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protocols::match::upstream::UpstreamResTypeGeometry 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 <UpstreamResTypeGeometry.hh>

Inheritance diagram for protocols::match::upstream::UpstreamResTypeGeometry:
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Public Types

typedef core::Size Size
 
typedef core::Real Real
 
typedef core::Vector Vector
 
typedef
numeric::HomogeneousTransform
< Real
HTReal
 

Public Member Functions

 ~UpstreamResTypeGeometry () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
 UpstreamResTypeGeometry ()
 
 UpstreamResTypeGeometry (core::chemical::ResidueType const &)
 
void initialize_from_residue_type (core::chemical::ResidueType const &)
 
std::string const & name () const
 the name of the residue type used to generate this geometry More...
 
core::Size natoms () const
 the number of atoms in this residue type More...
 
core::Size nchi () const
 
bool atom_controlled_by_any_chi (core::Size atomno) const
 
bool atom_is_chitip (core::Size atomno) const
 
utility::vector1< core::Size >
const & 
controlling_chi_for_atom () const
 
utility::vector1< core::Size >
const & 
which_point_for_atom () const
 
utility::vector1< core::Size >
const & 
chitip_atoms () const
 
core::Size chitip_atom (core::Size chi) const
 
HTReal const & pre_chitip_transform (core::Size chi) const
 
utility::vector1< HTReal > const & ht_for_chitip_atoms () const
 
HTReal const & ht_for_chitip_atom (core::Size chi) const
 
core::Size n_nonchitip_atoms_for_chi (core::Size chi) const
 
utility::vector1
< utility::vector1< core::Size >
> const & 
nonchitip_atoms () const
 
core::Size nonchitip_atom (core::Size chi, core::Size which_nonchitip_atom_for_chi) const
 
utility::vector1
< utility::vector1< Vector >
> const & 
points_for_nonchitip_atoms () const
 
utility::vector1< Vector > const & points_for_nonchitip_atoms (core::Size chi) const
 
Vector const & point_for_nonchitip_atom (core::Size atom)
 Convenience function: get the coordinate in the chitip frame for a particular atom. The atom must be a non-chitip atom that is not part of the backbone (it must be controlled by a chi angle). More...
 
core::Size N_atom_id () const
 
core::Size CA_atom_id () const
 
core::Size C_atom_id () const
 
core::Size O_atom_id () const
 
core::Size CB_atom_id () const
 
core::Size H_atom_id () const
 
core::Size HA_atom_id () const
 
bool has_N_atom () const
 
bool has_CA_atom () const
 
bool has_C_atom () const
 
bool has_O_atom () const
 
bool has_CB_atom () const
 
bool has_H_atom () const
 
bool has_HA_atom () const
 
bool atom_has_nonchi_coordinate (core::Size restype_atomid) const
 
Vector const & coordinate_for_nonchi_atom_in_ideal_frame (core::Size restype_atomid) const
 

Private Attributes

std::string restype_name_
 Data. More...
 
utility::vector1< core::Sizecontrolling_chi_for_atom_
 
utility::vector1< core::Sizewhich_point_for_atom_
 
utility::vector1< core::Sizechitip_atoms_
 
utility::vector1< HTRealpre_chitip_transforms_
 
utility::vector1< HTRealht_for_chitip_atoms_
 
utility::vector1
< utility::vector1< core::Size > > 
nonchitip_atoms_
 
utility::vector1
< utility::vector1< Vector > > 
points_for_nonchitip_atoms_
 
utility::vector1< core::Sizerestype_atom_id_2_nonchi_atom_id_
 
utility::vector1< core::Sizenonchi_atom_id_2_restype_atom_id_
 
utility::vector1< Vectornonchi_atoms_in_ideal_frame_
 
core::Size N_atom_id_
 
core::Size CA_atom_id_
 
core::Size C_atom_id_
 
core::Size O_atom_id_
 
core::Size CB_atom_id_
 
core::Size H_atom_id_
 
core::Size HA_atom_id_
 

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.

