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>
#include <utility/tools/make_vector1.hh>
#include <cmath>

Namespaces
	core
	A class for reading in the atom type properties.
	core::scoring
	core::scoring::dna

Typedefs
using	core::scoring::dna::Matrix = numeric::xyzMatrix< Real >
using	core::scoring::dna::Params = utility::vector1< Real >

Functions
static basic::Tracer	core::scoring::dna::TR ("core.scoring.dna.base_geometry")
Vector	core::scoring::dna::lsf_normal (utility::vector1< Vector > const &atoms_in)
	FWD. More...
void	core::scoring::dna::get_sugar_pucker (conformation::Residue const &rsd, std::pair< std::string, int > &pucker)
	this could be made faster... More...
void	core::scoring::dna::get_sugar_pucker_distr (conformation::Residue const &rsd, utility::vector1< core::Real > &puckerProb)
utility::vector1< utility::vector1< std::string > >	core::scoring::dna::sugar_torsion_atom_names ()
void	core::scoring::dna::get_sugar_torsions (conformation::Residue const &rsd, utility::vector1< Real > &torsions)
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::get_groove_widths (Size const i, pose::Pose const &pose, Real &major_width, Real &minor_width, Real &major_length)
void	core::scoring::dna::get_base_step_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Params &params)

Detailed Description

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