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core::chemical::rings Namespace Reference

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< RingConformerread_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

typedef numeric::xyzVector< Distance > core::chemical::rings::Coords
using core::chemical::rings::PoseCOP = typedef utility::pointer::shared_ptr< RingConformer const >
using core::chemical::rings::PoseOP = typedef utility::pointer::shared_ptr< RingConformer >
typedef utility::pointer::shared_ptr< RingConformerSet const > core::chemical::rings::RingConformerSetCOP
typedef utility::pointer::shared_ptr< RingConformerSet > core::chemical::rings::RingConformerSetOP

Enumeration Type Documentation

: 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 

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

Enumerator
PHI 
THETA 

: 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

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().

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.

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

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

Return the opposite axial/equatorial designation.

References AXIAL, EQUATORIAL, and NEITHER.

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