#include <Ramachandran2B.hh>

Inheritance diagram for core::scoring::Ramachandran2B:

Collaboration diagram for core::scoring::Ramachandran2B:

Public Types
typedef pose::Pose	Pose

typedef chemical::AA	AA

Public Member Functions
	Ramachandran2B ()

virtual	~Ramachandran2B ()

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, chemical::AA const left_aa, chemical::AA const right_aa, Real &rama, Real &drama_dphi, Real &drama_dpsi) const

Real	RamaE_Lower (conformation::Residue const &rsd, chemical::AA const &neighbor, Real &drama_dphi, Real &drama_dpsi) const

Real	RamaE_Lower (conformation::Residue const &rsd, chemical::AA const &neighbor) const

Real	RamaE_Upper (conformation::Residue const &rsd, chemical::AA const &neighbor, Real &drama_dphi, Real &drama_dpsi) const

Real	RamaE_Upper (conformation::Residue const &rsd, chemical::AA const &neighbor) const

Real	RamaE (conformation::Residue const &rsd, Real &drama_dphi, Real &drama_dpsi) const

Real	RamaE (conformation::Residue const &rsd) 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	IdealizeRamaEnergy (Real const phi, Real const psi, Real &rama, Real &drama_dphi, Real &drama_dpsi, Real const entropy, ObjexxFCL::FArray2A< Real > const &rama_for_res) const

void	random_phipsi_from_rama_left (AA const left_aa, AA const pos_aa, Real &phi, Real &psi) const

void	random_phipsi_from_rama_right (AA const pos_aa, AA const right_aa, Real &phi, Real &psi) const

void	random_phipsi_from_rama_by_torsion_bin_left (AA const left_aa, AA const pos_aa, Real &phi, Real &psi, char const torsion_bin) const
	function for torsion-bin specific but otherwise random phi/psi angles More...

void	random_phipsi_from_rama_by_torsion_bin_right (AA const pos_aa, AA const right_aa, Real &phi, Real &psi, char const torsion_bin) const

core::Size	get_torsion_bin_index (char torsion_bin) const

void	init_rama_sampling_tables_by_torsion_bin ()

void	get_entries_per_torsion_bin_left (AA const left_aa, AA const pos_aa, std::map< char, core::Size > &tb_frequencies) const

void	get_entries_per_torsion_bin_right (AA const pos_aa, AA const right_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

Private Member Functions
void	read_rama ()

void	init_rama_sampling_table_left (const char torsion_bin)
	based on the corresponding function for the Ramachandran class, but with adapted dimensions to accommodate the two neighbors More...

void	init_rama_sampling_table_right (const char torsion_bin)
	based on the corresponding function for the Ramachandran class, but with adapted dimensions to accommodate the two neighbors More...

Private Attributes
ObjexxFCL::FArray3D< Real >	ram_energ_

ObjexxFCL::FArray1D< Real >	ram_entropy_

ObjexxFCL::FArray4D< Real >	ram_energ_left_

ObjexxFCL::FArray2D< Real >	ram_entropy_left_

ObjexxFCL::FArray4D< Real >	ram_energ_right_

ObjexxFCL::FArray2D< Real >	ram_entropy_right_

Real const	rama_score_limit_

utility::vector1 < utility::vector1 < utility::vector1 < utility::vector1< Real > > > >	left_rama_sampling_table_

utility::vector1 < utility::vector1 < utility::vector1 < utility::vector1 < utility::vector1< Real > > > > >	left_rama_sampling_table_by_torsion_bin_

utility::vector1 < utility::vector1 < utility::vector1 < utility::vector1< Real > > > >	right_rama_sampling_table_

utility::vector1 < utility::vector1 < utility::vector1 < utility::vector1 < utility::vector1< Real > > > > >	right_rama_sampling_table_by_torsion_bin_

Static Private Attributes
static int const	n_phi_ = 36

static int const	n_psi_ = 36

static Real const	binw_

static int const	n_aa_ = 20

static int const	nullaa = 21

static ObjexxFCL::FArray4D< Real >	left_ram_probabil_

static ObjexxFCL::FArray4D< Real >	right_ram_probabil_

static Real const	rama_sampling_thold_

static Real const	rama_sampling_factor_

Detailed Description

Definition at line 48 of file Ramachandran2B.hh.

Member Typedef Documentation

typedef chemical::AA core::scoring::Ramachandran2B::AA

Definition at line 52 of file Ramachandran2B.hh.

typedef pose::Pose core::scoring::Ramachandran2B::Pose

Definition at line 51 of file Ramachandran2B.hh.

Constructor & Destructor Documentation

core::scoring::Ramachandran2B::Ramachandran2B ( )

Definition at line 75 of file Ramachandran2B.cc.

References read_rama().

core::scoring::Ramachandran2B::~Ramachandran2B ( )

virtual

Definition at line 64 of file Ramachandran2B.cc.

Member Function Documentation

void core::scoring::Ramachandran2B::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

Definition at line 93 of file Ramachandran2B.cc.

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

Real core::scoring::Ramachandran2B::eval_rama_score_residue	(	AA const	res_aa,
		Real const	phi,
		Real const	psi
	)		const

Definition at line 405 of file Ramachandran2B.cc.

References core::scoring::rama.

Referenced by core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), eval_rama_score_all(), eval_rama_score_residue(), and RamaE().

void core::scoring::Ramachandran2B::eval_rama_score_residue	(	conformation::Residue const &	res,
		chemical::AA const	left_aa,
		chemical::AA const	right_aa,
		Real &	rama,
		Real &	drama_dphi,
		Real &	drama_dpsi
	)		const

Definition at line 189 of file Ramachandran2B.cc.

References core::conformation::Residue::aa(), eval_rama_score_residue(), core::conformation::Residue::is_protein(), core::conformation::Residue::mainchain_torsion(), protocols::swa::phi(), protocols::swa::psi(), core::scoring::rama, RamaE(), RamaE_Lower(), and RamaE_Upper().

void core::scoring::Ramachandran2B::eval_rama_score_residue	(	conformation::Residue const &	res,
		Real &	rama,
		Real &	drama_dphi,
		Real &	drama_dpsi
	)		const

Definition at line 159 of file Ramachandran2B.cc.

References core::conformation::Residue::aa(), eval_rama_score_residue(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_terminus(), core::conformation::Residue::mainchain_torsion(), protocols::swa::phi(), protocols::swa::psi(), and core::scoring::rama.

void core::scoring::Ramachandran2B::eval_rama_score_residue	(	AA const	res_aa,
		Real const	phi,
		Real const	psi,
		Real &	rama,
		Real &	drama_dphi,
		Real &	drama_dpsi
	)		const

Definition at line 420 of file Ramachandran2B.cc.

References IdealizeRamaEnergy(), n_phi_, ram_energ_, and ram_entropy_.

void core::scoring::Ramachandran2B::get_entries_per_torsion_bin_left	(	AA const	left_aa,
		AA const	pos_aa,
		std::map< char, core::Size > &	tb_frequencies
	)		const

Definition at line 932 of file Ramachandran2B.cc.

References get_torsion_bin_index(), and left_rama_sampling_table_by_torsion_bin_.

Referenced by protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::refill_torsion_string_vector().

void core::scoring::Ramachandran2B::get_entries_per_torsion_bin_right	(	AA const	pos_aa,
		AA const	right_aa,
		std::map< char, core::Size > &	tb_frequencies
	)		const

Definition at line 949 of file Ramachandran2B.cc.

References get_torsion_bin_index(), and right_rama_sampling_table_by_torsion_bin_.

Referenced by protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::refill_torsion_string_vector().

core::Size core::scoring::Ramachandran2B::get_torsion_bin_index ( char torsion_bin) const

Definition at line 827 of file Ramachandran2B.cc.

Referenced by get_entries_per_torsion_bin_left(), get_entries_per_torsion_bin_right(), init_rama_sampling_table_left(), init_rama_sampling_table_right(), random_phipsi_from_rama_by_torsion_bin_left(), and random_phipsi_from_rama_by_torsion_bin_right().

void core::scoring::Ramachandran2B::IdealizeRamaEnergy	(	Real const	phi,
		Real const	psi,
		Real &	rama,
		Real &	drama_dphi,
		Real &	drama_dpsi,
		Real const	entropy,
		ObjexxFCL::FArray2A< Real > const &	rama_for_res
	)		const

Definition at line 237 of file Ramachandran2B.cc.

References binw_, n_phi_, core::scoring::rama, and rama_score_limit_.

Referenced by eval_rama_score_residue(), RamaE_Lower(), and RamaE_Upper().

void core::scoring::Ramachandran2B::init_rama_sampling_table_left ( const char torsion_bin)

private

based on the corresponding function for the Ramachandran class, but with adapted dimensions to accommodate the two neighbors

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

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

Definition at line 506 of file Ramachandran2B.cc.

References binw_, core::conformation::get_torsion_bin(), get_torsion_bin_index(), left_ram_probabil_, left_rama_sampling_table_, left_rama_sampling_table_by_torsion_bin_, n_aa_, n_phi_, n_psi_, rama_sampling_factor_, rama_sampling_thold_, and core::io::serialization::size().

Referenced by init_rama_sampling_tables_by_torsion_bin(), and random_phipsi_from_rama_left().

void core::scoring::Ramachandran2B::init_rama_sampling_table_right ( const char torsion_bin)

private

based on the corresponding function for the Ramachandran class, but with adapted dimensions to accommodate the two neighbors

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

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

Definition at line 669 of file Ramachandran2B.cc.

References binw_, core::conformation::get_torsion_bin(), get_torsion_bin_index(), n_aa_, n_phi_, n_psi_, rama_sampling_factor_, rama_sampling_thold_, right_ram_probabil_, right_rama_sampling_table_, right_rama_sampling_table_by_torsion_bin_, and core::io::serialization::size().

Referenced by init_rama_sampling_tables_by_torsion_bin(), and random_phipsi_from_rama_right().

void core::scoring::Ramachandran2B::init_rama_sampling_tables_by_torsion_bin ( )

Definition at line 834 of file Ramachandran2B.cc.

