core::scoring::packing Namespace Reference

Classes
class	Ball
class	HolesResult
	the result class holding the three scores and the per-atom scores More...
class	HolesEnergy
class	HolesEnergyCreator
class	HolesEnergyRes
class	HolesParams
class	HolesParamsRes
class	PoseBalls
class	PoseBallsLite
struct	SurfVol
struct	SurfVolDeriv
class	SurfEnergy
class	SurfEnergyCreator
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)
static basic::Tracer	TR ("core.scoring.packing.PoseBalls")
std::string	strip_whitespace (std::string const &name)
template<class T >
void	initialize_AtomID_Map (core::id::AtomID_Map< T > &map, PoseBalls const &pb)
static basic::Tracer	TR ("core.scoring.packing.PoseBallsLite")
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)
SurfVolDeriv	get_surf_vol_deriv (pose::Pose const &pose, core::Real const probe_radius)

Function Documentation

Real core::scoring::packing::compute_dec15_score

(

pose::Pose const &

pose)

Definition at line 173 of file compute_holes_score.cc.

References core::io::serialization::at(), core::scoring::packing::PoseBalls::atom_type(), compute_holes_surfs(), core::scoring::packing::PoseBalls::nballs(), core::scoring::packing::HolesParams::read_data_file(), core::scoring::packing::PoseBalls::secstruct(), core::scoring::packing::PoseBalls::smooth_nb(), 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
	)

Definition at line 308 of file compute_holes_score.cc.

References core::io::serialization::at(), core::scoring::packing::HolesResult::atom_scores, core::scoring::packing::PoseBalls::atom_type(), protocols::match::upstream::b, 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(), 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(), and TR().

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

Definition at line 453 of file compute_holes_score.cc.

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
	)

Definition at line 175 of file compute_holes_score_res.cc.

References core::scoring::packing::PoseBalls::atom_num(), protocols::match::upstream::b, core::scoring::packing::PoseBalls::ball(), core::scoring::packing::HolesParamsRes::have_params(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::scoring::packing::PoseBalls::nballs(), core::scoring::packing::HolesParamsRes::param(), core::scoring::packing::PoseBalls::res_name(), core::scoring::packing::PoseBalls::res_num(), core::pose::Pose::residue(), core::scoring::packing::HolesParamsRes::rho(), and core::pose::Pose::total_residue().

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
	)

Definition at line 283 of file compute_holes_score_res.cc.

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
	)

Definition at line 204 of file compute_holes_score.cc.

References core::io::serialization::at(), core::scoring::packing::HolesResult::atom_scores, core::scoring::packing::PoseBalls::atom_type(), compute_holes_surfs(), 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(), 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(), core::scoring::packing::PoseBalls::surf(), and TR().

Referenced by protocols::simple_filters::HolesFilter::compute(), 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

Definition at line 482 of file compute_holes_score.cc.

References compute_holes_score().

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

Definition at line 491 of file compute_holes_score.cc.

References compute_rosettaholes_score(), 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
	)

Definition at line 73 of file compute_holes_score_res.cc.

References core::scoring::packing::PoseBalls::atom_num(), protocols::match::upstream::b, core::scoring::packing::PoseBalls::ball(), core::scoring::packing::HolesParamsRes::have_params(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::scoring::packing::PoseBalls::nballs(), core::scoring::packing::HolesParamsRes::param(), core::scoring::packing::PoseBalls::res_name(), core::scoring::packing::PoseBalls::res_num(), core::pose::Pose::residue(), core::scoring::packing::HolesParamsRes::rho(), core::pose::Pose::total_residue(), 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

Definition at line 275 of file compute_holes_score_res.cc.

References compute_holes_score_res().

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

Definition at line 60 of file compute_holes_score.cc.

References protocols::match::upstream::b, core::scoring::packing::PoseBalls::ball(), core::scoring::packing::PoseBalls::nballs(), core::scoring::packing::PoseBalls::reset_surf(), core::scoring::packing::PoseBalls::set_surf(), and TR().

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
	)

Definition at line 120 of file compute_holes_score.cc.

References core::io::serialization::at(), core::scoring::packing::HolesResult::atom_scores, core::scoring::packing::PoseBalls::atom_type(), compute_holes_surfs(), 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(), 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(), 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
	)

Definition at line 440 of file compute_holes_score.cc.

References compute_rosettaholes_score(), 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
	)

Definition at line 463 of file compute_holes_score.cc.

References compute_rosettaholes_score().

HolesResult core::scoring::packing::compute_rosettaholes_score

(

pose::Pose const &

pose)

for the standard scores

Definition at line 474 of file compute_holes_score.cc.

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
	)

Definition at line 266 of file compute_holes_score.cc.

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(), core::scoring::packing::PoseBalls::secstruct(), sigmoidish_neighbor(), sigmoidish_neighbor_deriv(), 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
	)

Definition at line 66 of file surf_vol.cc.

References protocols::match::upstream::b, core::scoring::packing::PoseBallsLite::ball(), and core::scoring::packing::PoseBallsLite::nballs().

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
	)

Definition at line 115 of file surf_vol.cc.

References protocols::match::upstream::b, core::scoring::packing::PoseBallsLite::ball(), core::scoring::packing::PoseBallsLite::index_to_id(), and core::scoring::packing::PoseBallsLite::nballs().

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

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

Definition at line 169 of file surf_vol.cc.

References protocols::match::upstream::b, core::scoring::packing::PoseBalls::ball(), core::scoring::packing::PoseBalls::index_to_id(), and core::scoring::packing::PoseBalls::nballs().

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

template<class T >

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

Definition at line 91 of file PoseBallsLite.hh.

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
	)

Definition at line 160 of file PoseBalls.hh.

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

Definition at line 242 of file compute_holes_score.cc.

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

Definition at line 254 of file compute_holes_score.cc.

Referenced by compute_smooth_nb_deriv().

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

inline

Definition at line 237 of file compute_holes_score.cc.

Referenced by sigmoidish_neighbor().

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

inline

Remove spaces from given string.

Definition at line 63 of file PoseBalls.cc.

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

static

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().