Member Typedef Documentation

typedef numeric::HomogeneousTransform< Real > protocols::match::upstream::UpstreamResTypeGeometry::HTReal

Constructor & Destructor Documentation

protocols::match::upstream::UpstreamResTypeGeometry::~UpstreamResTypeGeometry ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

protocols::match::upstream::UpstreamResTypeGeometry::UpstreamResTypeGeometry ( )
protocols::match::upstream::UpstreamResTypeGeometry::UpstreamResTypeGeometry ( core::chemical::ResidueType const &  res)

Member Function Documentation

bool protocols::match::upstream::UpstreamResTypeGeometry::atom_controlled_by_any_chi ( core::Size  atomno) const
inline
bool protocols::match::upstream::UpstreamResTypeGeometry::atom_has_nonchi_coordinate ( core::Size  restype_atomid) const
bool protocols::match::upstream::UpstreamResTypeGeometry::atom_is_chitip ( core::Size  atomno) const
inline
core::Size protocols::match::upstream::UpstreamResTypeGeometry::C_atom_id ( ) const
inline
core::Size protocols::match::upstream::UpstreamResTypeGeometry::CA_atom_id ( ) const
inline
core::Size protocols::match::upstream::UpstreamResTypeGeometry::CB_atom_id ( ) const
inline
core::Size protocols::match::upstream::UpstreamResTypeGeometry::chitip_atom ( core::Size  chi) const
inline
utility::vector1< core::Size > const& protocols::match::upstream::UpstreamResTypeGeometry::chitip_atoms ( ) const
inline

References chitip_atoms_.

utility::vector1< core::Size > const& protocols::match::upstream::UpstreamResTypeGeometry::controlling_chi_for_atom ( ) const
inline
UpstreamResTypeGeometry::Vector const & protocols::match::upstream::UpstreamResTypeGeometry::coordinate_for_nonchi_atom_in_ideal_frame ( core::Size  restype_atomid) const
core::Size protocols::match::upstream::UpstreamResTypeGeometry::H_atom_id ( ) const
inline
core::Size protocols::match::upstream::UpstreamResTypeGeometry::HA_atom_id ( ) const
inline
bool protocols::match::upstream::UpstreamResTypeGeometry::has_C_atom ( ) const
inline

References C_atom_id_.

bool protocols::match::upstream::UpstreamResTypeGeometry::has_CA_atom ( ) const
inline

References CA_atom_id_.

bool protocols::match::upstream::UpstreamResTypeGeometry::has_CB_atom ( ) const
inline
bool protocols::match::upstream::UpstreamResTypeGeometry::has_H_atom ( ) const
inline
bool protocols::match::upstream::UpstreamResTypeGeometry::has_HA_atom ( ) const
inline
bool protocols::match::upstream::UpstreamResTypeGeometry::has_N_atom ( ) const
inline

References N_atom_id_.

bool protocols::match::upstream::UpstreamResTypeGeometry::has_O_atom ( ) const
inline

References O_atom_id_.

HTReal const& protocols::match::upstream::UpstreamResTypeGeometry::ht_for_chitip_atom ( core::Size  chi) const
inline
utility::vector1< HTReal > const& protocols::match::upstream::UpstreamResTypeGeometry::ht_for_chitip_atoms ( ) const
inline

References ht_for_chitip_atoms_.

void protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type ( core::chemical::ResidueType const &  res)
core::Size protocols::match::upstream::UpstreamResTypeGeometry::N_atom_id ( ) const
inline
core::Size protocols::match::upstream::UpstreamResTypeGeometry::n_nonchitip_atoms_for_chi ( core::Size  chi) const
inline
std::string const& protocols::match::upstream::UpstreamResTypeGeometry::name ( ) const
inline

the name of the residue type used to generate this geometry

References restype_name_.

core::Size protocols::match::upstream::UpstreamResTypeGeometry::natoms ( ) const
inline

the number of atoms in this residue type

References controlling_chi_for_atom_.

core::Size protocols::match::upstream::UpstreamResTypeGeometry::nchi ( ) const
inline

References chitip_atoms_.

