Classes
struct	RingConformer
	A structure for storing information for specific, idealized ring conformers. More...

class	RingConformerManager

class	RingConformerSet

Typedefs
using	PoseOP = utility::pointer::shared_ptr< RingConformer >

using	PoseCOP = utility::pointer::shared_ptr< RingConformer const >

typedef utility::pointer::shared_ptr< RingConformerSet >	RingConformerSetOP

typedef utility::pointer::shared_ptr< RingConformerSet const >	RingConformerSetCOP

typedef numeric::xyzVector< Distance >	Coords

Enumerations
enum	AxEqDesignation { NEITHER = 0 , AXIAL , EQUATORIAL }
	: The axial/equatorial designation for bonds/substituents on ring systems. More...

enum	CPParameter { q = 1 , PHI , THETA }
	Enumerators for the three Cremer-Pople "ring-puckering" parameters used to describe 4-, 5-, and 6-membered ring conformers. More...

enum	RingSaturationType { ALIPHATIC = 0 , AROMATIC }
	: An enumeration of saturation types for ring systems. More...

Functions
utility::vector1< RingConformer >	read_conformers_from_database_file_for_ring_size (std::string const &filename, core::Size ring_size)
	Return a list of ring conformers, read from a database file. More...

bool	operator== (RingConformer const &ring1, RingConformer const &ring2)

bool	operator!= (RingConformer const &ring1, RingConformer const &ring2)

std::ostream &	operator<< (std::ostream &output, RingConformer const &object_to_output)

std::ostream &	operator<< (std::ostream &output, RingConformerSet const &object_to_output)

AxEqDesignation	opposite_designation (AxEqDesignation designation)
	Return the opposite axial/equatorial designation. More...

AxEqDesignation	is_atom_axial_or_equatorial_to_ring (Coords const &query_atom, Coords const &attachment_atom, utility::vector1< Coords > const &ring_atoms)
	Are the query atom coordinates axial or equatorial to the given ring or neither? More...

Typedef Documentation

◆ Coords

typedef numeric::xyzVector< Distance > core::chemical::rings::Coords

◆ PoseCOP

using core::chemical::rings::PoseCOP = typedef utility::pointer::shared_ptr< RingConformer const >

◆ PoseOP

using core::chemical::rings::PoseOP = typedef utility::pointer::shared_ptr< RingConformer >

◆ RingConformerSetCOP

typedef utility::pointer::shared_ptr< RingConformerSet const > core::chemical::rings::RingConformerSetCOP

◆ RingConformerSetOP

typedef utility::pointer::shared_ptr< RingConformerSet > core::chemical::rings::RingConformerSetOP

Enumeration Type Documentation

◆ AxEqDesignation

enum core::chemical::rings::AxEqDesignation

: The axial/equatorial designation for bonds/substituents on ring systems.

Axial: "...[B]onds to ring atoms (and molecular entities attached to such bonds) are... axial... [if] the bonds make a relatively large... angle... with the plane containing or passing closest to a majority of the ring atoms. ...[A]xial bonds are approximately parallel to the C3 axis....
Equatorial: "...[B]onds to ring atoms (and molecular entities attached to such bonds) are... equatorial... [if] the bonds make a relatively small... angle... with the plane containing or passing closest to a majority of the ring atoms. ...[E]quatorial bonds [are] approximately parallel to two of the ring bonds. http://goldbook.iupac.org/A00546.html

Note: NEITHER has the value of 0 and so can be used in conditionals as false.

Enumerator
NEITHER
AXIAL
EQUATORIAL

◆ CPParameter

enum core::chemical::rings::CPParameter

Enumerators for the three Cremer-Pople "ring-puckering" parameters used to describe 4-, 5-, and 6-membered ring conformers.

Enumerator
q
PHI
THETA

◆ RingSaturationType

enum core::chemical::rings::RingSaturationType

: An enumeration of saturation types for ring systems.

The value labels if a ring is aliphatic, aromatic, or some other saturation state.

Note: Currently, the only options are ALIPHATIC and AROMATIC. In the future, other states will be added.

Enumerator
ALIPHATIC
AROMATIC

Function Documentation

◆ is_atom_axial_or_equatorial_to_ring()

AxEqDesignation core::chemical::rings::is_atom_axial_or_equatorial_to_ring	(	Coords const &	query_atom,
		Coords const &	attachment_atom,
		utility::vector1< Coords > const &	ring_atoms
	)

Are the query atom coordinates axial or equatorial to the given ring or neither?

This function calculates an average plane and determines whether the coordinates of a given atom are axial or equatorial to it (or neither).

Parameters

<query_atom>	The Cartesian coordinates of the atom in question.
<attachment_atom>	The Cartesian coordinates of the atom to which the query atom is attached, which must be a member of <ring_atoms>
<ring_atoms>	A list of Cartesian coordinates for the points of a monocyclic ring system in sequence.

Returns: An AxEqDesignation enum type value: AXIAL, EQUATORIAL, or NEITHER

References AXIAL, EQUATORIAL, NEITHER, and core::chemical::TR().

Referenced by core::conformation::is_atom_axial_or_equatorial_to_ring(), and protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs().

◆ operator!=()

bool core::chemical::rings::operator!=	(	RingConformer const &	ring1,
		RingConformer const &	ring2
	)

Two conformers are not equivalent if their CP parameters are not the same.

References core::chemical::rings::RingConformer::CP_parameters.

◆ operator<<() [1/2]

std::ostream & core::chemical::rings::operator<<	(	std::ostream &	output,
		RingConformer const &	object_to_output
	)

References core::chemical::rings::RingConformer::CP_parameters, core::chemical::rings::RingConformer::general_name, core::chemical::rings::RingConformer::nu_angles, and core::chemical::rings::RingConformer::specific_name.

◆ operator<<() [2/2]

std::ostream & core::chemical::rings::operator<<	(	std::ostream &	output,
		RingConformerSet const &	object_to_output
	)

References core::chemical::rings::RingConformerSet::show().

◆ operator==()

bool core::chemical::rings::operator==	(	RingConformer const &	ring1,
		RingConformer const &	ring2
	)

Two conformers are equivalent if their CP parameters are the same.

References core::chemical::rings::RingConformer::CP_parameters.

◆ opposite_designation()

AxEqDesignation core::chemical::rings::opposite_designation ( core::chemical::rings::AxEqDesignation designation )

Return the opposite axial/equatorial designation.

References AXIAL, EQUATORIAL, and NEITHER.

◆ read_conformers_from_database_file_for_ring_size()

utility::vector1< RingConformer > core::chemical::rings::read_conformers_from_database_file_for_ring_size	(	std::string const &	filename,
		core::Size	ring_size
	)

Return a list of ring conformers, read from a database file.

References core::chemical::rings::RingConformer::CP_parameters, core::chemical::rings::RingConformer::degeneracy, protocols::abinitio::filename(), core::chemical::rings::RingConformer::general_name, core::chemical::rings::RingConformer::nu_angles, core::chemical::rings::RingConformer::specific_name, core::chemical::rings::RingConformer::tau_angles, and core::chemical::TR().

Referenced by core::chemical::rings::RingConformerManager::get_conformers_for_ring_size_and_type().

Classes

Typedefs

Enumerations

Functions