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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  DarcParticleSwarmMinimizer
 
class  EggshellGrid
 @ More...
 
class  ElectrostaticpotentialGrid
 
class  FingerprintBase
 
class  FingerprintMultifunc
 Atom tree multifunction class. More...
 
class  GenPharmacophore
 
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
 
class  SmallMol
 
struct  spherical_coor_triplet
 
class  TargetPocketGrid
 @ More...
 
struct  triplet_and_originnum
 
class  UnionEdge
 

Typedefs

typedef
utility::pointer::shared_ptr
< DarcParticleSwarmMinimizer
DarcParticleSwarmMinimizerOP
 
typedef
utility::pointer::shared_ptr
< DarcParticleSwarmMinimizer
const > 
DarcParticleSwarmMinimizerCOP
 
typedef
utility::pointer::shared_ptr
< NonPlaidFingerprint
NonPlaidFingerprintOP
 
typedef
utility::pointer::shared_ptr
< NonPlaidFingerprint const > 
NonPlaidFingerprintCOP
 
typedef
utility::pointer::shared_ptr
< PlaidFingerprint
PlaidFingerprintOP
 
typedef
utility::pointer::shared_ptr
< PlaidFingerprint const > 
PlaidFingerprintCOP
 
typedef
utility::pointer::shared_ptr
< FingerprintManager > 
FingerprintManagerOP
 
typedef
utility::pointer::shared_ptr
< FingerprintManager const > 
FingerprintManagerCOP
 
typedef
utility::pointer::shared_ptr
< PocketConstraint
PocketConstraintOP
 
typedef
utility::pointer::shared_ptr
< PocketGrid
PocketGridOP
 
typedef
utility::pointer::shared_ptr
< PocketGrid const > 
PocketGridCOP
 

Functions

core::Real dD_dv1 (const core::Real x0, const core::Real x2, const core::Real x3, const core::Real y0, const core::Real y2, const core::Real y3, const core::Real z0, const core::Real z2, const core::Real z3, const core::Real r)
 
core::Real dD_dv2 (const core::Real x0, const core::Real x2, const core::Real x3, const core::Real y0, const core::Real y2, const core::Real y3, const core::Real z0, const core::Real z2, const core::Real z3, const core::Real r)
 
core::Real dD_dv3 (const core::Real x0, const core::Real x2, const core::Real x3, const core::Real y0, const core::Real y2, const core::Real y3, const core::Real z0, const core::Real z2, const core::Real z3, const core::Real r)
 
core::Real dD_dv4 (const core::Real x0, const core::Real x2, const core::Real x3, const core::Real y0, const core::Real y2, const core::Real y3, const core::Real z0, const core::Real z2, const core::Real z3, const core::Real r, const core::Real v4, const core::Real v5, const core::Real v6, const core::Real, const core::Real, const core::Real yc, const core::Real ys, const core::Real zc, const core::Real zs)
 
core::Real dD_dv5 (const core::Real x0, const core::Real x2, const core::Real x3, const core::Real y0, const core::Real y2, const core::Real y3, const core::Real z0, const core::Real z2, const core::Real z3, const core::Real r, const core::Real v4, const core::Real v5, const core::Real v6, const core::Real xc, const core::Real xs, const core::Real yc, const core::Real ys, const core::Real zc, const core::Real zs)
 
core::Real dD_dv6 (const core::Real x0, const core::Real x2, const core::Real x3, const core::Real y0, const core::Real y2, const core::Real y3, const core::Real z0, const core::Real z2, const core::Real z3, const core::Real r, const core::Real v4, const core::Real v5, const core::Real v6, const core::Real xc, const core::Real xs, const core::Real yc, const core::Real ys, const core::Real zc, const core::Real 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)
 
void convert_cartesian_to_grid (numeric::xyzVector< core::Real > const &cart_coord, numeric::xyzVector< core::Real > const &mid, numeric::xyzVector< core::Real > const &dim, core::Real const &spacing, numeric::xyzVector< core::Real > &grid_coord)
 
void convert_grid_to_cartesian (numeric::xyzVector< core::Real > const &grid_coord, numeric::xyzVector< core::Real > const &mid, numeric::xyzVector< core::Real > const &dim, core::Real const &spacing, numeric::xyzVector< core::Real > &cart_coord)
 
core::Real calDist (vector< core::Real > const &a1, vector< core::Real > const &a2)
 
static basic::Tracer TR ("core.scoring.constraints.PocketConstraint")
 
static basic::Tracer TR ("core.grid.Pockets.PocketGrid")
 
void convert_cartesian_to_grid (numeric::xyzVector< core::Real > const &cart_coord, numeric::xyzVector< core::Real > const &mid, numeric::xyzVector< core::Size > const &dim, core::Real const &spacing, numeric::xyzVector< core::Real > &grid_coord)
 
void convert_grid_to_cartesian (numeric::xyzVector< core::Real > &grid_coord, numeric::xyzVector< core::Real > const &mid, numeric::xyzVector< core::Size > const &dim, core::Real const &spacing, numeric::xyzVector< core::Real > &cart_coord)
 
void min_values_versus_cluster (core::Size &x, core::Size &y, core::Size &z, PCluster const &c2)
 
void max_values_versus_cluster (core::Size &x, core::Size &y, core::Size &z, PCluster const &c2)
 
void min_values_versus_cluster (core::Size &x, core::Size &y, core::Size &z, CCluster const &c2)
 
void max_values_versus_cluster (core::Size &x, core::Size &y, core::Size &z, CCluster const &c2)
 
