoring::electron_density_atomwise::TR.

void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::spline_coeffs ( ObjexxFCL::FArray3D< double > &  data, ObjexxFCL::FArray3D< double > &  coeffs  )

private

References core::scoring::electron_density::SplineInterp::compute_coefficients3().

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::spline_interpolation ( ObjexxFCL::FArray3D< double > &  coeffs, numeric::xyzVector< core::Real > const &  idxX  ) const

private

References core::scoring::electron_density::SplineInterp::interp3().

numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::trilinear_gradient ( ObjexxFCL::FArray3D< double > &  score, numeric::xyzVector< core::Real > const &  index  )

private

References grid.

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::trilinear_interpolation ( ObjexxFCL::FArray3D< double > &  score, numeric::xyzVector< core::Real > const &  index  )

private

References grid.

numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::xyz2index_in_cell ( numeric::xyzVector< core::Real > const &  xyz_vector )

private

References grid, and core::scoring::electron_density_atomwise::pos_mod().

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

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< double > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::unweighted_score_coeff

private

---

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

• src/core/scoring/electron_density_atomwise/ElectronDensityAtomwise.hh
• src/core/scoring/electron_density_atomwise/ElectronDensityAtomwise.cc