Rosetta 3.4
Public Types | Public Member Functions
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>

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List of all members.

Public Types

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

Public Member Functions

 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
Size natoms () const
 the number of atoms in this residue type
Size nchi () const
bool atom_controlled_by_any_chi (Size atomno) const
bool atom_is_chitip (Size atomno) const
utility::vector1< Size > const & controlling_chi_for_atom () const
utility::vector1< Size > const & which_point_for_atom () const
utility::vector1< Size > const & chitip_atoms () const
Size chitip_atom (Size chi) const
utility::vector1< HTReal > const & ht_for_chitip_atoms () const
HTReal const & ht_for_chitip_atom (Size chi) const
Size n_nonchitip_atoms_for_chi (Size chi) const
utility::vector1
< utility::vector1< Size >
> const & 
nonchitip_atoms () const
Size nonchitip_atom (Size chi, 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 (Size chi) const
Vector const & point_for_nonchitip_atom (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).
Size N_atom_id () const
Size CA_atom_id () const
Size C_atom_id () const
Size O_atom_id () const
Size CB_atom_id () const
Size H_atom_id () const
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 (Size restype_atomid) const
Vector const & coordinate_for_nonchi_atom_in_ideal_frame (Size restype_atomid) const

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

Member Function Documentation

bool protocols::match::upstream::UpstreamResTypeGeometry::atom_controlled_by_any_chi ( Size  atomno) const [inline]
bool protocols::match::upstream::UpstreamResTypeGeometry::atom_has_nonchi_coordinate ( Size  restype_atomid) const
bool protocols::match::upstream::UpstreamResTypeGeometry::atom_is_chitip ( Size  atomno) const [inline]
Size protocols::match::upstream::UpstreamResTypeGeometry::C_atom_id ( ) const [inline]
Size protocols::match::upstream::UpstreamResTypeGeometry::CA_atom_id ( ) const [inline]
Size protocols::match::upstream::UpstreamResTypeGeometry::CB_atom_id ( ) const [inline]
Size protocols::match::upstream::UpstreamResTypeGeometry::chitip_atom ( Size  chi) const [inline]
utility::vector1< Size > const& protocols::match::upstream::UpstreamResTypeGeometry::chitip_atoms ( ) const [inline]
utility::vector1< 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 ( Size  restype_atomid) const
Size protocols::match::upstream::UpstreamResTypeGeometry::H_atom_id ( ) const [inline]
Size protocols::match::upstream::UpstreamResTypeGeometry::HA_atom_id ( ) const [inline]
bool protocols::match::upstream::UpstreamResTypeGeometry::has_C_atom ( ) const [inline]
bool protocols::match::upstream::UpstreamResTypeGeometry::has_CA_atom ( ) const [inline]
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]
bool protocols::match::upstream::UpstreamResTypeGeometry::has_O_atom ( ) const [inline]
HTReal const& protocols::match::upstream::UpstreamResTypeGeometry::ht_for_chitip_atom ( Size  chi) const [inline]
utility::vector1< HTReal > const& protocols::match::upstream::UpstreamResTypeGeometry::ht_for_chitip_atoms ( ) const [inline]
void protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type ( core::chemical::ResidueType const &  res)
Size protocols::match::upstream::UpstreamResTypeGeometry::N_atom_id ( ) const [inline]
Size protocols::match::upstream::UpstreamResTypeGeometry::n_nonchitip_atoms_for_chi ( 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

Size protocols::match::upstream::UpstreamResTypeGeometry::natoms ( ) const [inline]

the number of atoms in this residue type

Size protocols::match::upstream::UpstreamResTypeGeometry::nchi ( ) const [inline]
Size protocols::match::upstream::UpstreamResTypeGeometry::nonchitip_atom ( Size  chi,
Size  which_nonchitip_atom_for_chi 
) const [inline]
utility::vector1< utility::vector1< Size > > const& protocols::match::upstream::UpstreamResTypeGeometry::nonchitip_atoms ( ) const [inline]
Size protocols::match::upstream::UpstreamResTypeGeometry::O_atom_id ( ) const [inline]
Vector const& protocols::match::upstream::UpstreamResTypeGeometry::point_for_nonchitip_atom ( 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(), and atom_is_chitip().

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 ( Size  chi) const [inline]
utility::vector1< Size > const& protocols::match::upstream::UpstreamResTypeGeometry::which_point_for_atom ( ) const [inline]

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