Referenced by initialize_from_residue_type().

core::Size protocols::match::upstream::UpstreamResTypeGeometry::nonchitip_atom ( core::Size  chi,
core::Size  which_nonchitip_atom_for_chi 
) const
inline
utility::vector1< utility::vector1< core::Size > > const& protocols::match::upstream::UpstreamResTypeGeometry::nonchitip_atoms ( ) const
inline

References nonchitip_atoms_.

core::Size protocols::match::upstream::UpstreamResTypeGeometry::O_atom_id ( ) const
inline
Vector const& protocols::match::upstream::UpstreamResTypeGeometry::point_for_nonchitip_atom ( core::Size  atom)
inline

Convenience function: get the coordinate in the chitip frame for a particular atom. The atom must be a non-chitip atom that is not part of the backbone (it must be controlled by a chi angle).

References atom_controlled_by_any_chi(), atom_is_chitip(), controlling_chi_for_atom_, points_for_nonchitip_atoms_, and which_point_for_atom_.

utility::vector1< utility::vector1< Vector > > const& protocols::match::upstream::UpstreamResTypeGeometry::points_for_nonchitip_atoms ( ) const
inline
utility::vector1< Vector > const& protocols::match::upstream::UpstreamResTypeGeometry::points_for_nonchitip_atoms ( core::Size  chi) const
inline
HTReal const& protocols::match::upstream::UpstreamResTypeGeometry::pre_chitip_transform ( core::Size  chi) const
inline
utility::vector1< core::Size > const& protocols::match::upstream::UpstreamResTypeGeometry::which_point_for_atom ( ) const
inline

References which_point_for_atom_.

Member Data Documentation

core::Size protocols::match::upstream::UpstreamResTypeGeometry::C_atom_id_
private
core::Size protocols::match::upstream::UpstreamResTypeGeometry::CA_atom_id_
private
core::Size protocols::match::upstream::UpstreamResTypeGeometry::CB_atom_id_
private
utility::vector1< core::Size > protocols::match::upstream::UpstreamResTypeGeometry::chitip_atoms_
private
utility::vector1< core::Size > protocols::match::upstream::UpstreamResTypeGeometry::controlling_chi_for_atom_
private
core::Size protocols::match::upstream::UpstreamResTypeGeometry::H_atom_id_
private
core::Size protocols::match::upstream::UpstreamResTypeGeometry::HA_atom_id_
private
utility::vector1< HTReal > protocols::match::upstream::UpstreamResTypeGeometry::ht_for_chitip_atoms_
private
core::Size protocols::match::upstream::UpstreamResTypeGeometry::N_atom_id_
private
utility::vector1< core::Size > protocols::match::upstream::UpstreamResTypeGeometry::nonchi_atom_id_2_restype_atom_id_
private
utility::vector1< Vector > protocols::match::upstream::UpstreamResTypeGeometry::nonchi_atoms_in_ideal_frame_
private
utility::vector1< utility::vector1< core::Size > > protocols::match::upstream::UpstreamResTypeGeometry::nonchitip_atoms_
private
core::Size protocols::match::upstream::UpstreamResTypeGeometry::O_atom_id_
private
utility::vector1< utility::vector1< Vector > > protocols::match::upstream::UpstreamResTypeGeometry::points_for_nonchitip_atoms_
private
utility::vector1< HTReal > protocols::match::upstream::UpstreamResTypeGeometry::pre_chitip_transforms_
private
utility::vector1< core::Size > protocols::match::upstream::UpstreamResTypeGeometry::restype_atom_id_2_nonchi_atom_id_
private

The ideal frame is defined at Calpha with the half point between N and C in the N plane-halfpoint-Calpha plane. i.g. HTReal( N, halfpoint, CAlpha); Non-chi dependendent atoms are measured from the ideal coordinate in this frame. This includes Cbeta and the Halphas. It also includes O and H, but since their geometry depends on phi and psi, this data would be inappropriate for them.

Referenced by atom_has_nonchi_coordinate(), coordinate_for_nonchi_atom_in_ideal_frame(), and initialize_from_residue_type().

std::string protocols::match::upstream::UpstreamResTypeGeometry::restype_name_
private

Data.

Referenced by initialize_from_residue_type(), and name().

utility::vector1< core::Size > protocols::match::upstream::UpstreamResTypeGeometry::which_point_for_atom_
private

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