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