core::scoring::packing Namespace Reference

Classes
class	Ball
class	HolesEnergy
class	HolesEnergyCreator
class	HolesEnergyRes
class	HolesParams
class	HolesParamsRes
class	HolesResult
	the result class holding the three scores and the per-atom scores More...
class	PoseBalls
class	PoseBallsLite
class	SurfEnergy
class	SurfEnergyCreator
struct	SurfVol
struct	SurfVolDeriv
class	SurfVolEnergy
class	SurfVolEnergyCreator

Functions
void	compute_holes_surfs (PoseBalls &pb, std::string)
HolesResult	compute_rosettaholes_score (pose::Pose const &pose, PoseBalls &pb, HolesParams const &resl_params, HolesParams const &dec_params, HolesParams const &dec15_params, bool use_cached_surfs, std::string cmd)
Real	compute_dec15_score (pose::Pose const &pose)
HolesResult	compute_holes_score (pose::Pose const &pose, PoseBalls &pb, HolesParams const &params, bool use_cached_surfs, std::string cmd)
core::Real	sqr (core::Real x)
core::Real	sigmoidish_neighbor (core::Real sqdist)
core::Real	sigmoidish_neighbor_deriv (core::Real sqdist)
core::Real	compute_smooth_nb_deriv (PoseBalls &pb, HolesParams const &params, core::id::AtomID_Map< numeric::xyzVector< core::Real > > &deriv)
HolesResult	compute_holes_deriv (pose::Pose const &, PoseBalls &pb, HolesParams const &params, core::id::AtomID_Map< numeric::xyzVector< core::Real > > &deriv)
HolesResult	compute_rosettaholes_score (pose::Pose const &pose, PoseBalls &pb)
HolesResult	compute_holes_deriv (pose::Pose const &pose, HolesParams const &params, core::id::AtomID_Map< numeric::xyzVector< core::Real > > &deriv)
	computes the cartesian space derivative WRT the given params More...
HolesResult	compute_rosettaholes_score (pose::Pose const &pose, HolesParams const &resl_params, HolesParams const &dec_params, HolesParams const &dec15_params)
HolesResult	compute_rosettaholes_score (pose::Pose const &pose)
	for the standard scores More...
HolesResult	compute_holes_score (pose::Pose const &pose, HolesParams const &params)
HolesResult	compute_holes_score (pose::Pose const &pose, std::string const &cmd)
Real	compute_holes_score_res (pose::Pose const &pose, PoseBalls const &pb, HolesParamsRes const &params)
Real	compute_holes_deriv_res (pose::Pose const &pose, PoseBalls const &pb, HolesParamsRes const &params, core::id::AtomID_Map< numeric::xyzVector< core::Real > > &derivs)
Real	compute_holes_score_res (pose::Pose const &pose, HolesParamsRes const &params)
	wrappers More...
Real	compute_holes_deriv_res (pose::Pose const &pose, HolesParamsRes const &params, core::id::AtomID_Map< numeric::xyzVector< core::Real > > &derivs)
std::string	strip_whitespace (std::string const &name)
template<class T >
void	initialize_AtomID_Map (core::id::AtomID_Map< T > &map, PoseBalls const &pb)
template<class T >
void	initialize_AtomID_Map (core::id::AtomID_Map< T > &map, PoseBallsLite const &pb)
Real	get_surf_tot (pose::Pose const &pose, core::Real const probe_radius)
SurfVol	get_surf_vol (pose::Pose const &pose, core::Real const probe_radius)
SurfVol	get_surf_vol (pose::Pose const &pose, core::id::AtomID_Mask const &whichatoms, core::Real const probe_radius)
SurfVolDeriv	get_surf_vol_deriv (pose::Pose const &pose, core::Real const probe_radius)
SurfVolDeriv	get_surf_vol_deriv (pose::Pose const &pose, core::id::AtomID_Mask const &whichatoms, core::Real const probe_radius)

Variables
static basic::Tracer	TR ("core.scoring.packing.PoseBalls")
static basic::Tracer	TR ("core.scoring.packing.PoseBallsLite")

Function Documentation

Real core::scoring::packing::compute_dec15_score

(

pose::Pose const &

pose

)

References core::io::serialization::at(), core::scoring::packing::PoseBalls::atom_type(), compute_holes_surfs(), basic::options::OptionKeys::holes::dalphaball, basic::database::full_name(), core::scoring::packing::PoseBalls::nballs(), basic::options::option, core::scoring::packing::HolesParams::read_data_file(), core::scoring::packing::PoseBalls::secstruct(), core::scoring::packing::PoseBalls::smooth_nb(), ss, core::scoring::packing::PoseBalls::surf(), and TR.

