Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Classes | Typedefs | Enumerations | Functions
protocols::sic_dock Namespace Reference

Classes

struct  XfoxmScore
 
struct  CBScoreVisitor
 
class  RigidScore
 
class  CBScore
 
class  LinkerScore
 
class  EdgeStandScore
 
class  HelixScore
 
class  BuriedPolarScore
 
class  JointScore
 
class  Rose
 
struct  CorrectionVisitor
 
class  SICFast
 
struct  Vec3
 
class  xyzStripeHashPose
 
class  xyzStripeHashPoseWithMeta
 

Typedefs

typedef numeric::xyzVector
< platform::Real
Vec
 
typedef numeric::xyzMatrix
< platform::Real
Mat
 
typedef core::Real Real
 
typedef core::Size Size
 
typedef core::pose::Pose Pose
 
typedef core::kinematics::Stub Stub
 
typedef utility::vector1< VecVecs
 
typedef utility::vector1< RealReals
 
typedef utility::vector1< SizeSizes
 
typedef utility::vector1< StubStubs
 
typedef utility::vector1
< RigidScoreCOP
Scores
 
typedef
utility::pointer::owning_ptr
< RigidScore
RigidScoreOP
 
typedef
utility::pointer::owning_ptr
< RigidScore const > 
RigidScoreCOP
 
typedef
utility::pointer::owning_ptr
< CBScore
CBScoreOP
 
typedef
utility::pointer::owning_ptr
< CBScore const > 
CBScoreCOP
 
typedef
utility::pointer::owning_ptr
< LinkerScore
LinkerScoreOP
 
typedef
utility::pointer::owning_ptr
< LinkerScore const > 
LinkerScoreCOP
 
typedef
utility::pointer::owning_ptr
< JointScore
JointScoreOP
 
typedef
utility::pointer::owning_ptr
< JointScore const > 
JointScoreCOP
 
typedef
utility::pointer::owning_ptr
< SICFast
SICFastOP
 
typedef
utility::pointer::owning_ptr
< SICFast const > 
SICFastCOP
 
typedef utility::vector1
< std::pair< platform::Size,
Vec3 > > 
TermInfo
 
typedef
utility::pointer::owning_ptr
< xyzStripeHashPose
xyzStripeHashPoseOP
 
typedef
utility::pointer::owning_ptr
< xyzStripeHashPose const > 
xyzStripeHashPoseCOP
 
typedef
utility::pointer::owning_ptr
< xyzStripeHashPoseWithMeta
xyzStripeHashPoseWithMetaOP
 
typedef
utility::pointer::owning_ptr
< xyzStripeHashPoseWithMeta
const > 
xyzStripeHashPoseWithMetaCOP
 

Enumerations

enum  PoseCoordPickMode {
  NBR, CA, CB, BB,
  BNP, HVY, ALL
}
 

Functions

void get_xform_stats (core::kinematics::Stub const &sir, core::kinematics::Stub const &sjr, Real &dx, Real &dy, Real &dz, Real &ex, Real &ey, Real &ez)
 
Vec3 get_leap_lower_stub (core::pose::Pose const &pose, Size ir)
 
Vec3 get_leap_upper_stub (core::pose::Pose const &pose, Size ir)
 
core::kinematics::Stub vec3_to_stub (Vec3 const &v3)
 
Stub vec3_to_stub (core::kinematics::Stub const &xform, Vec3 const &v3)
 
void get_termini_from_pose (core::pose::Pose const &pose, Size ir, TermInfo &lowers, TermInfo &uppers)
 
void get_termini_from_pose (core::pose::Pose const &pose, TermInfo &lowers, TermInfo &uppers)
 
numeric::geometry::hashing::Real6 get_leap_6dof (Stub const &lower, Stub const &upper)
 
Size count_linkers (Stub const &lower, Stub const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, Sizes const &loopsizes, core::Size radius)
 
core::Size dump_loophash_linkers (Stub const &lower, Stub const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, Sizes const &loopsizes, Size radius)
 
Real linker_count2score (Size count)
 
platform::Size count_linkers (core::kinematics::Stub const &lower, core::kinematics::Stub const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, utility::vector1< platform::Size > const &loopsizes, platform::Size radius=0)
 
platform::Size dump_loophash_linkers (core::kinematics::Stub const &lower, core::kinematics::Stub const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, utility::vector1< platform::Size > const &loopsizes, platform::Size radius=0)
 
static basic::Tracer TR ("propocols.sic_dock.RigidScore")
 
Real dist_score (Real const &sqdist, Real const &start, Real const &stop)
 
std::ostream & operator<< (std::ostream &out, Vec3 v)
 
template<typename T >
sqr (T x)
 
void dump_points_pdb (utility::vector1< Vec > const &p, std::string fn)
 
double dist_score (double const &sqdist, double const &start, double const &stop)
 
bool get_bounds_intersection (vector1< Vec > const &pb, vector1< Vec > const &pa, double &xmx, double &xmn, double &ymx, double &ymn)
 
void fill_plane_hash (vector1< Vec > const &pb, vector1< Vec > const &pa, double const &xmx, double const &xmn, double const &ymx, double const &ymn, double const &BIN, ObjexxFCL::FArray2D< Vec > &ha, ObjexxFCL::FArray2D< Vec > &hb, int &xlb, int &ylb, int &xub, int &yub)
 
double get_mindis_with_plane_hashes (int const &xlb, int const &ylb, int const &xub, int const &yub, ObjexxFCL::FArray2D< Vec > const &ha, ObjexxFCL::FArray2D< Vec > const &hb, double const &clashdis2)
 
double refine_mindis_with_xyzHash (xyzStripeHashPose *xh, core::kinematics::Stub const &xform_to_struct2_start, vector1< Vec > const &pa, Vec const &ori, double const &clash_dis_sq, double const &mindis_approx)
 
int neighbor_count (core::pose::Pose const &pose, int ires, double distance_threshold)
 
Real cb_weight (core::pose::Pose const &pose, Size ires, Real distance_threshold)
 
double slide_into_contact_and_score (protocols::sic_dock::SICFast const &sic, protocols::sic_dock::RigidScore const &sfxn, numeric::xyzTransform< core::Real > &xa, numeric::xyzTransform< core::Real > const &xb, numeric::xyzVector< platform::Real > const &ori, platform::Real &score)
 
double slide_into_contact_and_score (protocols::sic_dock::SICFast const &sic, protocols::sic_dock::RigidScore const &sfxn, core::kinematics::Stub &xa, core::kinematics::Stub const &xb, numeric::xyzVector< platform::Real > const &ori, platform::Real &score)
 
core::id::AtomID_Map< double > cb_weight_map_from_pose (core::pose::Pose const &pose)
 
utility::vector1< platform::Realcb_weights_from_pose (core::pose::Pose const &pose)
 
platform::Size count_CBs (core::pose::Pose const &pose)
 
core::pose::Pose const & pose_with_most_CBs (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
 
bool pose1_has_most_CBs (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
 
utility::vector1
< numeric::xyzVector
< platform::Real > > 
get_CB_Vecs (core::pose::Pose const &pose)
 
void xform_pose (core::pose::Pose &pose, core::kinematics::Stub const &s, Size sres, Size eres)
 
void xform_pose_rev (core::pose::Pose &pose, core::kinematics::Stub const &s, Size sres, Size eres)
 
void xform_pose (core::pose::Pose &pose, numeric::xyzTransform< core::Real > const &s, Size sres, Size eres)
 
void xform_pose_rev (core::pose::Pose &pose, numeric::xyzTransform< core::Real > const &s)
 
utility::vector1< platform::Sizerange (platform::Size beg, platform::Size end)
 
int flood_fill3D (int i, int j, int k, ObjexxFCL::FArray3D< double > &grid, double t)
 
core::kinematics::Stub multstubs (core::kinematics::Stub const &a, core::kinematics::Stub const &b)
 
core::kinematics::Stub invstub (core::kinematics::Stub const &a)
 

