#include <ElectronDensityAtomwise.hh>

Collaboration diagram for core::scoring::electron_density_atomwise::ElectronDensityAtomwise:

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

Detailed Description

Definition at line 47 of file ElectronDensityAtomwise.hh.

Constructor & Destructor Documentation

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

constructor

null constructor

Definition at line 83 of file ElectronDensityAtomwise.cc.

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
	)

Definition at line 1132 of file ElectronDensityAtomwise.cc.

References core::conformation::Residue::is_virtual(), core::pose::Pose::residue(), 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

Definition at line 660 of file ElectronDensityAtomwise.cc.

void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization ( pose::Pose const & pose)

Definition at line 872 of file ElectronDensityAtomwise.cc.

References core::chemical::aa_vrt, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::scoring::electron_density_atomwise::TR().

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

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

private

Definition at line 149 of file ElectronDensityAtomwise.cc.

References core::id::D, core::scoring::electron_density_atomwise::d2r(), 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

Definition at line 258 of file ElectronDensityAtomwise.cc.

References 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

Definition at line 676 of file ElectronDensityAtomwise.cc.

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::gaussian_1d ( core::Real const & dist)

private

Definition at line 731 of file ElectronDensityAtomwise.cc.

void core::scoring::electron_density_atomwise::ElectronDensityAtomwise::generate_gaussian_1d ( core::Real const & sigma)

private

Definition at line 716 of file ElectronDensityAtomwise.cc.

References PI.

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

private

Definition at line 739 of file ElectronDensityAtomwise.cc.

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

Definition at line 686 of file ElectronDensityAtomwise.cc.

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

private

Definition at line 694 of file ElectronDensityAtomwise.cc.

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

private

Definition at line 189 of file ElectronDensityAtomwise.cc.

References rot(), core::scoring::electron_density_atomwise::TR(), and trans().

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

inline

Is a map loaded?

Definition at line 53 of file ElectronDensityAtomwise.hh.

References is_map_loaded.

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

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

Definition at line 1008 of file ElectronDensityAtomwise.cc.

References 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.

Definition at line 408 of file ElectronDensityAtomwise.cc.

References core::scoring::electron_density_atomwise::CCP4HDSIZE, core::sequence::end, core::id::swap(), core::scoring::electron_density_atomwise::swap4_aligned(), and core::scoring::electron_density_atomwise::TR().

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)

Definition at line 1108 of file ElectronDensityAtomwise.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::conformation::Residue::seqpos(), core::scoring::total_score, 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

Definition at line 310 of file ElectronDensityAtomwise.cc.

References core::scoring::electron_density_atomwise::TR().

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

private

Definition at line 863 of file ElectronDensityAtomwise.cc.

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

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

private

Definition at line 853 of file ElectronDensityAtomwise.cc.

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

Definition at line 797 of file ElectronDensityAtomwise.cc.

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

private

Definition at line 759 of file ElectronDensityAtomwise.cc.

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

private

Definition at line 704 of file ElectronDensityAtomwise.cc.

References core::scoring::electron_density_atomwise::pos_mod().

Member Data Documentation

utility::vector1< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_gaussian_value

private

Definition at line 83 of file ElectronDensityAtomwise.hh.

utility::vector1< utility::vector1 < core::Size > > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_weight_stored

private

Definition at line 89 of file ElectronDensityAtomwise.hh.

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::avg_rho_obs

private

Definition at line 80 of file ElectronDensityAtomwise.hh.

numeric::xyzMatrix<core::Real> core::scoring::electron_density_atomwise::ElectronDensityAtomwise::c2f

private

Definition at line 76 of file ElectronDensityAtomwise.hh.

numeric::xyzMatrix<core::Real> core::scoring::electron_density_atomwise::ElectronDensityAtomwise::c2i

private

Definition at line 76 of file ElectronDensityAtomwise.hh.

numeric::xyzVector< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::cell_angles

private

Definition at line 94 of file ElectronDensityAtomwise.hh.

numeric::xyzVector< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::cell_dimensions

private

Definition at line 94 of file ElectronDensityAtomwise.hh.

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::cell_volume

private

Definition at line 80 of file ElectronDensityAtomwise.hh.

numeric::xyzVector< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::cos_r_cell_angles

private

Definition at line 94 of file ElectronDensityAtomwise.hh.

ObjexxFCL::FArray3D< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::density

private

Definition at line 86 of file ElectronDensityAtomwise.hh.

numeric::xyzMatrix<core::Real> core::scoring::electron_density_atomwise::ElectronDensityAtomwise::f2c

private

Definition at line 76 of file ElectronDensityAtomwise.hh.

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::gaussian_max_d

private

Definition at line 80 of file ElectronDensityAtomwise.hh.

numeric::xyzVector< int > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::grid

private

Definition at line 92 of file ElectronDensityAtomwise.hh.

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::grid_spacing

private

Definition at line 80 of file ElectronDensityAtomwise.hh.

numeric::xyzMatrix<core::Real> core::scoring::electron_density_atomwise::ElectronDensityAtomwise::i2c

private

Definition at line 76 of file ElectronDensityAtomwise.hh.

bool core::scoring::electron_density_atomwise::ElectronDensityAtomwise::is_map_loaded

private

Definition at line 78 of file ElectronDensityAtomwise.hh.

Referenced by isMapLoaded().

bool core::scoring::electron_density_atomwise::ElectronDensityAtomwise::is_score_precomputed

private

Definition at line 78 of file ElectronDensityAtomwise.hh.

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::map_reso

private

Definition at line 80 of file ElectronDensityAtomwise.hh.

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::max_del_grid

private

Definition at line 80 of file ElectronDensityAtomwise.hh.

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::normalization

private

Definition at line 80 of file ElectronDensityAtomwise.hh.

numeric::xyzVector< core::Real > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::orig

private

Definition at line 93 of file ElectronDensityAtomwise.hh.

numeric::xyzVector< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::r_cell_angles

private

Definition at line 94 of file ElectronDensityAtomwise.hh.

numeric::xyzVector< float > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::r_cell_dimensions

private

Definition at line 94 of file ElectronDensityAtomwise.hh.

core::Real core::scoring::electron_density_atomwise::ElectronDensityAtomwise::r_cell_volume

private

Definition at line 80 of file ElectronDensityAtomwise.hh.

utility::vector1< core::kinematics::RT > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::symmOps

private

Definition at line 97 of file ElectronDensityAtomwise.hh.

ObjexxFCL::FArray3D< double > core::scoring::electron_density_atomwise::ElectronDensityAtomwise::unweighted_score_coeff

private

Definition at line 87 of file ElectronDensityAtomwise.hh.

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

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation