#include <Ramachandran.hh>

Public Types
typedef pose::Pose	Pose

typedef chemical::AA	AA

Public Member Functions
	Ramachandran ()

	Ramachandran (std::string const &rama_map_filename, bool use_bicubic_interpolation)

virtual	~Ramachandran ()

bool	is_canonical_d_aminoacid (AA const res_aa) const
	Returns true if passed a core::chemical::AA corresponding to a D-amino acid, and false otherwise. More...

AA	get_l_equivalent (AA const d_aa) const
	When passed a d-amino acid, returns the l-equivalent. Returns aa_unk otherwise. More...

Real	eval_rama_score_residue (conformation::Residue const &res) const

Real	eval_rama_score_residue (AA const res_aa, Real const phi, Real const psi) const

void	eval_rama_score_residue (conformation::Residue const &res, Real &rama, Real &drama_dphi, Real &drama_dpsi) const

void	eval_rama_score_residue (AA const res_aa, Real const phi, Real const psi, Real &rama, Real &drama_dphi, Real &drama_dpsi) const

void	eval_rama_score_residue (bool use_bicubic_interpolation, bool rama_not_squared, AA const res_aa, Real const phi, Real const psi, Real &rama, Real &drama_dphi, Real &drama_dpsi) const

void	eval_rama_score_residue_nonstandard_connection (core::pose::Pose const &mypose, conformation::Residue const &res, Real &rama, Real &drama_dphi, Real &drama_dpsi) const
	Function to evaluate the rama score for residues whose connection partners are not necessarily adjacent in linear sequence (e.g. for backbone-cyclized peptides). Note that this assumes that rama is being used only for scoring alpha-amino acids (L- or D-). More...

void	random_phipsi_from_rama (AA const res_aa, Real &phi, Real &psi) const

void	uniform_phipsi_from_allowed_rama (AA const res_aa, Real &phi, Real &psi) const
	Return a phi/psi pair picked uniformly from the regions of rama space with nonzero weight. Sampling with this method will not give a rama distribution; it will give a flat distribution in only the allowed regions of rama space. More...

bool	phipsi_in_allowed_rama (AA const res_aa, Real phi, Real psi) const
	Return true if the given phi/psi pair is in the allowed space sampled by uniform_phipsi_from_allowed_rama. More...

bool	phipsi_in_forbidden_rama (AA const res_aa, Real phi, Real psi) const
	Return false if the given phi/psi pair is in the allowed space sampled by uniform_phipsi_from_allowed_rama. More...

void	random_phipsi_from_rama_by_torsion_bin (AA const res_aa, Real &phi, Real &psi, char const torsion_bin) const
	functions for torsion-bin specific but otherwise random phi/psi angles More...

core::Size	get_torsion_bin_index (char torsion_bin) const

void	init_rama_sampling_tables_by_torsion_bin () const

void	get_entries_per_torsion_bin (AA const res_aa, std::map< char, core::Size > &tb_frequencies) const

void	eval_rama_score_all (Pose &pose, ScoreFunction const &scorefxn) const
	evaluate rama score for each (protein) residue and store that score in the pose.energies() object More...

void	write_rama_score_all (Pose const &pose) const

void	eval_procheck_rama (Pose const &a_pose, Real &favorable, Real &allowed, Real &generous) const

bool	is_normally_connected (conformation::Residue const &res) const
	Function to do a quick check that the upper connection is seqpos+1 and the lower connection is seqpos-1. Returns true if this is so, false otherwise. More...

Private Member Functions
void	read_rama (std::string const &rama_map_filename, bool use_bicubic_interpolation)

void	read_rama_map_file (utility::io::izstream *iunit)

void	init_rama_sampling_table (char const torsion_bin) const

void	init_uniform_sampling_table () const

Private Attributes
utility::vector1 < numeric::interpolation::spline::BicubicSpline >	rama_energy_splines_

utility::vector1 < utility::vector1 < utility::vector1< Real > > >	rama_sampling_table_

utility::vector1 < utility::vector1 < utility::vector1 < utility::vector1< Real > > > >	rama_sampling_table_by_torsion_bin_

utility::vector1 < utility::vector1 < utility::vector1< Real > > >	uniform_sampling_table_
	Table containing a uniform distribution of allowed torsion bins. More...