Typedef Documentation

typedef platform::Real protocols::sic_dock::Real
typedef platform::Size protocols::sic_dock::Size

Enumeration Type Documentation

Enumerator
NBR 
CA 
CB 
BB 
BNP 
HVY 
ALL 

Function Documentation

core::Real protocols::sic_dock::cb_weight ( core::pose::Pose const &  pose,
Size  ires,
Real  distance_threshold 
)
core::id::AtomID_Map< double > protocols::sic_dock::cb_weight_map_from_pose ( core::pose::Pose const &  pose)
utility::vector1< platform::Real > protocols::sic_dock::cb_weights_from_pose ( core::pose::Pose const &  pose)
platform::Size protocols::sic_dock::count_CBs ( core::pose::Pose const &  pose)
platform::Size protocols::sic_dock::count_linkers ( core::kinematics::Stub const &  lower,
core::kinematics::Stub const &  upper,
protocols::loophash::LoopHashLibraryOP  loop_hash_library,
utility::vector1< platform::Size > const &  loopsizes,
platform::Size  radius = 0 
)
Size protocols::sic_dock::count_linkers ( Stub const &  lower,
Stub const &  upper,
protocols::loophash::LoopHashLibraryOP  loop_hash_library,
Sizes const &  loopsizes,
core::Size  radius 
)
Real protocols::sic_dock::dist_score ( Real const &  sqdist,
Real const &  start,
Real const &  stop 
)
inline
double protocols::sic_dock::dist_score ( double const &  sqdist,
double const &  start,
double const &  stop 
)
inline
platform::Size protocols::sic_dock::dump_loophash_linkers ( core::kinematics::Stub const &  lower,
core::kinematics::Stub const &  upper,
protocols::loophash::LoopHashLibraryOP  loop_hash_library,
utility::vector1< platform::Size > const &  loopsizes,
platform::Size  radius = 0 
)
core::Size protocols::sic_dock::dump_loophash_linkers ( Stub const &  lower,
Stub const &  upper,
protocols::loophash::LoopHashLibraryOP  loop_hash_library,
Sizes const &  loopsizes,
Size  radius 
)
void protocols::sic_dock::dump_points_pdb ( utility::vector1< Vec > const &  p,
std::string  fn 
)
void protocols::sic_dock::fill_plane_hash ( vector1< Vec > const &  pb,
vector1< Vec > const &  pa,
double const &  xmx,
double const &  xmn,
double const &  ymx,
double const &  ymn,
double const &  BIN,
ObjexxFCL::FArray2D< Vec > &  ha,
ObjexxFCL::FArray2D< Vec > &  hb,
int xlb,
int ylb,
int xub,
int yub 
)
inline
int protocols::sic_dock::flood_fill3D ( int  i,
int  j,
int  k,
ObjexxFCL::FArray3D< double > &  grid,
double  t 
)
bool protocols::sic_dock::get_bounds_intersection ( vector1< Vec > const &  pb,
vector1< Vec > const &  pa,
double &  xmx,
double &  xmn,
double &  ymx,
double &  ymn 
)
inline
utility::vector1< numeric::xyzVector< platform::Real > > protocols::sic_dock::get_CB_Vecs ( core::pose::Pose const &  pose)
numeric::geometry::hashing::Real6 protocols::sic_dock::get_leap_6dof ( Stub const &  lower,
Stub const &  upper 
)
Vec3 protocols::sic_dock::get_leap_lower_stub ( core::pose::Pose const &  pose,
Size  ir 
)
Vec3 protocols::sic_dock::get_leap_upper_stub ( core::pose::Pose const &  pose,
Size  ir 
)
double protocols::sic_dock::get_mindis_with_plane_hashes ( int const &  xlb,
int const &  ylb,
int const &  xub,
int const &  yub,
ObjexxFCL::FArray2D< Vec > const &  ha,
ObjexxFCL::FArray2D< Vec > const &  hb,
double const &  clashdis2 
)
inline
void protocols::sic_dock::get_termini_from_pose ( core::pose::Pose const &  pose,
Size  ir,
TermInfo &  lowers,
TermInfo &  uppers 
)
void protocols::sic_dock::get_termini_from_pose ( core::pose::Pose const &  pose,
TermInfo &  lowers,
TermInfo &  uppers 
)
void protocols::sic_dock::get_xform_stats ( core::kinematics::Stub const &  sir,
core::kinematics::Stub const &  sjr,
Real dx,
Real dy,
Real dz,
Real ex,
Real ey,
Real ez 
)
core::kinematics::Stub protocols::sic_dock::invstub ( core::kinematics::Stub const &  a)
inline
platform::Real protocols::sic_dock::linker_count2score ( Size  count)
core::kinematics::Stub protocols::sic_dock::multstubs ( core::kinematics::Stub const &  a,
core::kinematics::Stub const &  b 
)
inline
int protocols::sic_dock::neighbor_count ( core::pose::Pose const &  pose,
int  ires,
double  distance_threshold 
)
std::ostream& protocols::sic_dock::operator<< ( std::ostream &  out,
Vec3  v 
)
bool protocols::sic_dock::pose1_has_most_CBs ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 
)

