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core::chemical::ICoorAtomID Class Reference

Atom 's ID in internal coordinates in a ResidueType. More...

#include <AtomICoor.hh>

Public Types

typedef conformation::Residue Residue
 
typedef conformation::Conformation Conformation
 

Public Member Functions

 ICoorAtomID ()
 default constructor More...
 
 ICoorAtomID (std::string name, ResidueType const &rsd_type)
 construct ICoorAtomID by atom name and its ResidueType More...
 
Size atomno () const
 get ICoorAtomID atomno More...
 
void atomno (int const atomno_in)
 set ICoorAtomID atomno More...
 
ICoordAtomIDType const & type () const
 get ICoordAtomID type More...
 
bool is_internal () const
 
bool is_polymer_lower () const
 
bool is_polymer_upper () const
 
bool is_connect (Size const connid) const
 Returns true if this is the specified connection id. More...
 
bool is_connect () const
 Returns true if this is a connection. More...
 
std::string name (ResidueType const &rt) const
 Returns the string representation which will build this ICoorAtomID (e.g. atom name, UPPER, LOWER, CONN*. More...
 
Vector const & xyz (Residue const &rsd, Conformation const &conformation) const
 What is the coordinates corresponding to this ICoorAtomID, for the given residue and conformation. More...
 
Vector xyz (ResidueType const &rsd_type) const
 What is the coordinates corresponding to this ICoorAtomID, for the given idealized ResidueType. More...
 
Vector xyz (conformation::Residue const &rsd) const
 WARNING: Slightly dangerous function intended for black magic use only. Rebuilds atom location from stub atoms. If stub atom are not internal atoms, their location will be rebuilt from their residue stub atom's locations, as opposed to being retrieved from connected residues via a conformation. More...
 
id::AtomID atom_id (Residue const &rsd, Conformation const &conformation) const
 This ICoorAtomID (for the given residue) corresponds to which id::AtomID in the conformation? More...
 
bool buildable (Residue const &rsd, Conformation const &conformation) const
 Can valid coordinates be built for this ICoorAtomID, given the residue and conformation? More...
 
bool operator== (ICoorAtomID const &other) const
 
bool operator!= (ICoorAtomID const &other) const
 

Private Attributes

ICoordAtomIDType type_
 atom's "connection" type More...
 
Size atomno_
 atom's index number More...
 

Detailed Description

Atom 's ID in internal coordinates in a ResidueType.

Member Typedef Documentation

◆ Conformation

◆ Residue

Constructor & Destructor Documentation

◆ ICoorAtomID() [1/2]

core::chemical::ICoorAtomID::ICoorAtomID ( )

default constructor

References core::chemical::INTERNAL.

◆ ICoorAtomID() [2/2]

core::chemical::ICoorAtomID::ICoorAtomID ( std::string  name,
ResidueType const &  rsd_type 
)

construct ICoorAtomID by atom name and its ResidueType

After atom name is read in from residue param file, ICoorAtomID type_ and atomno_ is defined as:

  • Anything less than four character is considered as INTERNAL atom name and its atom index number is assigned as atomno_;
  • "LOWER" and "UPPER" for polymer lower and upper connections. Since they are unique, no atomno_ is given ( e.g., 0)
  • Non-polymer connections are flagged by "CONN*" in which * represents the index number of this connection in the ResidueType ( from 1 to ResidueType.n_connection() ). This number is assigned as atomno_.

References core::chemical::ResidueType::atom_index(), atomno_, core::chemical::CONNECT, core::chemical::get_connection_number(), core::chemical::ResidueType::has(), core::chemical::INTERNAL, core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueTypeBase::name(), name(), core::chemical::POLYMER_LOWER, core::chemical::POLYMER_UPPER, core::chemical::string_to_icoord_type(), core::chemical::TR(), and type_.

Member Function Documentation

◆ atom_id()

id::AtomID core::chemical::ICoorAtomID::atom_id ( Residue const &  rsd,
Conformation const &  conformation 
) const

◆ atomno() [1/2]

Size core::chemical::ICoorAtomID::atomno ( ) const
inline

get ICoorAtomID atomno

References atomno_.

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_amide_bond_cyclic_constraints(), protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper::add_angle_constraints(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::add_angle_constraints(), protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::add_angle_constraints(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::add_angle_constraints(), protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper::add_angle_constraints(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_closebond_logic_isopeptide(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_closebond_logic_thioether_lariat(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::add_dihedral_constraint_to_stream(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::add_dihedral_constraints(), protocols::ligand_docking::AddHydrogen::apply(), atom_id(), protocols::minimization_packing::MinimalRotamer::atom_is_ideal(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::select::util::calc_sc_neighbors(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), protocols::cyclic_peptide::crosslinker::correct_thioether_virtuals(), core::chemical::AtomICoor::depends_on_a_true_index(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds(), core::select::util::determine_whether_point_is_buried(), core::pack::rotamers::SingleLigandRotamerLibrary::fill_missing_atoms(), protocols::qsar::scoring_grid::ShapeGrid::get_point_score(), core::conformation::idealize_hydrogens(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Conformation::insert_ideal_geometry_at_residue_connection(), core::conformation::missing_stubs_build(), core::conformation::Residue::place(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), core::chemical::pretty_print_atomicoor(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_bond_length(), protocols::cyclic_peptide::crosslinker::set_up_thioether_constraints(), protocols::simple_moves::CyclizationMover::setup_constraints(), core::chemical::AtomICoor::show(), and core::conformation::update_cutpoint_virtual_atoms_if_connected().

◆ atomno() [2/2]

void core::chemical::ICoorAtomID::atomno ( int const  atomno_in)
inline

set ICoorAtomID atomno

References atomno_.

◆ buildable()

bool core::chemical::ICoorAtomID::buildable ( Residue const &  rsd,
Conformation const &  conformation 
) const

◆ is_connect() [1/2]

bool core::chemical::ICoorAtomID::is_connect ( ) const
inline

Returns true if this is a connection.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::CONNECT, and type_.

◆ is_connect() [2/2]

bool core::chemical::ICoorAtomID::is_connect ( Size const  connid) const
inline

Returns true if this is the specified connection id.

References atomno_, core::chemical::CONNECT, and type_.

Referenced by core::chemical::AtomICoor::depends_on_residue_connection().

◆ is_internal()

bool core::chemical::ICoorAtomID::is_internal ( ) const
inline

◆ is_polymer_lower()

bool core::chemical::ICoorAtomID::is_polymer_lower ( ) const
inline

◆ is_polymer_upper()

bool core::chemical::ICoorAtomID::is_polymer_upper ( ) const
inline

◆ name()

std::string core::chemical::ICoorAtomID::name ( ResidueType const &  rt) const

◆ operator!=()

bool core::chemical::ICoorAtomID::operator!= ( ICoorAtomID const &  other) const

References atomno_, and type_.

◆ operator==()

bool core::chemical::ICoorAtomID::operator== ( ICoorAtomID const &  other) const

References atomno_, and type_.

◆ type()

ICoordAtomIDType const& core::chemical::ICoorAtomID::type ( ) const
inline

◆ xyz() [1/3]

Vector core::chemical::ICoorAtomID::xyz ( conformation::Residue const &  rsd) const

WARNING: Slightly dangerous function intended for black magic use only. Rebuilds atom location from stub atoms. If stub atom are not internal atoms, their location will be rebuilt from their residue stub atom's locations, as opposed to being retrieved from connected residues via a conformation.

WARNING: Slightly dangerous function intended for black magic use only. Only to be used for situations where you know the ICoorAtomID can't be anything but a real atom on the given residue, and where a conformation is absolutely not availible. If you /can/ use ICoorAtomID::xyz( Residue const &, Conformation const &), you /should/.

References core::conformation::Residue::atom(), atomno_, core::chemical::AtomICoor::build(), core::chemical::CONNECT, core::chemical::ResidueConnection::icoor(), core::chemical::INTERNAL, core::chemical::ResidueType::lower_connect(), core::chemical::POLYMER_LOWER, core::chemical::POLYMER_UPPER, core::chemical::ResidueType::residue_connection(), core::conformation::Residue::type(), type_, core::chemical::ResidueType::upper_connect(), and core::conformation::Atom::xyz().

◆ xyz() [2/3]

Vector const & core::chemical::ICoorAtomID::xyz ( Residue const &  rsd,
Conformation const &  conformation 
) const

◆ xyz() [3/3]

Vector core::chemical::ICoorAtomID::xyz ( ResidueType const &  rsd_type) const

Member Data Documentation

◆ atomno_

Size core::chemical::ICoorAtomID::atomno_
private

◆ type_

ICoordAtomIDType core::chemical::ICoorAtomID::type_
private

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