HolesResult core::scoring::packing::compute_holes_deriv	(	pose::Pose const &	,
		PoseBalls &	pb,
		HolesParams const &	params,
		core::id::AtomID_Map< numeric::xyzVector< core::Real > > &	deriv
	)

References core::io::serialization::at(), core::scoring::packing::HolesResult::atom_scores, core::scoring::packing::PoseBalls::atom_type(), core::scoring::packing::PoseBalls::ball(), compute_smooth_nb_deriv(), core::scoring::packing::HolesParams::have_params(), core::scoring::packing::PoseBalls::index_to_id(), core::scoring::packing::HolesParams::intercept(), core::scoring::packing::HolesParams::nb_weight(), core::scoring::packing::PoseBalls::nballs(), basic::options::option, core::scoring::packing::HolesParams::sa_weight(), core::scoring::packing::HolesResult::score, core::scoring::packing::PoseBalls::secstruct(), core::id::AtomID_Map< T >::set(), core::scoring::packing::PoseBalls::smooth_nb(), ss, TR, and core::scoring::packing::Ball::x().

Referenced by compute_holes_deriv(), and core::scoring::packing::HolesEnergy::setup_for_derivatives().

HolesResult core::scoring::packing::compute_holes_deriv	(	pose::Pose const &	pose,
		HolesParams const &	params,
		core::id::AtomID_Map< numeric::xyzVector< core::Real > > &	deriv
	)

computes the cartesian space derivative WRT the given params

References compute_holes_deriv().

Real core::scoring::packing::compute_holes_deriv_res	(	pose::Pose const &	pose,
		PoseBalls const &	pb,
		HolesParamsRes const &	params,
		core::id::AtomID_Map< numeric::xyzVector< core::Real > > &	derivs
	)

References core::scoring::packing::PoseBalls::atom_num(), core::scoring::packing::PoseBalls::ball(), basic::DALPHABALL, basic::options::OptionKeys::holes::dalphaball, basic::DALPHABALL_DERIV, core::scoring::packing::HolesParamsRes::have_params(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::scoring::packing::PoseBalls::nballs(), basic::options::option, core::scoring::packing::HolesParamsRes::param(), PROF_START, PROF_STOP, core::scoring::packing::PoseBalls::res_name(), core::scoring::packing::PoseBalls::res_num(), core::pose::Pose::residue(), core::scoring::packing::HolesParamsRes::rho(), skip, core::pose::Pose::total_residue(), and core::scoring::packing::Ball::x().

Referenced by compute_holes_deriv_res(), and core::scoring::packing::HolesEnergyRes::setup_for_derivatives().

Real core::scoring::packing::compute_holes_deriv_res	(	pose::Pose const &	pose,
		HolesParamsRes const &	params,
		core::id::AtomID_Map< numeric::xyzVector< core::Real > > &	derivs
	)

References compute_holes_deriv_res().

HolesResult core::scoring::packing::compute_holes_score	(	pose::Pose const &	pose,
		PoseBalls &	pb,
		HolesParams const &	params,
		bool	use_cached_surfs,
		std::string	cmd
	)

References core::io::serialization::at(), core::scoring::packing::HolesResult::atom_scores, core::scoring::packing::PoseBalls::atom_type(), compute_holes_surfs(), basic::options::OptionKeys::holes::dalphaball, core::scoring::packing::PoseBalls::index_to_id(), core::pose::initialize_atomid_map(), core::scoring::packing::HolesParams::intercept(), core::scoring::packing::HolesParams::nb_weight(), core::scoring::packing::PoseBalls::nballs(), basic::options::option, core::scoring::packing::HolesParams::sa_weight(), core::scoring::packing::HolesResult::score, core::scoring::packing::PoseBalls::secstruct(), core::id::AtomID_Map< T >::set(), core::scoring::packing::PoseBalls::smooth_nb(), ss, core::scoring::packing::PoseBalls::surf(), and TR.

Referenced by compute_holes_score(), and core::scoring::packing::HolesEnergy::finalize_total_energy().

HolesResult core::scoring::packing::compute_holes_score	(	pose::Pose const &	pose,
		HolesParams const &	params
	)

if you have custom parameters, or want per-atom scores for a specific score result goes into the "score" field

References compute_holes_score().

HolesResult core::scoring::packing::compute_holes_score	(	pose::Pose const &	pose,
		std::string const &	cmd
	)

References compute_rosettaholes_score(), basic::database::full_name(), and core::scoring::packing::HolesParams::read_data_file().

