#include <Ramachandran.hh>

Inheritance diagram for core::scoring::Ramachandran:

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 ()

std::string	get_custom_rama_table_filename (Rama_Table_Type const type) const
	Given a custom Rama table type, get the filename of the database file containing the data. More...

Rama_Table_Type	get_ramatable_type_by_name (std::string const &name) const
	Given a Rama_Table_Type name, return the type. More...

std::string	get_ramatable_name_by_type (Rama_Table_Type const type) const
	Given a Rama_Table_Type, return the name. More...

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
	Generate random values for phi and psi, biased by the Ramachandran plot of a particular amino acid. More...

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 res_aa, Real &phi, Real &psi, conformation::ppo_torsion_bin torsion_bin) const
	functions for torsion-bin specific but otherwise random phi/psi angles More...

void	get_entries_per_torsion_bin (AA const res_aa, std::map< conformation::ppo_torsion_bin, 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

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...

Size	n_phi_bins () const

Size	n_psi_bins () const

Real	rama_probability (core::chemical::AA aa, Real phi, Real psi) const

Real	minimum_sampling_probability () const

utility::vector1< Real > const &	cdf_for_aa (core::chemical::AA aa) const

utility::vector1< Real > const &	cdf_for_aa_for_torsion_bin (chemical::AA aa, conformation::ppo_torsion_bin) const

void	draw_random_phi_psi_from_extra_cdf (Rama_Table_Type const type, Real &phi, Real &psi)
	Pick a random phi, psi value from a custom Rama table. More...

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

void	load_custom_rama_table (Rama_Table_Type const type)
	Load a custom Ramachandran table, in addition to the 20x3 standard ones that are always loaded. More...

void	symmetrize_gly_table ()
	If the -symmetric_gly_tables option is used, symmetrize the aa_gly table. More...

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

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

void	initialize_rama_sampling_tables ()

void	init_rama_sampling_table (conformation::ppo_torsion_bin torsion_bin)

void	init_uniform_sampling_table ()

void	draw_random_phi_psi_from_cdf (utility::vector1< Real > const &cdf, Real &phi, Real &psi) const
	Pick a random phi and psi value given a cumulative distribution function. More...

bool	has_custom_rama_probability_table (Rama_Table_Type const type) const
	Has a particular custom Rama probability table been loaded? More...

bool	has_custom_rama_count_table (Rama_Table_Type const type) const
	Has a particular custom Rama count table been loaded? More...

bool	has_custom_rama_energy_table (Rama_Table_Type const type) const
	Has a particular custom Rama energy table been loaded? More...

bool	has_custom_rama_cdf (Rama_Table_Type const type) const
	Has a particular custom Rama cumulative distribution function been generated? More...

void	generate_custom_rama_cdf (Rama_Table_Type const type)
	Generate a custom Rama cumulative distribution function from the corresponding energy table. More...

utility::vector1< core::Real > const &	custom_rama_cdf (Rama_Table_Type const type) const
	Get a custom (extra) cumulative distribution function (CDF). More...

core::Real const &	custom_rama_probability_table (Rama_Table_Type const type, core::Size const phi, core::Size const psi) const
	Get a custom (extra) rama probability table. More...

Private Attributes
ObjexxFCL::FArray4D< Real >	ram_probabil_
	The Ramachandran probability tables. More...

std::map< Rama_Table_Type, utility::vector1 < utility::vector1< core::Real > > >	extra_ram_probabil_
	Extra Ramachandran count tables. More...

ObjexxFCL::FArray4D_int	ram_counts_
	The Ramachandran count tables. More...

std::map< Rama_Table_Type, utility::vector1 < utility::vector1< core::Size > > >	extra_ram_counts_
	Extra Ramachandran count tables. More...

ObjexxFCL::FArray4D< Real >	ram_energ_
	The Ramachandran energy tables. More...

std::map< Rama_Table_Type, utility::vector1 < utility::vector1< core::Real > > >	extra_ram_energ_
	Extra Ramachandran energy tables. More...

ObjexxFCL::FArray2D< Real >	ram_entropy_

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

utility::vector1 < utility::vector1< Real > >	cdf_
	The cumulative distribution functions (CDF) for all phi/psi bins for each amino acid. More...

std::map< Rama_Table_Type, utility::vector1< Real > >	extra_cdf_
	Additional cumulative distribution functions (CDFs). More...

ObjexxFCL::FArray2D < utility::vector1< Real > >	cdf_by_torsion_bin_

ObjexxFCL::FArray2D< Size >	n_valid_pp_bins_by_ppo_torbin_

utility::vector1 < utility::vector1< Size > >	phi_psi_bins_above_thold_

Static Private Attributes
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

Detailed Description

Definition at line 68 of file Ramachandran.hh.

Member Typedef Documentation

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

Definition at line 72 of file Ramachandran.hh.

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

Definition at line 71 of file Ramachandran.hh.

Constructor & Destructor Documentation

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

Definition at line 87 of file Ramachandran.cc.

References read_rama(), and core::scoring::TR().

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

Definition at line 133 of file Ramachandran.cc.

References read_rama().

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

virtual

Definition at line 78 of file Ramachandran.cc.

Member Function Documentation

utility::vector1< Real > const & core::scoring::Ramachandran::cdf_for_aa ( core::chemical::AA aa ) const

Definition at line 736 of file Ramachandran.cc.

References cdf_.

utility::vector1< Real > const & core::scoring::Ramachandran::cdf_for_aa_for_torsion_bin	(	chemical::AA	aa,
		conformation::ppo_torsion_bin	torsion_bin
	)		const

Definition at line 742 of file Ramachandran.cc.

References cdf_by_torsion_bin_.

utility::vector1< core::Real > const& core::scoring::Ramachandran::custom_rama_cdf ( Rama_Table_Type const type ) const

inlineprivate

Get a custom (extra) cumulative distribution function (CDF).

This function is const. The CDF must already have been generated.

Definition at line 358 of file Ramachandran.hh.

References extra_cdf_, and has_custom_rama_cdf().

Referenced by draw_random_phi_psi_from_extra_cdf().

core::Real const& core::scoring::Ramachandran::custom_rama_probability_table	(	Rama_Table_Type const	type,
		core::Size const	phi,
		core::Size const	psi
	)		const

inlineprivate

Get a custom (extra) rama probability table.

This function is const. The probability table must already have been loaded. To keep this consistent with the older Rama probability tables, the phi- and psi-indices are zero-based (running from 0 to 35).

Definition at line 367 of file Ramachandran.hh.

References extra_ram_probabil_, has_custom_rama_probability_table(), n_phi_, and n_psi_.

Referenced by generate_custom_rama_cdf().

void core::scoring::Ramachandran::draw_random_phi_psi_from_cdf	(	utility::vector1< Real > const &	cdf,
		Real &	phi,
		Real &	psi
	)		const

private

Pick a random phi and psi value given a cumulative distribution function.

Parameters

[in]	cdf	The cumulative distribution function.
[out]	phi	The output phi value.
[out]	psi	The output psi value.

A random bin from the cumulative distribution function is chosen first. Then uniform randomness is added within the chosen bin to produce the final phi and psi values.

Definition at line 1254 of file Ramachandran.cc.

References binw_, n_phi_, n_psi_, and core::scoring::rg.

Referenced by draw_random_phi_psi_from_extra_cdf(), random_phipsi_from_rama(), and random_phipsi_from_rama_by_torsion_bin().

void core::scoring::Ramachandran::draw_random_phi_psi_from_extra_cdf	(	Rama_Table_Type const	type,
		Real &	phi,
		Real &	psi
	)

Pick a random phi, psi value from a custom Rama table.

The custom Rama table is lazily loaded, so this function is necessarily non-const. By default, only the 20 canonical Rama tables are loaded.

Parameters

[in]	type	The type of custom rama table (an enum value).
[out]	phi	Randomly-drawn phi value, biased by the custom rama table.
[out]	psi	Randomly-drawn psi value, biased by the custom rama table.

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

Definition at line 761 of file Ramachandran.cc.

References custom_rama_cdf(), draw_random_phi_psi_from_cdf(), core::scoring::flat_d_aa_ramatable, core::scoring::flat_d_aa_ramatable_stringent, core::scoring::flat_l_aa_ramatable, core::scoring::flat_l_aa_ramatable_stringent, generate_custom_rama_cdf(), and has_custom_rama_cdf().

Referenced by protocols::simple_moves::SetTorsion::apply(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_mainchain_torsions().

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

Definition at line 272 of file Ramachandran.cc.

References core::pose::Pose::energies(), eval_rama_score_residue(), eval_rama_score_residue_nonstandard_connection(), core::scoring::ScoreFunction::has_zero_weight(), is_normally_connected(), 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

Definition at line 501 of file Ramachandran.cc.

References core::scoring::rama.

Referenced by core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), eval_rama_score_all(), eval_rama_score_residue(), eval_rama_score_residue_nonstandard_connection(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_c_terminus(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_full(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_n_terminus(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_phi_only(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_psi_only(), protocols::simple_moves::SmallMover::make_move(), protocols::simple_moves::ShearMover::make_move(), 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

Definition at line 561 of file Ramachandran.cc.

References eval_rama_score_residue(), and core::scoring::rama.

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

Definition at line 512 of file Ramachandran.cc.

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

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

Definition at line 574 of file Ramachandran.cc.

References eval_rama_score_residue().

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

Definition at line 592 of file Ramachandran.cc.

References binw_, get_l_equivalent(), is_canonical_d_aminoacid(), n_phi_, ram_entropy_, ram_probabil_, core::scoring::rama, and rama_energy_splines_.

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

Definition at line 453 of file Ramachandran.cc.

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::conformation::Residue::backbone_aa(), core::conformation::Residue::connection_incomplete(), eval_rama_score_residue(), 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 protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_alpha_aa_rama_check(), core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), eval_rama_score_all(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), and core::scoring::methods::RamachandranEnergy::residue_energy().

void core::scoring::Ramachandran::generate_custom_rama_cdf ( Rama_Table_Type const type )

private

Generate a custom Rama cumulative distribution function from the corresponding energy table.

This is generated from the ENERGY table, not from the COUNTS. If the energy table has not been loaded, this function loads the energy table first.

This is generated from the PROBABILITY table, not from the ENERGY table. If the energy table has not been loaded, this function loads the energy table first.

Definition at line 1279 of file Ramachandran.cc.

References custom_rama_probability_table(), extra_cdf_, has_custom_rama_probability_table(), load_custom_rama_table(), n_phi_, n_psi_, and core::scoring::unknown_ramatable_type.

Referenced by draw_random_phi_psi_from_extra_cdf().

std::string core::scoring::Ramachandran::get_custom_rama_table_filename ( Rama_Table_Type const type ) const

Given a custom Rama table type, get the filename of the database file containing the data.

Accesses the options system for this information.

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

Definition at line 158 of file Ramachandran.cc.

References core::scoring::flat_d_aa_ramatable, core::scoring::flat_d_aa_ramatable_stringent, core::scoring::flat_l_aa_ramatable, core::scoring::flat_l_aa_ramatable_stringent, core::scoring::flat_symm_dl_aa_ramatable, core::scoring::flat_symm_dl_aa_ramatable_stringent, core::scoring::flat_symm_gly_ramatable, core::scoring::flat_symm_gly_ramatable_stringent, core::scoring::flat_symm_pro_ramatable, and core::scoring::flat_symm_pro_ramatable_stringent.

Referenced by load_custom_rama_table().

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

Definition at line 438 of file Ramachandran.cc.

References phi_psi_bins_above_thold_, core::conformation::ppo_torbin_A, core::conformation::ppo_torbin_B, core::conformation::ppo_torbin_E, core::conformation::ppo_torbin_G, and core::conformation::ppo_torbin_X.

Referenced by protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::get_entries_per_torsion_bin().

