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:

[legend]

Public Types
typedef core::Size	Size

typedef core::Real	Real

typedef utility::VirtualBase	parent

Public Member Functions
	BuildSet ()

	~BuildSet () override

	BuildSet (BuildSet const &)

BuildSet &	operator= (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::DownstreamAlgorithm &	algorithm ()

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::Size >	nbonds_from_bb_atom_

utility::vector1< ProbeRadius >	atom_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

typedef core::Real protocols::match::upstream::BuildSet::Real

typedef core::Size protocols::match::upstream::BuildSet::Size

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

References algorithm_.

Referenced by protocols::match::Matcher::add_external_geometry_samples_for_constraint(), and set_downstream_algorithm().

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

References backbone_only_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::add_build_set(), and set_residue_type().

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

References algorithm_.

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

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 )

References algorithm_, atom_radii_, backbone_only_, check_fa_dun_, fa_dun_cutoff_, nbonds_from_bb_atom_, restype_, restype_geom_, rot_prob_accumulation_limit_, and sample_strategy_for_chi_.

Real protocols::match::upstream::BuildSet::probability_limit ( ) const

inline

References rot_prob_accumulation_limit_.

core::chemical::ResidueType const& protocols::match::upstream::BuildSet::restype ( ) const

inline

References restype_.

Referenced by protocols::match::Matcher::create_ds_builder(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), and set_residue_type().

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

References sample_strategy_for_chi_.

Referenced by protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), and protocols::match::upstream::FullChiSampleSet::FullChiSampleSet().

void protocols::match::upstream::BuildSet::set_downstream_algorithm ( downstream::DownstreamAlgorithmOP algorithm )

References algorithm(), and algorithm_.

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

void protocols::match::upstream::BuildSet::set_fa_dun_cutoff ( core::Real cutoff )

References check_fa_dun_, and fa_dun_cutoff_.

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

void protocols::match::upstream::BuildSet::set_residue_type	(	core::chemical::ResidueTypeCOP	restype,
		bool	backbone_only = `false`
	)

initialization

References atom_radii_, backbone_only(), backbone_only_, nbonds_from_bb_atom_, protocols::match::probe_radius_for_atom_type(), restype(), restype_, restype_geom_, and sample_strategy_for_chi_.

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

void protocols::match::upstream::BuildSet::set_sample_strategy_for_chi	(	core::Size	chi,
		SampleStrategyData const &	data
	)

References sample_strategy_for_chi_.

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

Member Data Documentation

downstream::DownstreamAlgorithmOP protocols::match::upstream::BuildSet::algorithm_

Referenced by algorithm(), has_algorithm(), operator=(), and set_downstream_algorithm().

utility::vector1< ProbeRadius > protocols::match::upstream::BuildSet::atom_radii_

Referenced by atom_radius(), operator=(), and set_residue_type().

bool protocols::match::upstream::BuildSet::backbone_only_

Referenced by backbone_only(), operator=(), and set_residue_type().

bool protocols::match::upstream::BuildSet::check_fa_dun_

Referenced by check_fa_dun(), operator=(), and set_fa_dun_cutoff().

core::Real protocols::match::upstream::BuildSet::fa_dun_cutoff_

Referenced by fa_dun_cutoff(), operator=(), and set_fa_dun_cutoff().

utility::vector1< core::Size > protocols::match::upstream::BuildSet::nbonds_from_bb_atom_

Referenced by nbonds_from_bb_atom(), operator=(), and set_residue_type().

core::chemical::ResidueTypeCOP protocols::match::upstream::BuildSet::restype_

Referenced by has_restype(), operator=(), restype(), and set_residue_type().

UpstreamResTypeGeometryOP protocols::match::upstream::BuildSet::restype_geom_

Referenced by operator=(), restype_geometry(), and set_residue_type().

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_

Referenced by operator=(), sample_strategy_for_chi(), set_residue_type(), and set_sample_strategy_for_chi().

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

src/protocols/match/upstream/ProteinUpstreamBuilder.hh
src/protocols/match/upstream/ProteinUpstreamBuilder.cc

Public Types

Public Member Functions

Public Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation