Rosetta Protocols  2014.35
Namespaces | Functions
util.hh File Reference
#include <core/types.hh>
#include <core/kinematics/Stub.hh>
#include <core/conformation/Residue.fwd.hh>
#include <protocols/sic_dock/types.hh>
#include <protocols/sic_dock/RigidScore.fwd.hh>
#include <protocols/sic_dock/SICFast.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/id/AtomID_Map.hh>
#include <numeric/geometry/hashing/SixDHasher.fwd.hh>
#include <ObjexxFCL/FArray3D.fwd.hh>
#include <numeric/xyzTransform.hh>
#include <core/kinematics/Stub.fwd.hh>
#include <numeric/xyzVector.hh>
#include <numeric/numeric.functions.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzTriple.hh>
#include <numeric/Quaternion.hh>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::sic_dock
 

Functions

Real protocols::sic_dock::get_rg (core::pose::Pose const &pose)
 
int protocols::sic_dock::neighbor_count (core::pose::Pose const &pose, int ires, double distance_threshold)
 
Real protocols::sic_dock::cb_weight (core::pose::Pose const &pose, Size ires, Real distance_threshold)
 
void protocols::sic_dock::make_Cx (core::pose::Pose &pose, int N, numeric::xyzVector< core::Real > axis)
 
double protocols::sic_dock::slide_into_contact_and_score (protocols::sic_dock::SICFast const &sic, protocols::sic_dock::RigidScore const &sfxn, Xform &xa, Xform const &xb, numeric::xyzVector< core::Real > const &ori, core::Real &score)
 
double protocols::sic_dock::slide_into_contact_and_score_DEPRICATED (protocols::sic_dock::SICFast const &sic, protocols::sic_dock::RigidScore const &sfxn, core::kinematics::Stub &xa, core::kinematics::Stub const &xb, numeric::xyzVector< core::Real > const &ori, core::Real &score)
 
core::pose::Pose const & protocols::sic_dock::pose_with_most_CBs (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
 
bool protocols::sic_dock::pose1_has_most_CBs (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
 
core::Size protocols::sic_dock::count_CBs (core::pose::Pose const &pose)
 
core::id::AtomID_Map< doubleprotocols::sic_dock::cb_weight_map_from_pose (core::pose::Pose const &pose)
 
vector1< numeric::xyzVector
< core::Real > > 
protocols::sic_dock::get_CB_Vecs_from_pose (core::pose::Pose const &pose)
 
vector1< numeric::xyzVector
< core::Real > > 
protocols::sic_dock::get_CB_Vecs_from_map (core::pose::Pose const &pose, core::id::AtomID_Map< core::Real > const &map)
 
vector1< core::Realprotocols::sic_dock::cb_weights_from_pose (core::pose::Pose const &pose)
 
vector1< core::Realprotocols::sic_dock::cb_weights_from_map (core::pose::Pose const &pose, core::id::AtomID_Map< core::Real > const &map)
 
vector1< core::Sizeprotocols::sic_dock::range (core::Size beg, core::Size end)
 
Vec3 protocols::sic_dock::get_leap_lower_stub (core::pose::Pose const &pose, Size ir)
 
int protocols::sic_dock::flood_fill3D (int i, int j, int k, ObjexxFCL::FArray3D< double > &grid, double t)
 
Xform protocols::sic_dock::multstubs (Xform const &a, Xform const &b)
 
Xform protocols::sic_dock::invstub (Xform const &a)
 
bool protocols::sic_dock::residue_is_floppy (core::pose::Pose const &pose, Size const ir, Real const ttrim_cut, Size const nfold)
 
void protocols::sic_dock::auto_trim_floppy_termini (core::pose::Pose &pose, Real const ttrim_cut, Size const nfold)
 
Vec protocols::sic_dock::center_of_geom (core::pose::Pose const &pose, Size str, Size end)
 
void protocols::sic_dock::dump_points_pdb (utility::vector1< numeric::xyzVector< core::Real > > const &p, std::string fn)
 
void protocols::sic_dock::dump_points_pdb (utility::vector1< numeric::xyzVector< core::Real > > const &p, numeric::xyzVector< core::Real > t, std::string fn)
 
void protocols::sic_dock::trans_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &trans, core::Size start=1, core::Size end=0)
 
void protocols::sic_dock::rot_pose (core::pose::Pose &pose, numeric::xyzMatrix< core::Real > const &rot, core::Size start=1, core::Size end=0)
 
void protocols::sic_dock::rot_pose (core::pose::Pose &pose, numeric::xyzMatrix< core::Real > const &rot, numeric::xyzVector< core::Real > const &cen, core::Size start=1, core::Size end=0)
 
void protocols::sic_dock::rot_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &axis, core::Real const &ang, core::Size start=1, core::Size end=0)
 
void protocols::sic_dock::rot_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &axis, core::Real const &ang, numeric::xyzVector< core::Real > const &cen, core::Size start=1, core::Size end=0)
 
void protocols::sic_dock::alignaxis (core::pose::Pose &pose, numeric::xyzVector< core::Real > newaxis, numeric::xyzVector< core::Real > oldaxis, numeric::xyzVector< core::Real > cen=numeric::xyzVector< core::Real >(0, 0, 0))
 
numeric::xyzTransform< core::Realprotocols::sic_dock::alignaxis_xform (numeric::xyzVector< core::Real > newaxis, numeric::xyzVector< core::Real > oldaxis, numeric::xyzVector< core::Real > cen)
 
numeric::xyzVector< core::Realprotocols::sic_dock::projperp (numeric::xyzVector< core::Real > const &u, numeric::xyzVector< core::Real > const &v)
 
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)
 
core::kinematics::Stub protocols::sic_dock::getxform (core::conformation::Residue const &move_resi, core::conformation::Residue const &fixd_resi)
 
template<typename T >
T protocols::sic_dock::sqr (T x)