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)

Definition at line 260 of file Ramachandran.cc.

References core::chemical::get_L_equivalent().

Referenced by eval_rama_score_residue(), and random_phipsi_from_rama().

std::string core::scoring::Ramachandran::get_ramatable_name_by_type ( Rama_Table_Type const type ) const

Given a Rama_Table_Type, return the name.

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

Definition at line 212 of file Ramachandran.cc.

References core::scoring::flat_d_aa_ramatable, core::scoring::flat_d_aa_ramatable_stringent, core::scoring::flat_l_aa_ramatable, core::scoring::flat_l_aa_ramatable_stringent, core::scoring::flat_symm_dl_aa_ramatable, core::scoring::flat_symm_dl_aa_ramatable_stringent, core::scoring::flat_symm_gly_ramatable, core::scoring::flat_symm_gly_ramatable_stringent, core::scoring::flat_symm_pro_ramatable, and core::scoring::flat_symm_pro_ramatable_stringent.

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_rama_table_type_from_name(), get_ramatable_type_by_name(), load_custom_rama_table(), and protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_custom_rama_table().

Rama_Table_Type core::scoring::Ramachandran::get_ramatable_type_by_name ( std::string const & name ) const

Given a Rama_Table_Type name, return the type.

Calls get_rama_table_name_by_type().

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

Calls get_ramatable_name_by_type().

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

Definition at line 198 of file Ramachandran.cc.

References core::scoring::end_of_ramatable_type_list, get_ramatable_name_by_type(), and core::scoring::unknown_ramatable_type.

Referenced by protocols::simple_moves::SetTorsion::apply(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_rama_table_type_from_name(), and protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_custom_rama_table().

bool core::scoring::Ramachandran::has_custom_rama_cdf ( Rama_Table_Type const type ) const

inlineprivate

Has a particular custom Rama cumulative distribution function been generated?

Custom Rama tables are lazily loaded, and cumulative distribution functions are lazily generated.

Definition at line 345 of file Ramachandran.hh.

References extra_cdf_, core::scoring::flat_d_aa_ramatable, and core::scoring::flat_l_aa_ramatable.

Referenced by custom_rama_cdf(), and draw_random_phi_psi_from_extra_cdf().

bool core::scoring::Ramachandran::has_custom_rama_count_table ( Rama_Table_Type const type ) const

inlineprivate

Has a particular custom Rama count table been loaded?

Custom Rama tables are lazily loaded.

Definition at line 331 of file Ramachandran.hh.

References extra_ram_counts_, core::scoring::flat_d_aa_ramatable, and core::scoring::flat_l_aa_ramatable.

Referenced by load_custom_rama_table().

bool core::scoring::Ramachandran::has_custom_rama_energy_table ( Rama_Table_Type const type ) const

inlineprivate

Has a particular custom Rama energy table been loaded?

Custom Rama tables are lazily loaded.

Definition at line 338 of file Ramachandran.hh.

References extra_ram_energ_, core::scoring::flat_d_aa_ramatable, and core::scoring::flat_l_aa_ramatable.

Referenced by load_custom_rama_table().

bool core::scoring::Ramachandran::has_custom_rama_probability_table ( Rama_Table_Type const type ) const

inlineprivate

Has a particular custom Rama probability table been loaded?

Custom Rama tables are lazily loaded.

Definition at line 324 of file Ramachandran.hh.

References extra_ram_probabil_, core::scoring::flat_d_aa_ramatable, and core::scoring::flat_l_aa_ramatable.

Referenced by custom_rama_probability_table(), generate_custom_rama_cdf(), and load_custom_rama_table().

void core::scoring::Ramachandran::init_rama_sampling_table ( conformation::ppo_torsion_bin torsion_bin )

private

Definition at line 1159 of file Ramachandran.cc.

References binw_, cdf_, cdf_by_torsion_bin_, core::conformation::get_torsion_bin(), n_aa_, n_phi_, n_psi_, n_valid_pp_bins_by_ppo_torbin_, core::conformation::ppo_torbin_X, ram_probabil_, and rama_sampling_thold_.

Referenced by initialize_rama_sampling_tables().

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

private

Definition at line 1228 of file Ramachandran.cc.

References n_aa_, n_phi_, n_psi_, phi_psi_bins_above_thold_, ram_probabil_, and rama_sampling_thold_.

Referenced by initialize_rama_sampling_tables().

void core::scoring::Ramachandran::initialize_rama_sampling_tables ( )

private

Definition at line 1147 of file Ramachandran.cc.

References init_rama_sampling_table(), init_uniform_sampling_table(), core::conformation::ppo_torbin_A, core::conformation::ppo_torbin_B, core::conformation::ppo_torbin_E, core::conformation::ppo_torbin_G, and core::conformation::ppo_torbin_X.

Referenced by read_rama().

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)

Definition at line 248 of file Ramachandran.cc.

References core::chemical::is_canonical_D_aa().

Referenced by eval_rama_score_residue(), and random_phipsi_from_rama().

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

Definition at line 702 of file Ramachandran.cc.

References core::conformation::Residue::connect_map_size(), core::conformation::Residue::connection_incomplete(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::residue_connection_partner(), and core::conformation::Residue::seqpos().

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

void core::scoring::Ramachandran::load_custom_rama_table ( Rama_Table_Type const type )

private

Load a custom Ramachandran table, in addition to the 20x3 standard ones that are always loaded.

Detailed: Intended for sampling with alternative Ramachandran distributions. Custom: tables are lazily loaded so as not to add to total Rosetta memory footprint.

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

Definition at line 1062 of file Ramachandran.cc.

References extra_ram_counts_, extra_ram_energ_, extra_ram_probabil_, protocols::abinitio::filename(), get_custom_rama_table_filename(), get_ramatable_name_by_type(), has_custom_rama_count_table(), has_custom_rama_energy_table(), has_custom_rama_probability_table(), n_phi_, n_psi_, and core::scoring::TR().

Referenced by generate_custom_rama_cdf().

Real core::scoring::Ramachandran::minimum_sampling_probability ( ) const

Definition at line 730 of file Ramachandran.cc.

References rama_sampling_thold_.

Size core::scoring::Ramachandran::n_phi_bins ( ) const

Definition at line 718 of file Ramachandran.cc.

References n_phi_.

Referenced by core::scoring::bin_transitions::BinTransitionData::set_up_subbins().

Size core::scoring::Ramachandran::n_psi_bins ( ) const

Definition at line 720 of file Ramachandran.cc.

References n_psi_.

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.

return true if the bin that the given phi/psi pair falls in has a probability that exceeds the rama_sampling_thold_ constant.

Definition at line 391 of file Ramachandran.cc.

References binw_, ram_probabil_, and rama_sampling_thold_.

Referenced by phipsi_in_forbidden_rama().

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.

Definition at line 407 of file Ramachandran.cc.

References phipsi_in_allowed_rama().

Real core::scoring::Ramachandran::rama_probability	(	core::chemical::AA	aa,
		Real	phi,
		Real	psi
	)		const

Definition at line 722 of file Ramachandran.cc.

References binw_, and ram_probabil_.

Referenced by core::scoring::bin_transitions::BinTransitionData::set_up_subbins().

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

Generate random values for phi and psi, biased by the Ramachandran plot of a particular amino acid.

Parameters

[in]	res_aa	The amino acid in question.
[out]	phi	Output phi value.
[out]	psi	Output psi value.

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. Note2 – this function has been hackily patched to allow it to be used for D-amino acids. (VKM – 21 Aug 2014).

Definition at line 350 of file Ramachandran.cc.

References cdf_, draw_random_phi_psi_from_cdf(), get_l_equivalent(), and is_canonical_d_aminoacid().

Referenced by protocols::simple_moves::SetTorsion::apply(), protocols::hybridization::BackboneTorsionSampler::perturb(), protocols::hybridization::BackboneTorsionPerturbation::perturb(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_mainchain_torsions().

void core::scoring::Ramachandran::random_phipsi_from_rama_by_torsion_bin	(	AA	res_aa,
		Real &	phi,
		Real &	psi,
		conformation::ppo_torsion_bin	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

Definition at line 426 of file Ramachandran.cc.

References cdf_by_torsion_bin_, and draw_random_phi_psi_from_cdf().

Referenced by protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::get_random_phi_psi_for_residue(), and protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::perturb_chain().

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

private

Definition at line 967 of file Ramachandran.cc.

References initialize_rama_sampling_tables(), core::chemical::num_canonical_aas, ram_entropy_, ram_probabil_, rama_energy_splines_, read_rama_map_file(), read_rama_map_file_shapovalov(), and symmetrize_gly_table().

Referenced by Ramachandran().

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

private

Definition at line 895 of file Ramachandran.cc.

References n_aa_, ram_counts_, ram_energ_, ram_entropy_, and ram_probabil_.

Referenced by read_rama().

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

private

Definition at line 1311 of file Ramachandran.cc.

References core::chemical::aa_from_name(), ram_energ_, ram_entropy_, ram_probabil_, and core::scoring::TR().

Referenced by read_rama().

void core::scoring::Ramachandran::symmetrize_gly_table ( )

private

If the -symmetric_gly_tables option is used, symmetrize the aa_gly table.

By default, the gly table is asymmetric because it is based on statistics from the PDB (which disproportionately put glycine in the D-amino acid region of Ramachandran space). However, the intrinsic propensities of glycine make it equally inclined to favour right- or left-handed conformation. (Glycine is achrial, and can't have a preference.) Must be called AFTER gly table load, but prior to bicubic interpolation setup. Note that symmetrization is based on the probability table, and carries over to the energy table; the counts table is left as-is (asymmetric).

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

Definition at line 798 of file Ramachandran.cc.

References core::chemical::aa_gly, n_phi_, n_psi_, ram_energ_, ram_entropy_, ram_probabil_, and core::scoring::TR().

Referenced by read_rama().

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.

Definition at line 369 of file Ramachandran.cc.

References binw_, n_psi_, and phi_psi_bins_above_thold_.

Referenced by protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset_with_balance().

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

Definition at line 334 of file Ramachandran.cc.

Member Data Documentation

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

staticprivate

Definition at line 417 of file Ramachandran.hh.

Referenced by draw_random_phi_psi_from_cdf(), eval_rama_score_residue(), init_rama_sampling_table(), phipsi_in_allowed_rama(), rama_probability(), and uniform_phipsi_from_allowed_rama().

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

private

The cumulative distribution functions (CDF) for all phi/psi bins for each amino acid.

Definition at line 424 of file Ramachandran.hh.

Referenced by cdf_for_aa(), init_rama_sampling_table(), and random_phipsi_from_rama().

ObjexxFCL::FArray2D< utility::vector1< Real > > core::scoring::Ramachandran::cdf_by_torsion_bin_

private

Definition at line 436 of file Ramachandran.hh.

Referenced by cdf_for_aa_for_torsion_bin(), init_rama_sampling_table(), and random_phipsi_from_rama_by_torsion_bin().

std::map< Rama_Table_Type, utility::vector1< Real > > core::scoring::Ramachandran::extra_cdf_

private

Additional cumulative distribution functions (CDFs).

Used for several things. For example, for storing CDFs for flat L-alpha amino acid sampling.

Definition at line 429 of file Ramachandran.hh.

Referenced by custom_rama_cdf(), generate_custom_rama_cdf(), and has_custom_rama_cdf().

std::map< Rama_Table_Type, utility::vector1< utility::vector1 < core::Size > > > core::scoring::Ramachandran::extra_ram_counts_

private

Extra Ramachandran count tables.

This is a map of (energy table type -> 2D array of counts by phi, psi).

Definition at line 396 of file Ramachandran.hh.

Referenced by has_custom_rama_count_table(), and load_custom_rama_table().

std::map< Rama_Table_Type, utility::vector1< utility::vector1 < core::Real > > > core::scoring::Ramachandran::extra_ram_energ_

private

Extra Ramachandran energy tables.

