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base_geometry.cc File Reference
#include <core/scoring/dna/base_geometry.hh>
#include <core/scoring/dna/BasePartner.hh>
#include <core/scoring/dna/DNA_BasePotential.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <basic/basic.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
#include <core/kinematics/Stub.hh>
#include <core/pose/Pose.hh>
#include <numeric/conversions.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyz.functions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <utility/vector1.hh>

Namespaces

 core
 A class for defining atom parameters, known as atom_types.
 
 core::scoring
 
 core::scoring::dna
 

Constant Groups

 core
 A class for defining atom parameters, known as atom_types.
 
 core::scoring
 
 core::scoring::dna
 

Typedefs

typedef numeric::xyzMatrix< Realcore::scoring::dna::Matrix
 
typedef utility::vector1< Realcore::scoring::dna::Params
 

Functions

Vector core::scoring::dna::lsf_normal (utility::vector1< Vector > const &atoms_in)
 FWD. More...
 
void core::scoring::dna::get_base_pucker (conformation::Residue const &rsd, std::pair< std::string, int > &pucker)
 
std::string core::scoring::dna::dihedral_bin (Real phi)
 
std::string core::scoring::dna::get_DNA_backbone_bin (conformation::Residue const &rsd)
 
void core::scoring::dna::get_y_axis_atoms (chemical::ResidueType const &rsd_type, int const strand, std::string &a1, std::string &a2)
 
Vector core::scoring::dna::get_y_axis (conformation::Residue const &rsd, int const strand)
 
Vector core::scoring::dna::get_base_pair_y_axis_atom_xyz (conformation::Residue const &rsd)
 
Vector core::scoring::dna::get_z_axis (conformation::Residue const &rsd, Vector const &y_axis)
 
Vector core::scoring::dna::strand_orientation_vector (conformation::Residue const &rsd, int const strand)
 
Vector core::scoring::dna::get_z_axis (conformation::Residue const &rsd, Vector const &y_axis, int const strand, bool &flipped)
 
Vector core::scoring::dna::get_z_axis (conformation::Residue const &rsd, Vector const &y_axis, int const strand)
 
bool core::scoring::dna::is_orthonormal (numeric::xyzMatrix< Real > const &M, Real const tol)
 helper fxn More...
 
kinematics::Stub core::scoring::dna::get_base_stub (conformation::Residue const &rsd, int const strand)
 
kinematics::Stub core::scoring::dna::get_base_pair_stub (conformation::Residue const &rsd1, conformation::Residue const &rsd2)
 
kinematics::Stub core::scoring::dna::get_base_pair_stub_slow (conformation::Residue const &rsd1, conformation::Residue const &rsd2)
 
void core::scoring::dna::show_base_pair_params_with_z_scores (conformation::Residue const &rsd1, conformation::Residue const &rsd2, std::ostream &out)
 
void core::scoring::dna::show_base_pair_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2, std::ostream &out)
 
void core::scoring::dna::show_base_pair_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2)
 
void core::scoring::dna::get_stub_stub_params (kinematics::Stub const &stub1, kinematics::Stub const &stub2, Params &params)
 
void core::scoring::dna::get_base_pair_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Params &params)
 
void core::scoring::dna::get_base_step_params (conformation::Residue const &rsd11, conformation::Residue const &rsd12, conformation::Residue const &rsd21, conformation::Residue const &rsd22, Params &params)
 
bool core::scoring::dna::seqpos_is_base_step_anchor (Size const seqpos, pose::Pose const &pose)
 
void core::scoring::dna::show_base_step_params (Size const seqpos, pose::Pose const &pose, std::ostream &out)
 
void core::scoring::dna::show_new_base_step_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2)
 
void core::scoring::dna::show_base_step_params (pose::Pose const &pose, std::ostream &out)
 
void core::scoring::dna::show_base_pair_params (pose::Pose const &pose, std::ostream &out)
 
void core::scoring::dna::show_dna_geometry (pose::Pose const &pose, std::ostream &out)
 
void core::scoring::dna::get_base_pair_params_old (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Params &params)
 
void core::scoring::dna::get_base_step_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Params &params)
 
void core::scoring::dna::get_base_pucker (conformation::Residue const &rsd, std::pair< std::string, int > &pucker, Real &pseudorotation, Real &amplitude)
 
kinematics::Stub core::scoring::dna::get_midstep_stub (kinematics::Stub const &in_stub1, kinematics::Stub const &in_stub2)
 

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