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:

Collaboration diagram for protocols::match::upstream::UpstreamResTypeGeometry:

Public Types
typedef core::Size	Size
typedef core::Real	Real
typedef core::Vector	Vector
typedef numeric::HomogeneousTransform < Real >	HTReal

Public Member Functions
virtual	~UpstreamResTypeGeometry ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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...
Size	natoms () const
	the number of atoms in this residue type More...
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). More...
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

Private Attributes
std::string	restype_name_
	Data. More...
utility::vector1< Size >	controlling_chi_for_atom_
utility::vector1< Size >	which_point_for_atom_
utility::vector1< Size >	chitip_atoms_
utility::vector1< HTReal >	ht_for_chitip_atoms_
utility::vector1 < utility::vector1< Size > >	nonchitip_atoms_
utility::vector1 < utility::vector1< Vector > >	points_for_nonchitip_atoms_
utility::vector1< Size >	restype_atom_id_2_nonchi_atom_id_
utility::vector1< Size >	nonchi_atom_id_2_restype_atom_id_
utility::vector1< Vector >	nonchi_atoms_in_ideal_frame_
Size	N_atom_id_
Size	CA_atom_id_
Size	C_atom_id_
Size	O_atom_id_
Size	CB_atom_id_
Size	H_atom_id_
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

typedef core::Real protocols::match::upstream::UpstreamResTypeGeometry::Real

typedef core::Size protocols::match::upstream::UpstreamResTypeGeometry::Size

typedef core::Vector protocols::match::upstream::UpstreamResTypeGeometry::Vector

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

protocols::match::upstream::UpstreamResTypeGeometry::UpstreamResTypeGeometry

(

)

protocols::match::upstream::UpstreamResTypeGeometry::UpstreamResTypeGeometry

(

core::chemical::ResidueType const &

res)

References initialize_from_residue_type().

Member Function Documentation

bool protocols::match::upstream::UpstreamResTypeGeometry::atom_controlled_by_any_chi ( Size  atomno) const

inline

References controlling_chi_for_atom_.

Referenced by point_for_nonchitip_atom().

bool protocols::match::upstream::UpstreamResTypeGeometry::atom_has_nonchi_coordinate

(

Size

restype_atomid)

const

References restype_atom_id_2_nonchi_atom_id_.

bool protocols::match::upstream::UpstreamResTypeGeometry::atom_is_chitip ( Size  atomno) const

inline

References controlling_chi_for_atom_, and which_point_for_atom_.

Referenced by point_for_nonchitip_atom().

Size protocols::match::upstream::UpstreamResTypeGeometry::C_atom_id ( ) const

inline

References C_atom_id_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords().

Size protocols::match::upstream::UpstreamResTypeGeometry::CA_atom_id ( ) const

inline

References CA_atom_id_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords().

Size protocols::match::upstream::UpstreamResTypeGeometry::CB_atom_id ( ) const

inline

References CB_atom_id_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::compute_cb_frame(), and protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords().

Size protocols::match::upstream::UpstreamResTypeGeometry::chitip_atom ( Size  chi) const

inline

References chitip_atoms_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build(), and protocols::match::upstream::ProteinUpstreamBuilder::recover_hits().

utility::vector1< Size > const& protocols::match::upstream::UpstreamResTypeGeometry::chitip_atoms ( ) const

inline

References chitip_atoms_.

utility::vector1< Size > const& protocols::match::upstream::UpstreamResTypeGeometry::controlling_chi_for_atom ( ) const

inline

References controlling_chi_for_atom_.

UpstreamResTypeGeometry::Vector const & protocols::match::upstream::UpstreamResTypeGeometry::coordinate_for_nonchi_atom_in_ideal_frame

(

Size

restype_atomid)

const

References nonchi_atoms_in_ideal_frame_, and restype_atom_id_2_nonchi_atom_id_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::compute_cb_frame(), and protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords().

Size protocols::match::upstream::UpstreamResTypeGeometry::H_atom_id ( ) const

inline

References H_atom_id_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords().

Size protocols::match::upstream::UpstreamResTypeGeometry::HA_atom_id ( ) const

inline

References HA_atom_id_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords().

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

References CB_atom_id_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords().

bool protocols::match::upstream::UpstreamResTypeGeometry::has_H_atom ( ) const

inline

References H_atom_id_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords().

bool protocols::match::upstream::UpstreamResTypeGeometry::has_HA_atom ( ) const

inline

References HA_atom_id_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords().

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 ( Size  chi) const

inline

References ht_for_chitip_atoms_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build(), and protocols::match::upstream::ProteinUpstreamBuilder::recover_hits().

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)

References core::chemical::ResidueType::aa(), core::chemical::aa_gly, core::chemical::ResidueType::atom(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atoms_last_controlled_by_chi(), C_atom_id_, CA_atom_id_, CB_atom_id_, core::chemical::ResidueType::chi_atoms(), chitip_atoms_, controlling_chi_for_atom_, core::chemical::AtomICoor::d(), H_atom_id_, HA_atom_id_, core::chemical::ResidueType::has(), ht_for_chitip_atoms_, core::chemical::ResidueType::icoor(), core::chemical::Atom::ideal_xyz(), core::chemical::ResidueType::last_controlling_chi(), N_atom_id_, core::chemical::ResidueType::name(), core::chemical::ResidueType::natoms(), nchi(), core::chemical::ResidueType::nchi(), nonchi_atom_id_2_restype_atom_id_, nonchi_atoms_in_ideal_frame_, nonchitip_atoms_, O_atom_id_, points_for_nonchitip_atoms_, restype_atom_id_2_nonchi_atom_id_, restype_name_, core::chemical::AtomICoor::theta(), and which_point_for_atom_.

