util.hh File Reference

Helper functions for using the MIF-ST model developed Yang et al. More...

#include <protocols/inverse_folding/MIFST.fwd.hh>
#include <core/conformation/Conformation.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/select/residue_selector/ResidueSelector.hh>
#include <core/select/residue_selector/util.hh>
#include <core/select/util.hh>
#include <core/pose/Pose.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/VirtualBase.hh>
#include <utility/SingletonBase.hh>
#include <utility/vector1.hh>
#include <Eigen/Dense>
#include <cmath>

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

Functions
core::Real	protocols::inverse_folding::get_dihedrals (Eigen::Vector3d const &a, Eigen::Vector3d const &b, Eigen::Vector3d const &c, Eigen::Vector3d const &d)
	Helper function to return trRosetta style dihedrals. More...
core::Real	protocols::inverse_folding::get_angles (Eigen::Vector3d const &a, Eigen::Vector3d const &b, Eigen::Vector3d const &c)
	helper function to return trRosetta style angles More...
std::vector< Eigen::Vector3d >	protocols::inverse_folding::extract_coordinates (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset, std::string const &atom_name)
	get the coordinates of a specified ResidueSubset More...
Eigen::Vector3d	protocols::inverse_folding::calculate_Cb_position (Eigen::Vector3d const &N, Eigen::Vector3d const &Ca, Eigen::Vector3d const &C)
	Calculate the Cb position following the implementation of Yang et al. More...
Eigen::MatrixXd	protocols::inverse_folding::compute_distance_matrix (std::vector< Eigen::Vector3d > const &coordinates)
	Calculate the distance matrix of C betas. More...
std::vector< core::Size >	protocols::inverse_folding::tokenize (std::string const &seq, core::Size mask_position)
	function to tokenize sequence into MIF-ST Alphabet More...

Variables
static std::string	protocols::inverse_folding::PROTEIN_ALPHABET = "ACDEFGHIKLMNPQRSTVWYBZXJOU-*#@!"
static char	protocols::inverse_folding::MASK = '#'

Detailed Description

Helper functions for using the MIF-ST model developed Yang et al.

Author

moritzertelt (moritzertelt)