References init_rama_sampling_table_left(), and init_rama_sampling_table_right().

Referenced by random_phipsi_from_rama_by_torsion_bin_left(), and random_phipsi_from_rama_by_torsion_bin_right().

Real core::scoring::Ramachandran2B::RamaE	(	conformation::Residue const &	rsd,
		Real &	drama_dphi,
		Real &	drama_dpsi
	)		const

Definition at line 377 of file Ramachandran2B.cc.

References core::conformation::Residue::aa(), eval_rama_score_residue(), core::conformation::Residue::is_protein(), core::conformation::Residue::mainchain_torsion(), protocols::swa::phi(), and protocols::swa::psi().

Referenced by core::scoring::methods::RamachandranEnergy2B::eval_intrares_energy(), eval_rama_score_residue(), and RamaE().

Real core::scoring::Ramachandran2B::RamaE ( conformation::Residue const & rsd) const

Definition at line 368 of file Ramachandran2B.cc.

References RamaE().

Real core::scoring::Ramachandran2B::RamaE_Lower	(	conformation::Residue const &	rsd,
		chemical::AA const &	neighbor,
		Real &	drama_dphi,
		Real &	drama_dpsi
	)		const

Definition at line 286 of file Ramachandran2B.cc.

References core::conformation::Residue::aa(), IdealizeRamaEnergy(), core::conformation::Residue::is_protein(), core::conformation::Residue::mainchain_torsion(), n_phi_, protocols::swa::phi(), protocols::swa::psi(), ram_energ_left_, ram_entropy_left_, and core::scoring::rama.

Referenced by eval_rama_score_residue(), RamaE_Lower(), and core::scoring::methods::RamachandranEnergy2B::residue_pair_energy().

Real core::scoring::Ramachandran2B::RamaE_Lower	(	conformation::Residue const &	rsd,
		chemical::AA const &	neighbor
	)		const

Definition at line 276 of file Ramachandran2B.cc.

References RamaE_Lower().

Real core::scoring::Ramachandran2B::RamaE_Upper	(	conformation::Residue const &	rsd,
		chemical::AA const &	neighbor,
		Real &	drama_dphi,
		Real &	drama_dpsi
	)		const

Definition at line 332 of file Ramachandran2B.cc.

References core::conformation::Residue::aa(), IdealizeRamaEnergy(), core::conformation::Residue::is_protein(), core::conformation::Residue::mainchain_torsion(), n_phi_, protocols::swa::phi(), protocols::swa::psi(), ram_energ_right_, ram_entropy_right_, and core::scoring::rama.

Referenced by eval_rama_score_residue(), RamaE_Upper(), and core::scoring::methods::RamachandranEnergy2B::residue_pair_energy().

Real core::scoring::Ramachandran2B::RamaE_Upper	(	conformation::Residue const &	rsd,
		chemical::AA const &	neighbor
	)		const

Definition at line 322 of file Ramachandran2B.cc.

References RamaE_Upper().

void core::scoring::Ramachandran2B::random_phipsi_from_rama_by_torsion_bin_left	(	AA const	left_aa,
		AA const	pos_aa,
		Real &	phi,
		Real &	psi,
		char const	torsion_bin
	)		const

function 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

Definition at line 864 of file Ramachandran2B.cc.

References binw_, get_torsion_bin_index(), init_rama_sampling_tables_by_torsion_bin(), and left_rama_sampling_table_by_torsion_bin_.

Referenced by protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::perturb_chain().

void core::scoring::Ramachandran2B::random_phipsi_from_rama_by_torsion_bin_right	(	AA const	pos_aa,
		AA const	right_aa,
		Real &	phi,
		Real &	psi,
		char const	torsion_bin
	)		const

Definition at line 898 of file Ramachandran2B.cc.

References binw_, get_torsion_bin_index(), init_rama_sampling_tables_by_torsion_bin(), and right_rama_sampling_table_by_torsion_bin_.

Referenced by protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::perturb_chain().

void core::scoring::Ramachandran2B::random_phipsi_from_rama_left	(	AA const	left_aa,
		AA const	pos_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.

Definition at line 637 of file Ramachandran2B.cc.

References binw_, init_rama_sampling_table_left(), and left_rama_sampling_table_.

Referenced by protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::perturb_chain().

void core::scoring::Ramachandran2B::random_phipsi_from_rama_right	(	AA const	pos_aa,
		AA const	right_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.

Definition at line 803 of file Ramachandran2B.cc.

References binw_, init_rama_sampling_table_right(), and right_rama_sampling_table_.

Referenced by protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::perturb_chain().

void core::scoring::Ramachandran2B::read_rama ( )

private

Definition at line 441 of file Ramachandran2B.cc.

References left_ram_probabil_, n_aa_, nullaa, ram_energ_, ram_energ_left_, ram_energ_right_, ram_entropy_, ram_entropy_left_, ram_entropy_right_, right_ram_probabil_, and core::scoring::T().