#include <MainchainScoreTable.hh>

Inheritance diagram for core::chemical::mainchain_potential::MainchainScoreTable:

Public Member Functions
	MainchainScoreTable ()
	Default constructor. More...

MainchainScoreTableOP	clone () const
	Clone function: make a copy of this object and return an owning pointer to the copy. More...

void	parse_rama_map_file_shapovalov (std::string const &filename, std::string const &file_contents, std::string const &res_type_name, bool const use_polycubic_interpolation)
	Parse a Shapovalov-style rama database file and set up this MainchainScoreTable. More...

void	clear ()
	Reset this object completely. More...

void	initialize_for_de_novo_generation (core::chemical::ResidueType const &restype, utility::vector1< core::Size > const &dimensions, utility::vector1< core::Size > const &mainchain_torsions_covered, bool const symmetrize)
	Initialize this object for on-the-fly generation of a mainchain scoretable. More...

void	set_energy (utility::vector1< core::Size > const &coords, core::Real const &energy_in)
	Set an entry in the energies tensor. More...

bool	increment_energy_coords (utility::vector1< core::Size > &coords) const
	Given coordinates in the energy tensor, increment the coordinates. More...

void	finalize_de_novo_scoretable_from_energies (core::Real const &kbt, bool const normalize)
	After the energies tensor has been populated, compute all derived data. More...

void	write_mainchain_scoretable_to_stream (std::stringstream &outstream) const
	After the mainchain scoretable has been finalized, write it to a scorefile. More...

bool	initialized () const
	Has this MainchainScoreTable been initialized? More...

void	get_mainchain_torsions_from_coords (utility::vector1< core::Size > const &coords_in, utility::vector1< core::Real > &torsions_out, bool const offset_if_symmetric=true) const
	Given a vector of coordinates, get the corresponding vector of mainchain torsions. More...

core::Real const &	energy_tensor (utility::vector1< core::Size > const &coords) const
	Access an entry in the energy tensor. More...

core::Real	energy (utility::vector1< core::Real > coords) const
	Access values in this MainchainScoreTable. More...

void	gradient (utility::vector1< core::Real > coords_in, utility::vector1< core::Real > &gradient_out) const
	Get the gradient with respect to x1,x2,x3,...xn for this MainchainScoreTable. More...

void	set_symmetrize_gly (bool const setting_in)
	Set whether we should symmetrize tables for glycine. More...

bool	symmetrize_gly () const
	Return whether we should symmetrize tables for glycine. More...

void	draw_random_mainchain_torsion_values (utility::vector1< core::Real > &torsions) const
	Given the cumulative distribution function (pre-calculated), draw a random set of mainchain torsion values biased by the probability distribution. More...

utility::vector1< core::Size > const &	get_mainchain_torsions_covered () const
	Get a const reference to the vector of mainchain torsions indices that this mainchain potential covers. More...

Private Member Functions
void	set_initialized ()
	Sets the state of this MainchainScoreTable object to "initialized". More...

void	set_dimension_and_ntorsions_for_restype (core::chemical::ResidueType const &restype, utility::vector1< core::Size > const &dimensions, utility::vector1< core::Size > mainchain_torsions_covered)
	Given a residue type, set dimension_ and n_mainchain_torsions_total_, and resize all tensors appropriately. More...

void	set_up_cumulative_distribution_function (numeric::MathNTensorBaseCOP< core::Real > probs, numeric::MathNTensorBaseOP< core::Real > cdf) const
	Set up the cumulative distribution function. More...

void	energies_from_probs (numeric::MathNTensorBaseOP< core::Real > energies, numeric::MathNTensorBaseCOP< core::Real > probs, core::Real const &kbt) const
	Given a probabilities tensor, calculate the energies. More...

void	check_linestream (std::istringstream const &linestream, std::string const &filename, bool const fail_on_eof=true) const
	Check that the stringstream doesn't have bad or eof status, and throw an error message if it does. More...

void	initialize_tensors (utility::vector1< core::Size > dimensions)
	Initialize the energies_ and probabilities_ tensors to 0-containing N-tensors, of the dimensions given by the dimensions vector. More...

void	iteratively_correct_energy_tensor (core::Real const &entropy)
	Convert the energies from probabilities to Rosetta energy units, and add the entropic correction factor. More...

bool	increment_coords (utility::vector1< core::Size > &coords, numeric::MathNTensorBaseCOP< core::Real > tensor) const
	Given coordinates in the energy tensor, go to the next bin. More...

