Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Public Attributes | List of all members
protocols::match::upstream::BuildSet Class Reference

A simple class that describes the geometry for a particular residue type. It describes the coordinate frame geometry for the fourth atom defining each chi dihedral. The fourth atom is called the "chi tip" atom, as it's at the tip of the growing kinematic chain when building chi i. This class also describes the location of the atoms controlled by each chi which are not the chi-tip atoms; it measures their location in the coordinate frame of the chi-tip atom. More...

#include <ProteinUpstreamBuilder.hh>

Inheritance diagram for protocols::match::upstream::BuildSet:
Inheritance graph
[legend]

Public Types

typedef core::Size Size
 
typedef core::Real Real
 
typedef utility::VirtualBase parent
 

Public Member Functions

 BuildSet ()
 
 ~BuildSet () override
 
 BuildSet (BuildSet const &)
 
BuildSetoperator= (BuildSet const &rhs)
 
void set_residue_type (core::chemical::ResidueTypeCOP restype, bool backbone_only=false)
 initialization More...
 
void set_sample_strategy_for_chi (core::Size chi, SampleStrategyData const &data)
 
void set_downstream_algorithm (downstream::DownstreamAlgorithmOP)
 
bool has_restype () const
 accessors More...
 
core::chemical::ResidueType const & restype () const
 
bool backbone_only () const
 
UpstreamResTypeGeometry const & restype_geometry () const
 
Real probability_limit () const
 
SampleStrategyData const & sample_strategy_for_chi (core::Size chi) const
 
bool has_algorithm ()
 
downstream::DownstreamAlgorithm
const & 
algorithm () const
 
downstream::DownstreamAlgorithmalgorithm ()
 
core::Size nbonds_from_bb_atom (core::Size atom_index) const
 
ProbeRadius atom_radius (core::Size atomno) const
 
void set_fa_dun_cutoff (core::Real cutoff)
 
bool check_fa_dun () const
 
core::Real fa_dun_cutoff () const
 

Public Attributes

core::chemical::ResidueTypeCOP restype_
 
bool backbone_only_
 
UpstreamResTypeGeometryOP restype_geom_
 
Real rot_prob_accumulation_limit_
 
utility::vector1
< SampleStrategyData
sample_strategy_for_chi_
 
utility::vector1< core::Sizenbonds_from_bb_atom_
 
utility::vector1< ProbeRadiusatom_radii_
 
downstream::DownstreamAlgorithmOP algorithm_
 
bool check_fa_dun_
 
core::Real fa_dun_cutoff_
 

Detailed Description

A simple class that describes the geometry for a particular residue type. It describes the coordinate frame geometry for the fourth atom defining each chi dihedral. The fourth atom is called the "chi tip" atom, as it's at the tip of the growing kinematic chain when building chi i. This class also describes the location of the atoms controlled by each chi which are not the chi-tip atoms; it measures their location in the coordinate frame of the chi-tip atom.

To generate the coordinate of the chi-tip atom, the stored coordinate frame is multiplied by the coordinate frame at the third atom after that coordinate frame has been multipled by the chi-angle-z-axis rotation HT. Still sketchy on this class. It holds all of the data needed for describing the geometry of the downstream partner relative to the upstream partner for a single residue type. This class holds the data for deciding which base rotamers to consider, how each base rotamer should be expanded to produce a full set of chi rotamers, and how to orient the downstream partner relative to this rotamer. It also holds the UpstreamResTypeGeometry object for the restype being built.

Member Typedef Documentation

typedef utility::VirtualBase protocols::match::upstream::BuildSet::parent

Constructor & Destructor Documentation

protocols::match::upstream::BuildSet::BuildSet ( )
protocols::match::upstream::BuildSet::~BuildSet ( )
overridedefault
protocols::match::upstream::BuildSet::BuildSet ( BuildSet const &  other)

Member Function Documentation

downstream::DownstreamAlgorithm const& protocols::match::upstream::BuildSet::algorithm ( ) const
inline
downstream::DownstreamAlgorithm& protocols::match::upstream::BuildSet::algorithm ( )
inline

References algorithm_.

ProbeRadius protocols::match::upstream::BuildSet::atom_radius ( core::Size  atomno) const
inline

References atom_radii_.

bool protocols::match::upstream::BuildSet::backbone_only ( ) const
inline
bool protocols::match::upstream::BuildSet::check_fa_dun ( ) const
inline

References check_fa_dun_.

core::Real protocols::match::upstream::BuildSet::fa_dun_cutoff ( ) const
inline

References fa_dun_cutoff_.

bool protocols::match::upstream::BuildSet::has_algorithm ( )
inline
bool protocols::match::upstream::BuildSet::has_restype ( ) const
inline

accessors

References restype_.

Referenced by protocols::match::Matcher::create_ds_builder().

core::Size protocols::match::upstream::BuildSet::nbonds_from_bb_atom ( core::Size  atom_index) const
inline

References nbonds_from_bb_atom_.

BuildSet & protocols::match::upstream::BuildSet::operator= ( BuildSet const &  rhs)
Real protocols::match::upstream::BuildSet::probability_limit ( ) const
inline
core::chemical::ResidueType const& protocols::match::upstream::BuildSet::restype ( ) const
inline
UpstreamResTypeGeometry const& protocols::match::upstream::BuildSet::restype_geometry ( ) const
inline

References restype_geom_.

SampleStrategyData const& protocols::match::upstream::BuildSet::sample_strategy_for_chi ( core::Size  chi) const
inline
void protocols::match::upstream::BuildSet::set_downstream_algorithm ( downstream::DownstreamAlgorithmOP  algorithm)
void protocols::match::upstream::BuildSet::set_fa_dun_cutoff ( core::Real  cutoff)
void protocols::match::upstream::BuildSet::set_residue_type ( core::chemical::ResidueTypeCOP  restype,
bool  backbone_only = false 
)
void protocols::match::upstream::BuildSet::set_sample_strategy_for_chi ( core::Size  chi,
SampleStrategyData const &  data 
)

Member Data Documentation

downstream::DownstreamAlgorithmOP protocols::match::upstream::BuildSet::algorithm_
utility::vector1< ProbeRadius > protocols::match::upstream::BuildSet::atom_radii_
bool protocols::match::upstream::BuildSet::backbone_only_
bool protocols::match::upstream::BuildSet::check_fa_dun_
core::Real protocols::match::upstream::BuildSet::fa_dun_cutoff_
utility::vector1< core::Size > protocols::match::upstream::BuildSet::nbonds_from_bb_atom_
core::chemical::ResidueTypeCOP protocols::match::upstream::BuildSet::restype_
UpstreamResTypeGeometryOP protocols::match::upstream::BuildSet::restype_geom_
Real protocols::match::upstream::BuildSet::rot_prob_accumulation_limit_

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

utility::vector1< SampleStrategyData > protocols::match::upstream::BuildSet::sample_strategy_for_chi_

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