Size counting_atoms_in_residue (core::conformation::Residue const &rsd)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< FingerprintManager const > protocols::pockets::FingerprintManagerCOP
typedef utility::pointer::shared_ptr< FingerprintManager > protocols::pockets::FingerprintManagerOP
typedef utility::pointer::shared_ptr< NonPlaidFingerprint const > protocols::pockets::NonPlaidFingerprintCOP
typedef utility::pointer::shared_ptr< NonPlaidFingerprint > protocols::pockets::NonPlaidFingerprintOP
typedef utility::pointer::shared_ptr< PlaidFingerprint const > protocols::pockets::PlaidFingerprintCOP
typedef utility::pointer::shared_ptr< PlaidFingerprint > protocols::pockets::PlaidFingerprintOP
typedef utility::pointer::shared_ptr< PocketConstraint > protocols::pockets::PocketConstraintOP
typedef utility::pointer::shared_ptr< PocketGrid const > protocols::pockets::PocketGridCOP
typedef utility::pointer::shared_ptr< PocketGrid > protocols::pockets::PocketGridOP

Function Documentation

core::Real protocols::pockets::calDist ( vector< core::Real > const &  a1,
vector< core::Real > const &  a2 
)
void protocols::pockets::convert_cartesian_to_grid ( numeric::xyzVector< core::Real > const &  cart_coord,
numeric::xyzVector< core::Real > const &  mid,
numeric::xyzVector< core::Real > const &  dim,
core::Real const &  spacing,
numeric::xyzVector< core::Real > &  grid_coord 
)
inline
void protocols::pockets::convert_cartesian_to_grid ( numeric::xyzVector< core::Real > const &  cart_coord,
numeric::xyzVector< core::Real > const &  mid,
numeric::xyzVector< core::Size > const &  dim,
core::Real const &  spacing,
numeric::xyzVector< core::Real > &  grid_coord 
)
inline
void protocols::pockets::convert_cartesian_to_spherical_coor_triplet ( numeric::xyzVector< core::Real > const &  coord,
spherical_coor_triplet &  triplet 
)
inline
void protocols::pockets::convert_grid_to_cartesian ( numeric::xyzVector< core::Real > const &  grid_coord,
numeric::xyzVector< core::Real > const &  mid,
numeric::xyzVector< core::Real > const &  dim,
core::Real const &  spacing,
numeric::xyzVector< core::Real > &  cart_coord 
)
inline
void protocols::pockets::convert_grid_to_cartesian ( numeric::xyzVector< core::Real > &  grid_coord,
numeric::xyzVector< core::Real > const &  mid,
numeric::xyzVector< core::Size > const &  dim,
core::Real const &  spacing,
numeric::xyzVector< core::Real > &  cart_coord 
)
inline
void protocols::pockets::convert_spherical_coor_triplet_to_cartesian ( spherical_coor_triplet const &  triplet,
numeric::xyzVector< core::Real > &  coord 
)
inline
Size protocols::pockets::counting_atoms_in_residue ( core::conformation::Residue const &  rsd)
core::Real protocols::pockets::dD_dv1 ( const core::Real  x0,
const core::Real  x2,
const core::Real  x3,
const core::Real  y0,
const core::Real  y2,
const core::Real  y3,
const core::Real  z0,
const core::Real  z2,
const core::Real  z3,
const core::Real  r 
)
core::Real protocols::pockets::dD_dv2 ( const core::Real  x0,
const core::Real  x2,
const core::Real  x3,
const core::Real  y0,
const core::Real  y2,
const core::Real  y3,
const core::Real  z0,
const core::Real  z2,
const core::Real  z3,
const core::Real  r 
)
core::Real protocols::pockets::dD_dv3 ( const core::Real  x0,
const core::Real  x2,
const core::Real  x3,
const core::Real  y0,
const core::Real  y2,
const core::Real  y3,
const core::Real  z0,
const core::Real  z2,
const core::Real  z3,
const core::Real  r 
)
core::Real protocols::pockets::dD_dv4 ( const core::Real  x0,
const core::Real  x2,
const core::Real  x3,
const core::Real  y0,
const core::Real  y2,
const core::Real  y3,
const core::Real  z0,
const core::Real  z2,
const core::Real  z3,
const core::Real  r,
const core::Real  v4,
const core::Real  v5,
const core::Real  v6,
const core::Real  ,
const core::Real  ,
const core::Real  yc,
const core::Real  ys,
const core::Real  zc,
const core::Real  zs 
)

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

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

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

core::Real protocols::pockets::dD_dv6 ( const core::Real  x0,
const core::Real  x2,
const core::Real  x3,
const core::Real  y0,
const core::Real  y2,
const core::Real  y3,
const core::Real  z0,
const core::Real  z2,
const core::Real  z3,
const core::Real  r,
const core::Real  v4,
const core::Real  v5,
const core::Real  v6,
const core::Real  xc,
const core::Real  xs,
const core::Real  yc,
const core::Real  ys,
const core::Real  zc,
const core::Real  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 
)
void protocols::pockets::max_values_versus_cluster ( core::Size x,
core::Size y,
core::Size z,
PCluster const &  c2 
)
void protocols::pockets::max_values_versus_cluster ( core::Size x,
core::Size y,
core::Size z,
CCluster const &  c2 
)
void protocols::pockets::min_values_versus_cluster ( core::Size x,
core::Size y,
core::Size z,
PCluster const &  c2 
)
void protocols::pockets::min_values_versus_cluster ( core::Size x,
core::Size y,
core::Size z,
CCluster const &  c2 
)
static basic::Tracer protocols::pockets::TR ( "core.scoring.constraints.PocketConstraint"  )
static
static basic::Tracer protocols::pockets::TR ( "core.grid.Pockets.PocketGrid"  )
static