Referenced by UpstreamResTypeGeometry().

Size protocols::match::upstream::UpstreamResTypeGeometry::N_atom_id ( ) const

inline

References N_atom_id_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords().

Size protocols::match::upstream::UpstreamResTypeGeometry::n_nonchitip_atoms_for_chi ( Size  chi) const

inline

References nonchitip_atoms_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build(), and protocols::match::upstream::ProteinUpstreamBuilder::recover_hits().

std::string const& protocols::match::upstream::UpstreamResTypeGeometry::name ( ) const

inline

the name of the residue type used to generate this geometry

References restype_name_.

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

inline

the number of atoms in this residue type

References controlling_chi_for_atom_.

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

inline

References chitip_atoms_.

Referenced by initialize_from_residue_type().

Size protocols::match::upstream::UpstreamResTypeGeometry::nonchitip_atom ( Size  chi, Size  which_nonchitip_atom_for_chi  ) const

inline

References nonchitip_atoms_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build(), and protocols::match::upstream::ProteinUpstreamBuilder::recover_hits().

utility::vector1< utility::vector1< Size > > const& protocols::match::upstream::UpstreamResTypeGeometry::nonchitip_atoms ( ) const

inline

References nonchitip_atoms_.

Size protocols::match::upstream::UpstreamResTypeGeometry::O_atom_id ( ) const

inline

References O_atom_id_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords().

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(), 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

References points_for_nonchitip_atoms_.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build(), and protocols::match::upstream::ProteinUpstreamBuilder::recover_hits().

utility::vector1< Vector > const& protocols::match::upstream::UpstreamResTypeGeometry::points_for_nonchitip_atoms ( Size  chi) const

inline

References points_for_nonchitip_atoms_.

utility::vector1< Size > const& protocols::match::upstream::UpstreamResTypeGeometry::which_point_for_atom ( ) const

inline

References which_point_for_atom_.

Member Data Documentation

Size protocols::match::upstream::UpstreamResTypeGeometry::C_atom_id_

private

Referenced by C_atom_id(), has_C_atom(), and initialize_from_residue_type().

Size protocols::match::upstream::UpstreamResTypeGeometry::CA_atom_id_

private

Referenced by CA_atom_id(), has_CA_atom(), and initialize_from_residue_type().

Size protocols::match::upstream::UpstreamResTypeGeometry::CB_atom_id_

private

Referenced by CB_atom_id(), has_CB_atom(), and initialize_from_residue_type().

utility::vector1< Size > protocols::match::upstream::UpstreamResTypeGeometry::chitip_atoms_

private

Referenced by chitip_atom(), chitip_atoms(), initialize_from_residue_type(), and nchi().

utility::vector1< Size > protocols::match::upstream::UpstreamResTypeGeometry::controlling_chi_for_atom_

private

Referenced by atom_controlled_by_any_chi(), atom_is_chitip(), controlling_chi_for_atom(), initialize_from_residue_type(), natoms(), and point_for_nonchitip_atom().

Size protocols::match::upstream::UpstreamResTypeGeometry::H_atom_id_

private

Referenced by H_atom_id(), has_H_atom(), and initialize_from_residue_type().

Size protocols::match::upstream::UpstreamResTypeGeometry::HA_atom_id_

private

Referenced by HA_atom_id(), has_HA_atom(), and initialize_from_residue_type().

utility::vector1< HTReal > protocols::match::upstream::UpstreamResTypeGeometry::ht_for_chitip_atoms_

private

Referenced by ht_for_chitip_atom(), ht_for_chitip_atoms(), and initialize_from_residue_type().

Size protocols::match::upstream::UpstreamResTypeGeometry::N_atom_id_

private

Referenced by has_N_atom(), initialize_from_residue_type(), and N_atom_id().

utility::vector1< Size > protocols::match::upstream::UpstreamResTypeGeometry::nonchi_atom_id_2_restype_atom_id_

private

Referenced by initialize_from_residue_type().

utility::vector1< Vector > protocols::match::upstream::UpstreamResTypeGeometry::nonchi_atoms_in_ideal_frame_

private

Referenced by coordinate_for_nonchi_atom_in_ideal_frame(), and initialize_from_residue_type().

utility::vector1< utility::vector1< Size > > protocols::match::upstream::UpstreamResTypeGeometry::nonchitip_atoms_

private

Referenced by initialize_from_residue_type(), n_nonchitip_atoms_for_chi(), nonchitip_atom(), and nonchitip_atoms().

Size protocols::match::upstream::UpstreamResTypeGeometry::O_atom_id_

private

Referenced by has_O_atom(), initialize_from_residue_type(), and O_atom_id().

utility::vector1< utility::vector1< Vector > > protocols::match::upstream::UpstreamResTypeGeometry::points_for_nonchitip_atoms_

private

Referenced by initialize_from_residue_type(), point_for_nonchitip_atom(), and points_for_nonchitip_atoms().

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

private

Referenced by atom_is_chitip(), initialize_from_residue_type(), point_for_nonchitip_atom(), and which_point_for_atom().

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

• src/protocols/match/upstream/UpstreamResTypeGeometry.hh
• src/protocols/match/upstream/UpstreamResTypeGeometry.cc