Real core::scoring::packing::compute_holes_score_res	(	pose::Pose const &	pose,
		PoseBalls const &	pb,
		HolesParamsRes const &	params
	)

References core::scoring::packing::PoseBalls::atom_num(), core::scoring::packing::PoseBalls::ball(), basic::options::OptionKeys::holes::dalphaball, basic::DALPHABALL, numeric::xyzVector< class >::distance_squared(), core::scoring::packing::HolesParamsRes::have_params(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::scoring::packing::PoseBalls::nballs(), basic::options::option, core::scoring::packing::HolesParamsRes::param(), PROF_START, PROF_STOP, core::scoring::packing::PoseBalls::res_name(), core::scoring::packing::PoseBalls::res_num(), core::pose::Pose::residue(), core::scoring::packing::HolesParamsRes::rho(), skip, core::pose::Pose::total_residue(), utility_exit_with_message, core::scoring::packing::Ball::x(), and core::scoring::packing::Ball::xyz().

Referenced by compute_holes_score_res(), and core::scoring::packing::HolesEnergyRes::finalize_total_energy().

Real core::scoring::packing::compute_holes_score_res	(	pose::Pose const &	pose,
		HolesParamsRes const &	params
	)

wrappers

References compute_holes_score_res().

void core::scoring::packing::compute_holes_surfs	(	PoseBalls &	pb,
		std::string
	)

References core::scoring::packing::PoseBalls::ball(), utility::io::ozstream::close(), core::pack::interaction_graph::debug, getline(), core::scoring::packing::PoseBalls::nballs(), basic::options::option, option, out, core::scoring::packing::PoseBalls::reset_surf(), core::scoring::packing::PoseBalls::set_surf(), TR, utility_exit_with_message, and core::scoring::packing::Ball::x().

Referenced by compute_dec15_score(), compute_holes_score(), and compute_rosettaholes_score().

HolesResult core::scoring::packing::compute_rosettaholes_score	(	pose::Pose const &	pose,
		PoseBalls &	pb,
		HolesParams const &	resl_params,
		HolesParams const &	dec_params,
		HolesParams const &	dec15_params,
		bool	use_cached_surfs,
		std::string	cmd
	)

References core::io::serialization::at(), core::scoring::packing::HolesResult::atom_scores, core::scoring::packing::PoseBalls::atom_type(), compute_holes_surfs(), basic::options::OptionKeys::holes::dalphaball, core::scoring::packing::HolesResult::dec15_score, core::scoring::packing::HolesResult::decoy_score, core::scoring::packing::PoseBalls::index_to_id(), core::pose::initialize_atomid_map(), core::scoring::packing::HolesParams::intercept(), core::scoring::packing::HolesResult::natom, core::scoring::packing::HolesParams::nb_weight(), core::scoring::packing::PoseBalls::nballs(), basic::options::option, core::scoring::packing::HolesResult::resl_score, core::scoring::packing::HolesParams::sa_weight(), core::scoring::packing::HolesResult::score, core::scoring::packing::PoseBalls::secstruct(), core::id::AtomID_Map< T >::set(), core::scoring::packing::PoseBalls::smooth_nb(), ss, core::scoring::packing::PoseBalls::surf(), and TR.

Referenced by compute_holes_score(), and compute_rosettaholes_score().

HolesResult core::scoring::packing::compute_rosettaholes_score	(	pose::Pose const &	pose,
		PoseBalls &	pb
	)

References compute_rosettaholes_score(), basic::database::full_name(), and core::scoring::packing::HolesParams::read_data_file().

HolesResult core::scoring::packing::compute_rosettaholes_score	(	pose::Pose const &	pose,
		HolesParams const &	resl_params,
		HolesParams const &	dec_params,
		HolesParams const &	dec15_params
	)

References compute_rosettaholes_score().

HolesResult core::scoring::packing::compute_rosettaholes_score

(

pose::Pose const &

pose

)

for the standard scores

References compute_rosettaholes_score().

core::Real core::scoring::packing::compute_smooth_nb_deriv	(	PoseBalls &	pb,
		HolesParams const &	params,
		core::id::AtomID_Map< numeric::xyzVector< core::Real > > &	deriv
	)

References core::scoring::packing::PoseBalls::atom_type(), core::scoring::packing::PoseBalls::ball(), core::scoring::packing::HolesParams::have_params(), core::scoring::packing::PoseBalls::index_to_id(), core::scoring::packing::PoseBalls::is_heavy(), core::scoring::packing::HolesParams::nb_weight(), core::scoring::packing::PoseBalls::nballs(), numeric::xyzVector< class >::normalize(), core::scoring::packing::PoseBalls::secstruct(), sigmoidish_neighbor(), sigmoidish_neighbor_deriv(), ss1, ss2, w(), and core::scoring::packing::Ball::xyz().