References count_CBs().

core::pose::Pose const & protocols::sic_dock::pose_with_most_CBs ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 
)

References count_CBs().

utility::vector1< platform::Size > protocols::sic_dock::range ( platform::Size  beg,
platform::Size  end 
)
double protocols::sic_dock::refine_mindis_with_xyzHash ( xyzStripeHashPose *  xh,
core::kinematics::Stub const &  xform_to_struct2_start,
vector1< Vec > const &  pa,
Vec const &  ori,
double const &  clash_dis_sq,
double const &  mindis_approx 
)
inline
double protocols::sic_dock::slide_into_contact_and_score ( protocols::sic_dock::SICFast const &  sic,
protocols::sic_dock::RigidScore const &  sfxn,
numeric::xyzTransform< core::Real > &  xa,
numeric::xyzTransform< core::Real > const &  xb,
numeric::xyzVector< platform::Real > const &  ori,
platform::Real score 
)
double protocols::sic_dock::slide_into_contact_and_score ( protocols::sic_dock::SICFast const &  sic,
protocols::sic_dock::RigidScore const &  sfxn,
core::kinematics::Stub xa,
core::kinematics::Stub const &  xb,
numeric::xyzVector< platform::Real > const &  ori,
platform::Real score 
)
template<typename T >
T protocols::sic_dock::sqr ( x)
inline
static basic::Tracer protocols::sic_dock::TR ( "propocols.sic_dock.RigidScore"  )
static
core::kinematics::Stub protocols::sic_dock::vec3_to_stub ( Vec3 const &  v3)
core::kinematics::Stub protocols::sic_dock::vec3_to_stub ( core::kinematics::Stub const &  xform,
Vec3 const &  v3 
)
void protocols::sic_dock::xform_pose ( core::pose::Pose pose,
core::kinematics::Stub const &  s,
Size  sres,
Size  eres 
)
void protocols::sic_dock::xform_pose ( core::pose::Pose pose,
numeric::xyzTransform< core::Real > const &  s,
Size  sres,
Size  eres 
)
void protocols::sic_dock::xform_pose_rev ( core::pose::Pose pose,
core::kinematics::Stub const &  s,
Size  sres,
Size  eres 
)
void protocols::sic_dock::xform_pose_rev ( core::pose::Pose pose,
numeric::xyzTransform< core::Real > const &  s 
)