void	get_opposite_coord (utility::vector1< core::Size > const &coord, numeric::MathNTensorBaseCOP< core::Real > tensor, utility::vector1< core::Size > &opposite_coord) const
	Given a set of coordinates in a MathNTensor, get the opposite coordinates. More...

void	set_up_polycubic_interpolation (utility::vector1< core::Real > const &offsets, utility::vector1< core::Size > const &dimensions)
	Once the internal MathNTensor has been set up, set up polycubic interpolation. More...

void	symmetrize_tensor (numeric::MathNTensorBaseOP< core::Real > tensor) const
	Given a tensor, symmetrize it. More...

Private Attributes
bool	initialized_
	Has this object been initialized? More...

core::Size	dimension_
	Dimensionality of this MainchainScoreTable. More...

utility::pointer::DeepCopyOP < numeric::MathNTensorBase < core::Real > >	energies_
	N-dimensional tensor for storing energies data. More...

utility::pointer::DeepCopyOP < numeric::MathNTensorBase < core::Real > >	probabilities_
	N-dimensional tensor for storing probabilities data. More...

utility::pointer::DeepCopyOP < numeric::MathNTensorBase < core::Real > >	cdf_
	N-dimensional tensor for storing the cumulative distribution function. More...

bool	use_polycubic_interpolation_
	Is this MainchainScoreTable set up with polycubic interpolation? More...

utility::pointer::DeepCopyOP < numeric::interpolation::spline::CubicSpline >	energies_spline_1D_
	Interpolation spline for the 1D case. More...

utility::pointer::DeepCopyOP < numeric::interpolation::spline::BicubicSpline >	energies_spline_2D_
	Interpolation spline for the 2D case. More...

utility::pointer::DeepCopyOP < numeric::interpolation::spline::PolycubicSplineBase >	energies_spline_ND_
	Interpolation spline for the N-dimensional case, where N > 2. More...

core::Size	n_mainchain_torsions_total_
	What is the total number of mainchain torsions for this residue type? More...

utility::vector1< core::Size >	mainchain_torsions_covered_
	If only a subset of mainchain torsions are provided, which ones are the relevant ones? More...

bool	symmetrize_gly_
	Symmetrize glycine tables? More...

Constructor & Destructor Documentation

core::chemical::mainchain_potential::MainchainScoreTable::MainchainScoreTable ( )

Default constructor.

References symmetrize_gly_.

Member Function Documentation

void core::chemical::mainchain_potential::MainchainScoreTable::check_linestream	(	std::istringstream const &	linestream,
		std::string const &	filename,
		bool const	fail_on_eof = `true`
	)		const

private

Check that the stringstream doesn't have bad or eof status, and throw an error message if it does.

Referenced by parse_rama_map_file_shapovalov().

void core::chemical::mainchain_potential::MainchainScoreTable::clear ( )

Reset this object completely.

References cdf_, dimension_, energies_, energies_spline_1D_, energies_spline_2D_, energies_spline_ND_, initialized_, mainchain_torsions_covered_, n_mainchain_torsions_total_, probabilities_, symmetrize_gly_, and use_polycubic_interpolation_.

Referenced by initialize_for_de_novo_generation().

MainchainScoreTableOP core::chemical::mainchain_potential::MainchainScoreTable::clone ( ) const

Clone function: make a copy of this object and return an owning pointer to the copy.

void core::chemical::mainchain_potential::MainchainScoreTable::draw_random_mainchain_torsion_values ( utility::vector1< core::Real > & torsions ) const

Given the cumulative distribution function (pre-calculated), draw a random set of mainchain torsion values biased by the probability distribution.

output is in the range (-180, 180].

Note: The dimensionality of the torsions vector will match the total degrees of freedom of the residue. If the mainchain potential is a function of fewer mainchain degrees of freedom, then those torsions on which the potential does NOT depend will have values of 0 in the torsions vector. Use the get_mainchain_torsions_covered() function to get the vector of mainchiain torsion indices that are covered.

output is in the range (-180, 180].

Note: The dimensionality of the torsions vector will match the degrees of freedom covered by the mainchain potential, NOT the total mainchain degrees of freedom. Use the get_mainchain_torsions_covered() function to get the vector of mainchiain torsion indices that are covered.

References cdf_, protocols::simple_filters::coords(), increment_coords(), initialized(), mainchain_torsions_covered_, n_mainchain_torsions_total_, and core::scoring::rg.

void core::chemical::mainchain_potential::MainchainScoreTable::energies_from_probs	(	numeric::MathNTensorBaseOP< core::Real >	energies,
		numeric::MathNTensorBaseCOP< core::Real >	probs,
		core::Real const &	kbt
	)		const

private

Given a probabilities tensor, calculate the energies.

Tensors must be the same size. Contents of the probabilities tensor are overwritten.

Parameters

[out]	energies	Tensor of energies.
[in]	probs	Tensor of probabilities.
[in]	kbt	Boltzmann temperature (k_B*T), in Rosetta energy units.

References protocols::simple_filters::coords(), and increment_coords().

Referenced by finalize_de_novo_scoretable_from_energies(), and parse_rama_map_file_shapovalov().

core::Real core::chemical::mainchain_potential::MainchainScoreTable::energy ( utility::vector1< core::Real > coords ) const

Access values in this MainchainScoreTable.

Note that the vector is deliberately not passed by reference. The function copies the vector and ensures that all coordinates are in the range [0, 360).

Note: The full vector of mainchain torsions should be passed in. If the potential is a function of fewer degrees of freedom, this function will disregard the appropraite entries in the coords vector.

References dimension_, energies_spline_1D_, energies_spline_2D_, energies_spline_ND_, initialized(), mainchain_torsions_covered_, and n_mainchain_torsions_total_.

core::Real const & core::chemical::mainchain_potential::MainchainScoreTable::energy_tensor ( utility::vector1< core::Size > const & coords ) const

Access an entry in the energy tensor.

Note that bounds checking only occurs in debug mode!

Note: Intended for unit testing.

References energies_, and initialized().

void core::chemical::mainchain_potential::MainchainScoreTable::finalize_de_novo_scoretable_from_energies	(	core::Real const &	kbt,
		bool const	normalize
	)

After the energies tensor has been populated, compute all derived data.

If "normalize" is true, the probabilities are normalized to 1, and the energies adjusted accordingly. (This has the effect of raising or lowering all of the energies by some constant.) If "symmetrize_gly_" is true, the tensors are made symmetric.

Note: Sets initalized_ to true.

References protocols::simple_filters::coords(), energies_, energies_from_probs(), increment_energy_coords(), initialized_, probabilities_, symmetrize_gly_, and symmetrize_tensor().

utility::vector1< core::Size > const& core::chemical::mainchain_potential::MainchainScoreTable::get_mainchain_torsions_covered ( ) const

inline

Get a const reference to the vector of mainchain torsions indices that this mainchain potential covers.

For example, for an oligourea, this would return {1, 2, 3}, since the Rama maps for oligoureas cover phi, theta, and psi (mainchain torsions 1, 2, and 3, respectively), but not mu or omega (mainchain torsions 4 and 5).

References mainchain_torsions_covered_.

void core::chemical::mainchain_potential::MainchainScoreTable::get_mainchain_torsions_from_coords	(	utility::vector1< core::Size > const &	coords_in,
		utility::vector1< core::Real > &	torsions_out,
		bool const	offset_if_symmetric = `true`
	)		const

Given a vector of coordinates, get the corresponding vector of mainchain torsions.

Bounds-checking only in debug mode!

Note: Offset is 0 if symmetrize_gly_ is false, 1/2 well if symmetrize_gly_ is true. Offset is only added if offset_if_symmetric is set to true.

References energies_, and symmetrize_gly_.

Referenced by write_mainchain_scoretable_to_stream().

void core::chemical::mainchain_potential::MainchainScoreTable::get_opposite_coord	(	utility::vector1< core::Size > const &	coord,
		numeric::MathNTensorBaseCOP< core::Real >	tensor,
		utility::vector1< core::Size > &	opposite_coord
	)		const

private

Given a set of coordinates in a MathNTensor, get the opposite coordinates.

For example, in a 2D 5x5 tensor, (1, 3) would yield an opposite of (3, 1).

Referenced by symmetrize_tensor().

void core::chemical::mainchain_potential::MainchainScoreTable::gradient	(	utility::vector1< core::Real >	coords_in,
		utility::vector1< core::Real > &	gradient_out
	)		const

Get the gradient with respect to x1,x2,x3,...xn for this MainchainScoreTable.

Parameters

[in]	coords_in	The coordinates at which to evaluate the gradient.
[out]	gradient_out	The resulting gradient.

Note: The full vector of mainchain torsions should be passed in. If the potential is a function of fewer degrees of freedom, this function will disregard the appropraite entries in the coords vector.

References dimension_, energies_spline_1D_, energies_spline_2D_, energies_spline_ND_, initialized(), mainchain_torsions_covered_, and n_mainchain_torsions_total_.

bool core::chemical::mainchain_potential::MainchainScoreTable::increment_coords	(	utility::vector1< core::Size > &	coords,
		numeric::MathNTensorBaseCOP< core::Real >	tensor
	)		const

private

Given coordinates in the energy tensor, go to the next bin.

As row ends are reached, the row resets to 1 and the next column is selected (and so forth down the dimensions).

Returns: Returns "true" if increment was successful, "false" if the end of the tensor has been reached.

As row ends are reached, the row resets to 1 and the next column is selected (and so forth down the dimensions). Returns "true" if increment was successful, "false" if the end of the tensor has been reached.

Referenced by draw_random_mainchain_torsion_values(), energies_from_probs(), increment_energy_coords(), iteratively_correct_energy_tensor(), set_up_cumulative_distribution_function(), and symmetrize_tensor().

bool core::chemical::mainchain_potential::MainchainScoreTable::increment_energy_coords ( utility::vector1< core::Size > & coords ) const

Given coordinates in the energy tensor, increment the coordinates.

Returns: Returns "true" if increment was successful, "false" if the end of the tensor has been reached.

References energies_, and increment_coords().

Referenced by finalize_de_novo_scoretable_from_energies(), and write_mainchain_scoretable_to_stream().

void core::chemical::mainchain_potential::MainchainScoreTable::initialize_for_de_novo_generation	(	core::chemical::ResidueType const &	restype,
		utility::vector1< core::Size > const &	dimensions,
		utility::vector1< core::Size > const &	mainchain_torsions_covered,
		bool const	symmetrize
	)

Initialize this object for on-the-fly generation of a mainchain scoretable.

Calls clear() first.

References clear(), set_dimension_and_ntorsions_for_restype(), and set_symmetrize_gly().

void core::chemical::mainchain_potential::MainchainScoreTable::initialize_tensors ( utility::vector1< core::Size > dimensions )

private

Initialize the energies_ and probabilities_ tensors to 0-containing N-tensors, of the dimensions given by the dimensions vector.

References cdf_, dimension_, energies_, energies_spline_1D_, energies_spline_2D_, energies_spline_ND_, and probabilities_.

Referenced by parse_rama_map_file_shapovalov(), and set_dimension_and_ntorsions_for_restype().

bool core::chemical::mainchain_potential::MainchainScoreTable::initialized ( ) const

inline

Has this MainchainScoreTable been initialized?

False if no score table has been read yet; true otherwise.

References initialized_.

Referenced by draw_random_mainchain_torsion_values(), energy(), energy_tensor(), gradient(), parse_rama_map_file_shapovalov(), and set_initialized().

void core::chemical::mainchain_potential::MainchainScoreTable::iteratively_correct_energy_tensor ( core::Real const & entropy )

private

Convert the energies from probabilities to Rosetta energy units, and add the entropic correction factor.

References protocols::simple_filters::coords(), energies_, and increment_coords().

Referenced by parse_rama_map_file_shapovalov().

void core::chemical::mainchain_potential::MainchainScoreTable::parse_rama_map_file_shapovalov	(	std::string const &	filename,
		std::string const &	file_contents,
		std::string const &	res_type_name,
		bool const	use_polycubic_interpolation
	)

Parse a Shapovalov-style rama database file and set up this MainchainScoreTable.

Sets initialized_ to true.

Parameters

[in]	filename	The name of the file that was read. (Just used for output messages – this function does not file read).
[in]	file_contents	The slurped contents of the file to parse.
[in]	res_type_name	The name of the ResidueType for which we're reading data. Data lines for other residue types will be ignored.
[in]	use_polycubic_interpolation	If true, uses polycubic interpolation; if false, uses polylinear interpolation.

References cdf_, check_linestream(), energies_, energies_from_probs(), initialize_tensors(), initialized(), iteratively_correct_energy_tensor(), mainchain_torsions_covered_, n_mainchain_torsions_total_, probabilities_, protocols::noesy_assign::round(), set_initialized(), set_up_cumulative_distribution_function(), set_up_polycubic_interpolation(), symmetrize_gly_, symmetrize_tensor(), and use_polycubic_interpolation_.

void core::chemical::mainchain_potential::MainchainScoreTable::set_dimension_and_ntorsions_for_restype	(	core::chemical::ResidueType const &	restype,
		utility::vector1< core::Size > const &	dimensions,
		utility::vector1< core::Size >	mainchain_torsions_covered
	)

private

Given a residue type, set dimension_ and n_mainchain_torsions_total_, and resize all tensors appropriately.

Assumes that all data have already been cleared. Call clear() before invoking this method.

Note: The mainchain_torsions_covered vector is deliberately passed by copy.

References core::chemical::ResidueTypeBase::base_name(), dimension_, initialize_tensors(), mainchain_torsions_covered_, n_mainchain_torsions_total_, and core::chemical::ResidueTypeBase::name().

Referenced by initialize_for_de_novo_generation().

void core::chemical::mainchain_potential::MainchainScoreTable::set_energy	(	utility::vector1< core::Size > const &	coords,
		core::Real const &	energy_in
	)

Set an entry in the energies tensor.

Note: Bounds checking only in debug build!

References energies_.

void core::chemical::mainchain_potential::MainchainScoreTable::set_initialized ( )

private

Sets the state of this MainchainScoreTable object to "initialized".

Double-checks that it's not already initialized, and throws an error if it is.

References initialized(), and initialized_.

Referenced by parse_rama_map_file_shapovalov().

void core::chemical::mainchain_potential::MainchainScoreTable::set_symmetrize_gly ( bool const setting_in )

Set whether we should symmetrize tables for glycine.

References symmetrize_gly_.

Referenced by initialize_for_de_novo_generation().

void core::chemical::mainchain_potential::MainchainScoreTable::set_up_cumulative_distribution_function	(	numeric::MathNTensorBaseCOP< core::Real >	probs,
		numeric::MathNTensorBaseOP< core::Real >	cdf
	)		const

private

Set up the cumulative distribution function.

The CDF is used for drawing random mainchain torsion values biased by the relative probabilities of mainchain torsion values.

Note: Each bin stores the probability of being in the current bin or an earlier bin (so the final bin should store a probability of 1). This differs from the convention used in Ramachandran.cc, but allows for a simpler drawing algorithm: I pick a uniformly-distributed random number from 0 to 1, loop through my bins, and stop when I get to a bin with a value greater than the value that I have drawn.

Parameters

[in]	probs	Tensor of probabilities. Need not be normalized (sum to 1).
[out]	cdf	Tensor for the cumulative distribution function.

References protocols::simple_filters::coords(), and increment_coords().

Referenced by parse_rama_map_file_shapovalov().

void core::chemical::mainchain_potential::MainchainScoreTable::set_up_polycubic_interpolation	(	utility::vector1< core::Real > const &	offsets,
		utility::vector1< core::Size > const &	dimensions
	)

private

Once the internal MathNTensor has been set up, set up polycubic interpolation.

This function includes special-case logic for setting up cubic interpolation in the 1D case and bicubic interpolation in the 2D case, since these are not handled by the PolycubicSpline class.

Parameters

[in]	offsets	Vector of offset values, from 0 to 1 – where centres are, as fraction of bin width.
[in]	dimensions	Vector of number of entries in each dimension. Bin widths are inferred from this: 36 entries would correspond to 10-degree bins.

References dimension_, energies_, energies_spline_2D_, energies_spline_ND_, and probabilities_.

Referenced by parse_rama_map_file_shapovalov().

bool core::chemical::mainchain_potential::MainchainScoreTable::symmetrize_gly ( ) const

inline

Return whether we should symmetrize tables for glycine.

References symmetrize_gly_.

void core::chemical::mainchain_potential::MainchainScoreTable::symmetrize_tensor ( numeric::MathNTensorBaseOP< core::Real > tensor ) const

private

Given a tensor, symmetrize it.

Assumes that tensor stores probabilities; normalizes tensor in the process.

References get_opposite_coord(), increment_coords(), and protocols::hybridization::val.

Referenced by finalize_de_novo_scoretable_from_energies(), and parse_rama_map_file_shapovalov().

void core::chemical::mainchain_potential::MainchainScoreTable::write_mainchain_scoretable_to_stream ( std::stringstream & outstream ) const

After the mainchain scoretable has been finalized, write it to a scorefile.

References protocols::simple_filters::coords(), dimension_, energies_, get_mainchain_torsions_from_coords(), increment_energy_coords(), mainchain_torsions_covered_, n_mainchain_torsions_total_, probabilities_, and protocols::noesy_assign::round().

Member Data Documentation

utility::pointer::DeepCopyOP< numeric::MathNTensorBase< core::Real > > core::chemical::mainchain_potential::MainchainScoreTable::cdf_

private

N-dimensional tensor for storing the cumulative distribution function.

This is used for drawing random mainchain torsion values biased by the relative probabilities of having a set of mainchain torsion values.

Referenced by clear(), draw_random_mainchain_torsion_values(), initialize_tensors(), and parse_rama_map_file_shapovalov().

core::Size core::chemical::mainchain_potential::MainchainScoreTable::dimension_

private

Dimensionality of this MainchainScoreTable.

Minimum 1, maximum 9. A value of 0 indicates that it is uninitialized.

Referenced by clear(), energy(), gradient(), initialize_tensors(), set_dimension_and_ntorsions_for_restype(), set_up_polycubic_interpolation(), and write_mainchain_scoretable_to_stream().

utility::pointer::DeepCopyOP< numeric::MathNTensorBase< core::Real > > core::chemical::mainchain_potential::MainchainScoreTable::energies_

private

N-dimensional tensor for storing energies data.

Referenced by clear(), energy_tensor(), finalize_de_novo_scoretable_from_energies(), get_mainchain_torsions_from_coords(), increment_energy_coords(), initialize_tensors(), iteratively_correct_energy_tensor(), parse_rama_map_file_shapovalov(), set_energy(), set_up_polycubic_interpolation(), and write_mainchain_scoretable_to_stream().

utility::pointer::DeepCopyOP< numeric::interpolation::spline::CubicSpline > core::chemical::mainchain_potential::MainchainScoreTable::energies_spline_1D_

private

Interpolation spline for the 1D case.

Only used if use_polycubic_interpolation_ is true and the energies_ MathNTensor is 1D. Null otherwise.

Referenced by clear(), energy(), gradient(), and initialize_tensors().

utility::pointer::DeepCopyOP< numeric::interpolation::spline::BicubicSpline > core::chemical::mainchain_potential::MainchainScoreTable::energies_spline_2D_

private

Interpolation spline for the 2D case.

Only used if use_polycubic_interpolation_ is true and the energies_ MathNTensor is 2D. Null otherwise.

Referenced by clear(), energy(), gradient(), initialize_tensors(), and set_up_polycubic_interpolation().

utility::pointer::DeepCopyOP< numeric::interpolation::spline::PolycubicSplineBase > core::chemical::mainchain_potential::MainchainScoreTable::energies_spline_ND_

private

Interpolation spline for the N-dimensional case, where N > 2.

Only used if use_polycubic_interpolation_ is true and the energies_ MathNTensor is N-dimensional, where N > 2. Null otherwise.

Referenced by clear(), energy(), gradient(), initialize_tensors(), and set_up_polycubic_interpolation().

bool core::chemical::mainchain_potential::MainchainScoreTable::initialized_

private

Has this object been initialized?

Referenced by clear(), finalize_de_novo_scoretable_from_energies(), initialized(), and set_initialized().

utility::vector1< core::Size > core::chemical::mainchain_potential::MainchainScoreTable::mainchain_torsions_covered_

private

If only a subset of mainchain torsions are provided, which ones are the relevant ones?

For oligoureas, for example, this would be {1, 2, 3}, since only phi, theta, and psi are covered by the mainchain potential, and mu and theta (torsions 4 and 5) are covered by the omega score term.

Referenced by clear(), draw_random_mainchain_torsion_values(), energy(), get_mainchain_torsions_covered(), gradient(), parse_rama_map_file_shapovalov(), set_dimension_and_ntorsions_for_restype(), and write_mainchain_scoretable_to_stream().

core::Size core::chemical::mainchain_potential::MainchainScoreTable::n_mainchain_torsions_total_

private

What is the total number of mainchain torsions for this residue type?

Could be different than the dimension of the tensors, if certain torsions are fixed. Note that this excludes omega (the inter-residue torsion), so for an alpha-amino acid, it should be "2". In the case of an oligourea, it is "3" instead of "4", since mu is fixed at 180 and enforced (along with omega) by the OmegaTetherEnergy.

Referenced by clear(), draw_random_mainchain_torsion_values(), energy(), gradient(), parse_rama_map_file_shapovalov(), set_dimension_and_ntorsions_for_restype(), and write_mainchain_scoretable_to_stream().