Static Private Attributes
static bool	rama_initialized_

static ObjexxFCL::FArray4D< Real >	ram_probabil_

static ObjexxFCL::FArray4D_int	ram_counts_

static ObjexxFCL::FArray4D< Real >	ram_energ_

static int const	n_phi_ = 36

static int const	n_psi_ = 36

static Real const	binw_

static Real const	rama_sampling_thold_

static Real const	rama_sampling_factor_

static int const	n_aa_ = 20

static ObjexxFCL::FArray2D< Real >	ram_entropy_

Member Typedef Documentation

typedef chemical::AA core::scoring::Ramachandran::AA

typedef pose::Pose core::scoring::Ramachandran::Pose

Constructor & Destructor Documentation

core::scoring::Ramachandran::Ramachandran ( )

References option.

core::scoring::Ramachandran::Ramachandran	(	std::string const &	rama_map_filename,
		bool	use_bicubic_interpolation
	)

core::scoring::Ramachandran::~Ramachandran ( )

virtual

Member Function Documentation

void core::scoring::Ramachandran::eval_procheck_rama	(	Pose const &	a_pose,
		Real &	favorable,
		Real &	allowed,
		Real &	generous
	)		const

void core::scoring::Ramachandran::eval_rama_score_all	(	pose::Pose &	pose,
		ScoreFunction const &	scorefxn
	)		const

evaluate rama score for each (protein) residue and store that score in the pose.energies() object

References core::pose::Pose::energies(), core::scoring::ScoreFunction::has_zero_weight(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_terminus(), core::conformation::Residue::is_virtual_residue(), core::scoring::rama, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Real core::scoring::Ramachandran::eval_rama_score_residue ( conformation::Residue const & res ) const

References core::scoring::rama.

Referenced by core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), and core::scoring::methods::RamachandranEnergy::residue_energy().

Real core::scoring::Ramachandran::eval_rama_score_residue	(	AA const	res_aa,
		Real const	phi,
		Real const	psi
	)		const

References core::scoring::rama.

void core::scoring::Ramachandran::eval_rama_score_residue	(	conformation::Residue const &	res,
		Real &	rama,
		Real &	drama_dphi,
		Real &	drama_dpsi
	)		const

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::conformation::Residue::backbone_aa(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_terminus(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::mainchain_torsion(), and nonnegative_principal_angle_degrees().

void core::scoring::Ramachandran::eval_rama_score_residue	(	AA const	res_aa,
		Real const	phi,
		Real const	psi,
		Real &	rama,
		Real &	drama_dphi,
		Real &	drama_dpsi
	)		const

References option.

void core::scoring::Ramachandran::eval_rama_score_residue	(	bool	use_bicubic_interpolation,
		bool	rama_not_squared,
		AA const	res_aa,
		Real const	phi,
		Real const	psi,
		Real &	rama,
		Real &	drama_dphi,
		Real &	drama_dpsi
	)		const

References bilinearly_interpolated(), core::scoring::rama, and ss_type.

void core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection	(	core::pose::Pose const &	mypose,
		conformation::Residue const &	res,
		Real &	rama,
		Real &	drama_dphi,
		Real &	drama_dpsi
	)		const

Function to evaluate the rama score for residues whose connection partners are not necessarily adjacent in linear sequence (e.g. for backbone-cyclized peptides). Note that this assumes that rama is being used only for scoring alpha-amino acids (L- or D-).

Author: Vikram K. Mulligan

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::conformation::Residue::backbone_aa(), core::conformation::Residue::connection_incomplete(), numeric::dihedral_degrees(), numeric::nonnegative_principal_angle_degrees(), basic::options::option, basic::options::OptionKeys::score::rama_score_nonstandard_connections, core::pose::Pose::residue(), core::conformation::Residue::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), and core::conformation::Residue::xyz().

Referenced by core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), and core::scoring::methods::RamachandranEnergy::residue_energy().

void core::scoring::Ramachandran::get_entries_per_torsion_bin	(	AA const	res_aa,
		std::map< char, core::Size > &	tb_frequencies
	)		const

core::chemical::AA core::scoring::Ramachandran::get_l_equivalent ( AA const d_aa ) const

When passed a d-amino acid, returns the l-equivalent. Returns aa_unk otherwise.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::get_L_equivalent().

core::Size core::scoring::Ramachandran::get_torsion_bin_index ( char torsion_bin ) const

void core::scoring::Ramachandran::init_rama_sampling_table ( char const torsion_bin ) const

private

Initialize the table holding the sample-able torsion space for each residue with each torsion given indices proportionate to its probability

References core::conformation::get_torsion_bin(), j, core::io::serialization::size(), ss_type, and torsion().

void core::scoring::Ramachandran::init_rama_sampling_tables_by_torsion_bin ( ) const

void core::scoring::Ramachandran::init_uniform_sampling_table ( ) const

private

References j, and torsion().

bool core::scoring::Ramachandran::is_canonical_d_aminoacid ( AA const res_aa ) const

Returns true if passed a core::chemical::AA corresponding to a D-amino acid, and false otherwise.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::is_canonical_D_aa().

bool core::scoring::Ramachandran::is_normally_connected ( conformation::Residue const & res ) const

Function to do a quick check that the upper connection is seqpos+1 and the lower connection is seqpos-1. Returns true if this is so, false otherwise.

Author: Vikram K. Mulligan

References core::conformation::Residue::connection_incomplete(), basic::options::option, basic::options::OptionKeys::score::rama_score_nonstandard_connections, core::conformation::Residue::residue_connection_partner(), and core::conformation::Residue::seqpos().

