Classes
class	MIFSTProbabilitiesMetric
	A PerResidueProbabilitiesMetric that stores amino acid probabilities predicted by the MIF-ST model. More...

class	MIFSTProbabilitiesMetricCreator

Typedefs
using	MIFSTOP = utility::pointer::shared_ptr< MIFST >

using	MIFSTCOP = utility::pointer::shared_ptr< MIFST const >

using	MIFSTProbabilitiesMetricOP = utility::pointer::shared_ptr< MIFSTProbabilitiesMetric >

using	MIFSTProbabilitiesMetricCOP = utility::pointer::shared_ptr< MIFSTProbabilitiesMetric const >

Functions
core::Real	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	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 >	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	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	compute_distance_matrix (std::vector< Eigen::Vector3d > const &coordinates)
	Calculate the distance matrix of C betas. More...

std::vector< core::Size >	tokenize (std::string const &seq, core::Size mask_position)
	function to tokenize sequence into MIF-ST Alphabet More...

Variables
static std::string	PROTEIN_ALPHABET = "ACDEFGHIKLMNPQRSTVWYBZXJOU-*#@!"

static char	MASK = '#'

Typedef Documentation

◆ MIFSTCOP

using protocols::inverse_folding::MIFSTCOP = typedef utility::pointer::shared_ptr< MIFST const >

◆ MIFSTOP

using protocols::inverse_folding::MIFSTOP = typedef utility::pointer::shared_ptr< MIFST >

◆ MIFSTProbabilitiesMetricCOP

using protocols::inverse_folding::MIFSTProbabilitiesMetricCOP = typedef utility::pointer::shared_ptr< MIFSTProbabilitiesMetric const >

◆ MIFSTProbabilitiesMetricOP

using protocols::inverse_folding::MIFSTProbabilitiesMetricOP = typedef utility::pointer::shared_ptr< MIFSTProbabilitiesMetric >

Function Documentation

◆ calculate_Cb_position()

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.

References core::pose::motif::a(), protocols::match::upstream::b, core::chemical::element::C, core::chemical::element::Ca, and core::chemical::element::N.

◆ compute_distance_matrix()

Eigen::MatrixXd protocols::inverse_folding::compute_distance_matrix ( std::vector< Eigen::Vector3d > const & coordinates )

Calculate the distance matrix of C betas.

◆ extract_coordinates()

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

References core::conformation::Residue::has(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::TR(), and core::conformation::Residue::xyz().

◆ get_angles()

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

References core::pose::motif::a(), protocols::match::upstream::b, protocols::mean_field::max(), and protocols::mean_field::min().

◆ get_dihedrals()

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.

References core::pose::motif::a(), and protocols::match::upstream::b.

◆ tokenize()

std::vector< core::Size > protocols::inverse_folding::tokenize	(	std::string const &	seq,
		core::Size	mask_position
	)

function to tokenize sequence into MIF-ST Alphabet

References MASK, PROTEIN_ALPHABET, and protocols::TR().

Variable Documentation

◆ MASK

char protocols::inverse_folding::MASK = '#'

static

Referenced by tokenize().

◆ PROTEIN_ALPHABET

std::string protocols::inverse_folding::PROTEIN_ALPHABET = "ACDEFGHIKLMNPQRSTVWYBZXJOU-*#@!"