Rosetta Protocols  2014.35
Classes | Typedefs | Functions | Variables
protocols::pockets Namespace Reference

Classes

class  CCluster
 @ Cluster of exemplar points More...
 
class  CClusterSet
 @ Set of clusters of exemplar points More...
 
class  ComparisonGrid
 @ More...
 
class  DarcElectrostaticsBase
 
class  DarcParticleSwarmMinimizer
 
class  DelphiElectrostatics
 
class  EggshellGrid
 @ More...
 
class  FingerprintBase
 
class  FingerprintMultifunc
 Atom tree multifunction class. More...
 
class  NonPlaidFingerprint
 
class  PCluster
 @ Cluster of Pocket points More...
 
class  PClusterSet
 @ Set of cluster of pocket points More...
 
class  PlaidFingerprint
 
class  PocketConstraint
 This constraint favors creating a pocket suitable for a small-molecule. More...
 
class  PocketConstraintCreator
 Mover creator for the PocketConstraint constraint. More...
 
class  PocketExemplarMultifunc
 Pocket multifunction class, does objective function of optimization. More...
 
class  PocketGrid
 @ More...
 
struct  ray_distance_derivs
 
struct  spherical_coor_triplet
 
class  TargetPocketGrid
 @ More...
 

Typedefs

typedef
utility::pointer::owning_ptr
< DelphiElectrostatics
DelphiElectrostaticsOP
 
typedef
utility::pointer::owning_ptr
< DelphiElectrostatics const > 
DelphiElectrostaticsCOP
 
typedef
utility::pointer::owning_ptr
< DarcParticleSwarmMinimizer
DarcParticleSwarmMinimizerOP
 
typedef
utility::pointer::owning_ptr
< DarcParticleSwarmMinimizer
const > 
DarcParticleSwarmMinimizerCOP
 
typedef
utility::pointer::owning_ptr
< NonPlaidFingerprint
NonPlaidFingerprintOP
 
typedef
utility::pointer::owning_ptr
< NonPlaidFingerprint const > 
NonPlaidFingerprintCOP
 
typedef
utility::pointer::owning_ptr
< PlaidFingerprint
PlaidFingerprintOP
 
typedef
utility::pointer::owning_ptr
< PlaidFingerprint const > 
PlaidFingerprintCOP
 
typedef
utility::pointer::owning_ptr
< PocketConstraint
PocketConstraintOP
 
typedef
utility::pointer::owning_ptr
< PocketGrid
PocketGridOP
 
typedef
utility::pointer::owning_ptr
< PocketGrid const > 
PocketGridCOP
 

Functions

double dD_dv1 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r)
 
double dD_dv2 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r)
 
double dD_dv3 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r)
 
double dD_dv4 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r, const double v4, const double v5, const double v6, const double, const double, const double yc, const double ys, const double zc, const double zs)
 
double dD_dv5 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r, const double v4, const double v5, const double v6, const double xc, const double xs, const double yc, const double ys, const double zc, const double zs)
 
double dD_dv6 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r, const double v4, const double v5, const double v6, const double xc, const double xs, const double yc, const double ys, const double zc, const double zs)
 
core::Real Find_Closest_Intersect_SQ (core::Real const &phiAngle, core::Real const &psiAngle, core::Real const &atomX, core::Real const &atomY, core::Real const &atomZ, core::Real const &atom_radius)
 
void convert_cartesian_to_spherical_coor_triplet (numeric::xyzVector< core::Real > const &coord, spherical_coor_triplet &triplet)
 
void convert_spherical_coor_triplet_to_cartesian (spherical_coor_triplet const &triplet, numeric::xyzVector< core::Real > &coord)
 

Variables

static basic::Tracer TR ("core.scoring.constraints.PocketConstraint")
 
static basic::Tracer TR ("core.grid.Pockets.PocketGrid", basic::t_debug)
 

Typedef Documentation

Function Documentation

void protocols::pockets::convert_cartesian_to_spherical_coor_triplet ( numeric::xyzVector< core::Real > const &  coord,
spherical_coor_triplet &  triplet 
)
inline
void protocols::pockets::convert_spherical_coor_triplet_to_cartesian ( spherical_coor_triplet const &  triplet,
numeric::xyzVector< core::Real > &  coord 
)
inline
double protocols::pockets::dD_dv1 ( const double  x0,
const double  x2,
const double  x3,
const double  y0,
const double  y2,
const double  y3,
const double  z0,
const double  z2,
const double  z3,
const double  r 
)

References protocols::match::upstream::b, and c.

Referenced by dD_dv4(), dD_dv5(), and dD_dv6().

double protocols::pockets::dD_dv2 ( const double  x0,
const double  x2,
const double  x3,
const double  y0,
const double  y2,
const double  y3,
const double  z0,
const double  z2,
const double  z3,
const double  r 
)

References protocols::match::upstream::b, and c.

Referenced by dD_dv4(), dD_dv5(), and dD_dv6().

double protocols::pockets::dD_dv3 ( const double  x0,
const double  x2,
const double  x3,
const double  y0,
const double  y2,
const double  y3,
const double  z0,
const double  z2,
const double  z3,
const double  r 
)

References protocols::match::upstream::b, and c.

Referenced by dD_dv4(), dD_dv5(), and dD_dv6().

double protocols::pockets::dD_dv4 ( const double  x0,
const double  x2,
const double  x3,
const double  y0,
const double  y2,
const double  y3,
const double  z0,
const double  z2,
const double  z3,
const double  r,
const double  v4,
const double  v5,
const double  v6,
const double  ,
const double  ,
const double  yc,
const double  ys,
const double  zc,
const double  zs 
)

References dD_dv1(), dD_dv2(), and dD_dv3().

double protocols::pockets::dD_dv5 ( const double  x0,
const double  x2,
const double  x3,
const double  y0,
const double  y2,
const double  y3,
const double  z0,
const double  z2,
const double  z3,
const double  r,
const double  v4,
const double  v5,
const double  v6,
const double  xc,
const double  xs,
const double  yc,
const double  ys,
const double  zc,
const double  zs 
)

References dD_dv1(), dD_dv2(), and dD_dv3().

double protocols::pockets::dD_dv6 ( const double  x0,
const double  x2,
const double  x3,
const double  y0,
const double  y2,
const double  y3,
const double  z0,
const double  z2,
const double  z3,
const double  r,
const double  v4,
const double  v5,
const double  v6,
const double  xc,
const double  xs,
const double  yc,
const double  ys,
const double  zc,
const double  zs 
)

References dD_dv1(), dD_dv2(), and dD_dv3().

core::Real protocols::pockets::Find_Closest_Intersect_SQ ( core::Real const &  phiAngle,
core::Real const &  psiAngle,
core::Real const &  atomX,
core::Real const &  atomY,
core::Real const &  atomZ,
core::Real const &  atom_radius 
)

Variable Documentation

basic::Tracer protocols::pockets::TR("core.grid.Pockets.PocketGrid", basic::t_debug)
static
basic::Tracer protocols::pockets::TR("core.scoring.constraints.PocketConstraint")
static