This is a map of (energy table type -> 2D array of energies by phi, psi).

Definition at line 407 of file Ramachandran.hh.

Referenced by has_custom_rama_energy_table(), and load_custom_rama_table().

std::map< Rama_Table_Type, utility::vector1< utility::vector1 < core::Real > > > core::scoring::Ramachandran::extra_ram_probabil_

private

Extra Ramachandran count tables.

This is a map of (energy table type -> 2D array of probabilities by phi, psi).

Definition at line 385 of file Ramachandran.hh.

Referenced by custom_rama_probability_table(), has_custom_rama_probability_table(), and load_custom_rama_table().

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

staticprivate

Definition at line 420 of file Ramachandran.hh.

Referenced by init_rama_sampling_table(), init_uniform_sampling_table(), and read_rama_map_file().

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

staticprivate

Definition at line 415 of file Ramachandran.hh.

Referenced by custom_rama_probability_table(), draw_random_phi_psi_from_cdf(), eval_rama_score_residue(), generate_custom_rama_cdf(), init_rama_sampling_table(), init_uniform_sampling_table(), load_custom_rama_table(), n_phi_bins(), and symmetrize_gly_table().

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

staticprivate

Definition at line 416 of file Ramachandran.hh.

Referenced by custom_rama_probability_table(), draw_random_phi_psi_from_cdf(), generate_custom_rama_cdf(), init_rama_sampling_table(), init_uniform_sampling_table(), load_custom_rama_table(), n_psi_bins(), symmetrize_gly_table(), and uniform_phipsi_from_allowed_rama().

ObjexxFCL::FArray2D< Size > core::scoring::Ramachandran::n_valid_pp_bins_by_ppo_torbin_

private

Definition at line 439 of file Ramachandran.hh.

Referenced by init_rama_sampling_table().

utility::vector1< utility::vector1< Size > > core::scoring::Ramachandran::phi_psi_bins_above_thold_

private

Definition at line 442 of file Ramachandran.hh.

Referenced by get_entries_per_torsion_bin(), init_uniform_sampling_table(), and uniform_phipsi_from_allowed_rama().

ObjexxFCL::FArray4D_int core::scoring::Ramachandran::ram_counts_

private

The Ramachandran count tables.

This is a FORTRAN-style 4D array. The first two dimensions are for phi and psi, respectively. The third is for secondary structure (helix, sheet, loop), though only the loop values are used nowadays. The fourth is for the amino acid type (20 entries). This is another horrible data structure that should be replaced by something much more intuitive.

Definition at line 392 of file Ramachandran.hh.

Referenced by read_rama_map_file().

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

private

The Ramachandran energy tables.

This is a FORTRAN-style 4D array. The first two dimensions are for phi and psi, respectively. The third is for secondary structure (helix, sheet, loop), though only the loop values are used nowadays. The fourth is for the amino acid type (20 entries). This is also a horrible data structure that should be replaced by something much more intuitive.

Definition at line 403 of file Ramachandran.hh.

Referenced by read_rama_map_file(), read_rama_map_file_shapovalov(), and symmetrize_gly_table().

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

private

Definition at line 409 of file Ramachandran.hh.

Referenced by eval_rama_score_residue(), read_rama(), read_rama_map_file(), read_rama_map_file_shapovalov(), and symmetrize_gly_table().

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

private

The Ramachandran probability tables.

This is a FORTRAN-style 4D array. The first two dimensions are for phi and psi, respectively. The third is for secondary structure (helix, sheet, loop), though only the loop values are used nowadays. The fourth is for the amino acid type (20 entries). This is a horrible data structure that should be replaced by something much more intuitive.

Definition at line 372 of file Ramachandran.hh.

Referenced by eval_rama_score_residue(), init_rama_sampling_table(), init_uniform_sampling_table(), phipsi_in_allowed_rama(), rama_probability(), read_rama(), read_rama_map_file(), read_rama_map_file_shapovalov(), and symmetrize_gly_table().