Referenced by compute_holes_deriv().

Real core::scoring::packing::get_surf_tot	(	pose::Pose const &	pose,
		core::Real const	probe_radius
	)

References core::scoring::packing::PoseBallsLite::ball(), basic::options::OptionKeys::holes::dalphaball, basic::DALPHABALL, core::scoring::packing::PoseBallsLite::nballs(), basic::options::option, PROF_START, PROF_STOP, and core::scoring::packing::Ball::x().

Referenced by core::scoring::packing::SurfEnergy::finalize_total_energy().

SurfVol core::scoring::packing::get_surf_vol	(	pose::Pose const &	pose,
		core::Real const	probe_radius
	)

References core::pose::initialize_atomid_map_heavy_only().

Referenced by core::scoring::packing::SurfVolEnergy::finalize_total_energy().

SurfVol core::scoring::packing::get_surf_vol	(	pose::Pose const &	pose,
		core::id::AtomID_Mask const &	whichatoms,
		core::Real const	probe_radius
	)

References core::scoring::packing::PoseBallsLite::ball(), basic::options::OptionKeys::holes::dalphaball, basic::DALPHABALL, core::scoring::packing::PoseBallsLite::index_to_id(), core::scoring::packing::PoseBallsLite::nballs(), basic::options::option, PROF_START, PROF_STOP, s, and core::scoring::packing::Ball::x().

SurfVolDeriv core::scoring::packing::get_surf_vol_deriv	(	pose::Pose const &	pose,
		core::Real const	probe_radius
	)

References core::pose::initialize_atomid_map_heavy_only().

Referenced by core::scoring::packing::SurfVolEnergy::setup_for_derivatives(), and core::scoring::packing::SurfEnergy::setup_for_derivatives().

SurfVolDeriv core::scoring::packing::get_surf_vol_deriv	(	pose::Pose const &	pose,
		core::id::AtomID_Mask const &	whichatoms,
		core::Real const	probe_radius
	)

References core::scoring::packing::PoseBalls::ball(), basic::options::OptionKeys::holes::dalphaball, basic::DALPHABALL, core::scoring::packing::PoseBalls::index_to_id(), core::scoring::packing::PoseBalls::nballs(), basic::options::option, PROF_START, PROF_STOP, s, and core::scoring::packing::Ball::x().

template<class T >

void core::scoring::packing::initialize_AtomID_Map	(	core::id::AtomID_Map< T > &	map,
		PoseBallsLite const &	pb
	)

References core::scoring::packing::PoseBallsLite::atom_num(), core::id::AtomID_Map< T >::n_atom(), core::scoring::packing::PoseBallsLite::nballs(), core::scoring::packing::PoseBallsLite::res_num(), core::id::AtomID_Map< T >::resize(), and core::id::AtomID_Map< T >::size().

template<class T >

void core::scoring::packing::initialize_AtomID_Map	(	core::id::AtomID_Map< T > &	map,
		PoseBalls const &	pb
	)

References core::scoring::packing::PoseBalls::atom_num(), core::id::AtomID_Map< T >::n_atom(), core::scoring::packing::PoseBalls::nballs(), core::scoring::packing::PoseBalls::res_num(), core::id::AtomID_Map< T >::resize(), and core::id::AtomID_Map< T >::size().

core::Real core::scoring::packing::sigmoidish_neighbor ( core::Real  sqdist )

inline

References sqr().

Referenced by core::scoring::packing::PoseBalls::compute_smooth_nb(), and compute_smooth_nb_deriv().

core::Real core::scoring::packing::sigmoidish_neighbor_deriv ( core::Real  sqdist )

inline

Referenced by compute_smooth_nb_deriv().

core::Real core::scoring::packing::sqr ( core::Real  x )

inline

Referenced by sigmoidish_neighbor().

std::string core::scoring::packing::strip_whitespace ( std::string const &  name )

inline

Remove spaces from given string.

References trim().

Variable Documentation

basic::Tracer core::scoring::packing::TR("core.scoring.packing.PoseBallsLite")

static

basic::Tracer core::scoring::packing::TR("core.scoring.packing.PoseBalls")

static

Referenced by compute_dec15_score(), compute_holes_deriv(), compute_holes_score(), compute_holes_surfs(), and compute_rosettaholes_score().