Referenced by core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), and core::scoring::methods::RamachandranEnergy::residue_energy().

bool core::scoring::Ramachandran::phipsi_in_allowed_rama	(	AA const	res_aa,
		Real	phi,
		Real	psi
	)		const

Return true if the given phi/psi pair is in the allowed space sampled by uniform_phipsi_from_allowed_rama.

References numeric::nonnegative_principal_angle_degrees().

bool core::scoring::Ramachandran::phipsi_in_forbidden_rama	(	AA const	res_aa,
		Real	phi,
		Real	psi
	)		const

Return false if the given phi/psi pair is in the allowed space sampled by uniform_phipsi_from_allowed_rama.

void core::scoring::Ramachandran::random_phipsi_from_rama	(	AA const	res_aa,
		Real &	phi,
		Real &	psi
	)		const

Sample phi/psi torsions with probabilities proportionate to their Ramachandran probabilities Note – this function had previously required that the option loops::nonpivot_torsion_sampling be active. This function now performs a just-in-time check to initialize these tables the first time they are requested – To properly multi-thread this code, the function should nab a mutex so that no two threads try to execute the code at once.

References numeric::random::random_range(), and numeric::random::uniform().

void core::scoring::Ramachandran::random_phipsi_from_rama_by_torsion_bin	(	AA const	res_aa,
		Real &	phi,
		Real &	psi,
		char const	torsion_bin
	)		const

functions for torsion-bin specific but otherwise random phi/psi angles

Author: Amelie Stein

Sample phi/psi torsions with probabilities proportionate to their Ramachandran probabilities – this version performs lookup restricted to specified torsion bins based on random_phipsi_from_rama and has the same issue for parallel running

Author: Amelie Stein (ameli.nosp@m.e.st.nosp@m.ein@u.nosp@m.csf..nosp@m.edu)

Date: Fri May 11 15:52:01 PDT 2012

returns a random phi/psi combination within the given torsion bin – WARNING: this will only work for the torsion bins that are currently implemented

References numeric::random::random_range(), and numeric::random::uniform().

void core::scoring::Ramachandran::read_rama	(	std::string const &	rama_map_filename,
		bool	use_bicubic_interpolation
	)

private

References utility::io::izstream::clear(), utility::io::izstream::close(), e_Periodic, utility::io::izstream::good(), core::chemical::num_canonical_aas, basic::database::open(), utility::io::izstream::open(), numeric::interpolation::spline::BicubicSpline::train(), and utility_exit_with_message.

void core::scoring::Ramachandran::read_rama_map_file ( utility::io::izstream * iunit )

private

References utility::io::izstream::clear(), utility::io::izstream::eof(), utility::io::izstream::fail(), utility::io::izstream::getline(), j, and ss_type.

void core::scoring::Ramachandran::uniform_phipsi_from_allowed_rama	(	AA const	res_aa,
		Real &	phi,
		Real &	psi
	)		const

Return a phi/psi pair picked uniformly from the regions of rama space with nonzero weight. Sampling with this method will not give a rama distribution; it will give a flat distribution in only the allowed regions of rama space.

References numeric::random::random_range(), random_range(), uniform(), and numeric::random::uniform().

void core::scoring::Ramachandran::write_rama_score_all ( Pose const & pose ) const

Member Data Documentation

Real const core::scoring::R::binw_

staticprivate

int const core::scoring::Ramachandran::n_aa_ = 20

staticprivate

int const core::scoring::Ramachandran::n_phi_ = 36

staticprivate

int const core::scoring::Ramachandran::n_psi_ = 36

staticprivate

ObjexxFCL::FArray4D_int core::scoring::R::ram_counts_

staticprivate

ObjexxFCL::FArray4D< Real > core::scoring::R::ram_energ_

staticprivate

ObjexxFCL::FArray2D< Real > core::scoring::R::ram_entropy_

staticprivate

ObjexxFCL::FArray4D< Real > core::scoring::R::ram_probabil_

staticprivate

utility::vector1< numeric::interpolation::spline::BicubicSpline > core::scoring::Ramachandran::rama_energy_splines_

private

bool core::scoring::R::rama_initialized_

staticprivate

Real const core::scoring::R::rama_sampling_factor_

staticprivate

utility::vector1< utility::vector1< utility::vector1< Real > > > core::scoring::Ramachandran::rama_sampling_table_

mutableprivate

utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > core::scoring::Ramachandran::rama_sampling_table_by_torsion_bin_

mutableprivate

Real const core::scoring::R::rama_sampling_thold_

staticprivate

utility::vector1< utility::vector1< utility::vector1< Real > > > core::scoring::Ramachandran::uniform_sampling_table_

mutableprivate

Table containing a uniform distribution of allowed torsion bins.

The indices are: table[amino acid][list][torsion]. The amino acid index comes from the AA enum and probably just goes from 1-20. The list index is what should be randomly chosen to produce uniform sampling. The torsion indices of 1 and 2 give the phi and psi bins, respectively.

The documentation for this class was generated from the following files:

symlinks/rosetta/src/core/scoring/Ramachandran.hh
symlinks/rosetta/src/core/scoring/Ramachandran.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation