#include <RingConformerSet.hh>

Inheritance diagram for core::chemical::rings::RingConformerSet:

Public Member Functions
	RingConformerSet (core::Size const ring_size, std::string const &lowest_conformer, utility::vector1< std::string > const &low_conformers)
	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...

bool	low_energy_conformers_are_known () const
	Are the low-energy conformers known for this 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 const &	get_ideal_conformer_from_nus (utility::vector1< core::Angle > const &angles, core::Real limit=90.0) const
	Return the conformer that is the best fit for the provided list of nu angles. More...

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

utility::vector1< RingConformer >	get_local_min_conformers () const

Private Member Functions
	RingConformerSet ()

void	init (core::Size const ring_size, std::string const &lowest_conformer_in, utility::vector1< std::string > const &low_conformers)

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

Private Attributes
core::Size	ring_size_

utility::vector1< RingConformer >	nondegenerate_conformers_

utility::vector1< RingConformer >	degenerate_conformers_

RingConformer	energy_minimum_conformer_

utility::vector1< RingConformer >	energy_minima_conformers_

Constructor & Destructor Documentation

core::chemical::rings::RingConformerSet::RingConformerSet	(	core::Size const	ring_size,
		std::string const &	lowest_conformer,
		utility::vector1< std::string > const &	low_conformers
	)

Standard constructor.

Parameters

<ring_size>	an unsigned integer expressing the size of the ring
<lowest_conformer>	IUPAC name for the lowest-energy ring conformer, if known
<low_conformers>	IUPAC name for other low-energy ring conformers

References init().

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

Copy constructor.

References copy_data().

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

virtual

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

private

Member Function Documentation

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

private

References degenerate_conformers_, energy_minima_conformers_, energy_minimum_conformer_, nondegenerate_conformers_, and ring_size_.

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

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

Return a list of all nondegenerate conformers in the set.

References nondegenerate_conformers_.

RingConformer const & core::chemical::rings::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::rings::RingConformer::CP_parameters, nondegenerate_conformers_, core::chemical::rings::PHI, core::chemical::rings::q, ring_size_, size(), core::chemical::rings::THETA, and core::chemical::TR().

RingConformer const & core::chemical::rings::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_, size(), and core::chemical::rings::RingConformer::specific_name.

RingConformer const & core::chemical::rings::RingConformerSet::get_ideal_conformer_from_nus	(	utility::vector1< core::Angle > const &	angles,
		core::Real	limit = `90.0`
	)		const

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

Parameters

<angles> an appropriate, ordered list of nu angles in degrees, one less than the ring size.

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::rings::RingConformer::nu_angles, ring_size_, size(), and core::chemical::TR().

utility::vector1< RingConformer > core::chemical::rings::RingConformerSet::get_local_min_conformers ( ) const

References energy_minima_conformers_.

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

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

References energy_minimum_conformer_.

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

Return a random conformer from the set.

References degenerate_conformers_, and core::scoring::rg.

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

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

References energy_minima_conformers_, and core::scoring::rg.

void core::chemical::rings::RingConformerSet::init	(	core::Size const	ring_size,
		std::string const &	lowest_conformer_in,
		utility::vector1< std::string > const &	low_conformers
	)