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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)
 
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)
 
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)
 

Function Documentation

Real core::scoring::packing::compute_dec15_score ( pose::Pose const &  pose)
HolesResult core::scoring::packing::compute_holes_deriv ( pose::Pose const &  ,
PoseBalls &  pb,
HolesParams const &  params,
core::id::AtomID_Map< numeric::xyzVector< core::Real > > &  deriv 
)
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 
)
Real core::scoring::packing::compute_holes_deriv_res ( pose::Pose const &  pose,
HolesParamsRes const &  params,
core::id::AtomID_Map< numeric::xyzVector< core::Real > > &  derivs 
)
HolesResult core::scoring::packing::compute_holes_score ( pose::Pose const &  pose,
PoseBalls &  pb,
HolesParams const &  params,
bool  use_cached_surfs,
std::string  cmd 
)
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 
)
Real core::scoring::packing::compute_holes_score_res ( pose::Pose const &  pose,
PoseBalls const &  pb,
HolesParamsRes const &  params 
)
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   
)
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 
)
HolesResult core::scoring::packing::compute_rosettaholes_score ( pose::Pose const &  pose,
PoseBalls &  pb 
)
HolesResult core::scoring::packing::compute_rosettaholes_score ( pose::Pose const &  pose,
HolesParams const &  resl_params,
HolesParams const &  dec_params,
HolesParams const &  dec15_params 
)
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 
)
Real core::scoring::packing::get_surf_tot ( pose::Pose const &  pose,
core::Real const  probe_radius 
)
SurfVol core::scoring::packing::get_surf_vol ( pose::Pose const &  pose,
core::Real const  probe_radius 
)
SurfVol core::scoring::packing::get_surf_vol ( pose::Pose const &  pose,
core::id::AtomID_Mask const &  whichatoms,
core::Real const  probe_radius 
)
SurfVolDeriv core::scoring::packing::get_surf_vol_deriv ( pose::Pose const &  pose,
core::Real const  probe_radius 
)
SurfVolDeriv core::scoring::packing::get_surf_vol_deriv ( pose::Pose const &  pose,
core::id::AtomID_Mask const &  whichatoms,
core::Real const  probe_radius 
)
template<class T >
void core::scoring::packing::initialize_AtomID_Map ( core::id::AtomID_Map< T > &  map,
PoseBallsLite const &  pb 
)
template<class T >
void core::scoring::packing::initialize_AtomID_Map ( core::id::AtomID_Map< T > &  map,
PoseBalls const &  pb 
)
core::Real core::scoring::packing::sigmoidish_neighbor ( core::Real  sqdist)
inline
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.

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