#include <RingConformerSet.hh>

Public Member Functions
	RingConformerSet (core::uint const ring_size)
	Standard constructor. More...

	RingConformerSet (RingConformerSet const &object_to_copy)
	Copy constructor. More...

RingConformerSet &	operator= (RingConformerSet const &object_to_copy)

virtual	~RingConformerSet ()

virtual void	show (std::ostream &output=std::cout) const
	Generate string representation of RingConformerSet for debugging purposes. More...

core::Size	ring_size () const
	Return the ring size of the conformers in this set. More...

core::Size	size () const
	Return the size of the conformer set. More...

utility::vector1 < RingConformer > const &	get_all_nondegenerate_conformers () const
	Return a list of all nondegenerate conformers in the set. More...

RingConformer const &	get_ideal_conformer_by_name (std::string const name) const
	Return the conformer corresponding to the requested name. More...

RingConformer const &	get_ideal_conformer_by_CP_parameters (utility::vector1< core::Real > const parameters) const
	Return the conformer that is the best fit for the provided Cremer-Pople parameters. More...

RingConformer	get_ideal_conformer_from_nus (utility::vector1< core::Angle > const angles) const
	Return the conformer that is the best fit for the provided list of nu angles. More...

RingConformer	get_lowest_energy_conformer () const
	Return the conformer that is known from studies (if available) to be the lowest energy ring conformer. More...

RingConformer const &	get_random_conformer () const
	Return a random conformer from the set. More...

RingConformer	get_random_local_min_conformer () const
	Return a random conformer from the subset of conformers that are local minima. More...

Private Member Functions
	RingConformerSet ()

void	init (core::uint const ring_size)

void	copy_data (RingConformerSet &object_to_copy_to, RingConformerSet const &object_to_copy_from)

Static Private Member Functions
static utility::vector1 < RingConformer > const &	conformers_for_ring_size (core::Size ring_size)
	A set of ring conformers for the requested ring size. More...

Private Attributes
core::Size	ring_size_

utility::vector1< RingConformer >	nondegenerate_conformers_

utility::vector1< RingConformer >	degenerate_conformers_

utility::vector1< RingConformer >	energy_minima_conformers_

utility::vector1< RingConformer >	energy_maxima_conformers_

Constructor & Destructor Documentation

core::chemical::RingConformerSet::RingConformerSet ( core::uint const ring_size )

Standard constructor.

Parameters

<ring_size> an unsigned integer expressing the size of the saccharide ring

References init().

core::chemical::RingConformerSet::RingConformerSet ( RingConformerSet const & object_to_copy )

Copy constructor.

References copy_data().

core::chemical::RingConformerSet::~RingConformerSet ( )

virtual

core::chemical::RingConformerSet::RingConformerSet ( )

private

References init().

Member Function Documentation

utility::vector1< RingConformer > const & core::chemical::RingConformerSet::conformers_for_ring_size ( core::Size ring_size )

staticprivate

A set of ring conformers for the requested ring size.

References filename(), basic::database::full_name(), core::chemical::read_conformers_from_database_file_for_ring_size(), and ring_size().

Referenced by init().

void core::chemical::RingConformerSet::copy_data	(	RingConformerSet &	object_to_copy_to,
		RingConformerSet const &	object_to_copy_from
	)

private

References degenerate_conformers_, nondegenerate_conformers_, and ring_size_.

Referenced by operator=(), and RingConformerSet().

utility::vector1< RingConformer > const & core::chemical::RingConformerSet::get_all_nondegenerate_conformers ( ) const

Return a list of all nondegenerate conformers in the set.

References nondegenerate_conformers_.

RingConformer const & core::chemical::RingConformerSet::get_ideal_conformer_by_CP_parameters ( utility::vector1< core::Real > const parameters ) const

Return the conformer that is the best fit for the provided Cremer-Pople parameters.

Parameters

<parameter> an appropriate, ordered list of C-P parameters, with angles in degrees:

For 4-membered rings, provide q.
For 5-membered rings, provide q, phi.
For 6-membered rings, provide q, phi, theta. For ideal conformers, q is ignored, if non-zero, except for 4-membered rings, where only the sign matters.

Returns: matching RingConformer or exits, if no match is found

Note: This is slow, but it should not be called by most protocols, which will pull randomly from various subsets.

References core::chemical::RingConformer::CP_parameters, nondegenerate_conformers_, nonnegative_principal_angle_degrees(), core::chemical::PHI, core::chemical::q, ring_size_, core::chemical::THETA, core::chemical::TR, and utility_exit_with_message.

RingConformer const & core::chemical::RingConformerSet::get_ideal_conformer_by_name ( std::string const name ) const

Return the conformer corresponding to the requested name.

Parameters

<name> the IUPAC name for a specific ring conformation, e.g., "1C4"

For a saccharide residue, the provided name assumes a ring with the anomeric carbon labeled 1. That is, for a 2-ketopyranose in the 2C5 chair form, provide 1C4.

Returns: matching RingConformer or exits, if no match is found

Note: This is slow, but it should not be called by most protocols, which will pull randomly from various subsets.

References nondegenerate_conformers_, core::chemical::RingConformer::specific_name, and utility_exit_with_message.

RingConformer core::chemical::RingConformerSet::get_ideal_conformer_from_nus ( utility::vector1< core::Angle > const angles ) const

Return the conformer that is the best fit for the provided list of nu angles.

RingConformer core::chemical::RingConformerSet::get_lowest_energy_conformer ( ) const

Return the conformer that is known from studies (if available) to be the lowest energy ring conformer.

RingConformer const & core::chemical::RingConformerSet::get_random_conformer ( ) const

Return a random conformer from the set.

References degenerate_conformers_, RG, and numeric::random::RandomGenerator::uniform().

RingConformer core::chemical::RingConformerSet::get_random_local_min_conformer ( ) const

Return a random conformer from the subset of conformers that are local minima.

void core::chemical::RingConformerSet::init ( core::uint const ring_size )

private

References conformers_for_ring_size(), core::chemical::RingConformer::degeneracy, degenerate_conformers_, nondegenerate_conformers_, ring_size(), and ring_size_.

Referenced by RingConformerSet().

RingConformerSet & core::chemical::RingConformerSet::operator= ( RingConformerSet const & object_to_copy )

References copy_data().

core::Size core::chemical::RingConformerSet::ring_size ( ) const

inline

Return the ring size of the conformers in this set.

References ring_size_.

Referenced by conformers_for_ring_size(), and init().

void core::chemical::RingConformerSet::show ( std::ostream & output = std::cout ) const

virtual

Generate string representation of RingConformerSet for debugging purposes.

References nondegenerate_conformers_.

Referenced by core::chemical::operator<<().

core::Size core::chemical::RingConformerSet::size ( ) const

Return the size of the conformer set.

References nondegenerate_conformers_.

Member Data Documentation

utility::vector1<RingConformer> core::chemical::RingConformerSet::degenerate_conformers_

private

Referenced by copy_data(), get_random_conformer(), and init().

utility::vector1<RingConformer> core::chemical::RingConformerSet::energy_maxima_conformers_

private

utility::vector1<RingConformer> core::chemical::RingConformerSet::energy_minima_conformers_

private

utility::vector1<RingConformer> core::chemical::RingConformerSet::nondegenerate_conformers_

private

Referenced by copy_data(), get_all_nondegenerate_conformers(), get_ideal_conformer_by_CP_parameters(), get_ideal_conformer_by_name(), init(), show(), and size().

core::Size core::chemical::RingConformerSet::ring_size_

private

Referenced by copy_data(), get_ideal_conformer_by_CP_parameters(), init(), and ring_size().

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

src/core/chemical/RingConformerSet.hh
src/core/chemical/RingConformerSet.cc

Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation