core::chemical::ResidueConnection Class Reference

A simple class marking atoms at inter-residue connections. More...

#include <ResidueConnection.hh>

Public Member Functions
	ResidueConnection ()
	default constructor More...
	ResidueConnection (int const atomno_in)
	constructor with atom index number More...
	ResidueConnection (int const atomno_in, AtomICoor const &icoor_in, int const index)
	constructor with atom index number, AtomICoor, and connection index More...
int	atomno () const
	get atom index number More...
void	atomno (Size const atomno_in)
	set atom index number More...
AtomICoor const &	icoor () const
	get atom's AtomICoor More...
void	icoor (AtomICoor const &ic)
	set atom's AtomICoor More...
int	index () const
void	index (int index_in)

Private Attributes
int	atomno_
	atom index number More...
AtomICoor	icoor_
	atom AtomICoor More...
int	index_
	Which residue connection # am I in my owners list of residue connections? More...

Detailed Description

A simple class marking atoms at inter-residue connections.

Each residue type specifies some number of positions at which it is expecting to form a chemical bond with another residue. Think of them as ports: they are parts of the residue where there are chemical bonds beyond the intra-residue chemical bonds are expected – places where they can be chemically linked to the outside world. A conformation::Residue will require that its ResidueConnections be fulfilled by other Residues – the ResConnID class describes how two residues are connected: e.g., the third ResConnID for residue 10 would say "I connect to residue 58 at residue 58's third residue connection" if residue 10 and residue 58 were disulfide bonded as the disulfide connection id is "3" for two mid-protein cystine residues. The advantages of separating ResidueConnections from atoms themselves are that 1) it allows multiple residue connections to stem from the same atom – useful for single-atom residues, such as coordinated metals (Zn, Mg), and 2) it allows one residue to change its set of atoms without invalidating the bond information (e.g. the atom index) on its partner. For example, if a chain-break were placed between residues 57 and 58, then residue 58 will get an extra C-prev virtual atom, and the index of SG will change. Residue 10, if it had recorded the SG index would have to find SG's new index. If instead, the connection point is represented simply as connection point 3, and if the new residue type (the chainbreak disulfide residue) has the same number of residue connections as the original residue type (it will!) then nothing about residue 10 needs to be updated.

Constructor & Destructor Documentation

ResidueConnection() [1/3]

core::chemical::ResidueConnection::ResidueConnection ( )

inline

default constructor

ResidueConnection() [2/3]

core::chemical::ResidueConnection::ResidueConnection ( int const  atomno_in )

inline

constructor with atom index number

ResidueConnection() [3/3]

core::chemical::ResidueConnection::ResidueConnection ( int const  atomno_in, AtomICoor const &  icoor_in, int const  index  )

inline

constructor with atom index number, AtomICoor, and connection index

Member Function Documentation

atomno() [1/2]

int core::chemical::ResidueConnection::atomno ( ) const

inline

get atom index number

References atomno_.

Referenced by core::util::add_constraints_to_metal(), core::conformation::Conformation::append_residue_by_bond(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::chemical::compare_residue_connection(), core::conformation::Residue::connect_atom(), core::scoring::mm::connection_indices(), core::chemical::MutableResidueType::copy_other_info(), core::conformation::Residue::copy_residue_connections(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::pose::create_chemical_edge(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::conformation::Conformation::declare_chemical_bond(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::energy_methods::LK_hack::distribute_pseudo_base_atom_derivatives(), core::conformation::disulfide_bonds(), protocols::cyclic_peptide::dump_debug_output(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_cycpep_pose_copy(), core::energy_methods::LK_PolarNonPolarEnergy::get_base_vector(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::conformation::get_disulf_partner(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), protocols::drug_design::ConformationSelectionToRDMol::Mol(), core::conformation::orient_residue_for_ideal_bond(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::energy_methods::LK_hack::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::conformation::Residue::resolve_partial_atom_id(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), protocols::simple_moves::CyclizationMover::setup_constraints(), core::conformation::setup_corresponding_atoms(), and core::chemical::write_topology_file().

atomno() [2/2]

void core::chemical::ResidueConnection::atomno ( Size const  atomno_in )

inline

set atom index number

References atomno_.

icoor() [1/2]

AtomICoor const& core::chemical::ResidueConnection::icoor ( ) const

inline

get atom's AtomICoor

References icoor_.

Referenced by protocols::ligand_docking::AddHydrogen::apply(), core::chemical::compare_residue_connection(), core::conformation::Residue::connection_distance(), core::chemical::MutableResidueType::copy_other_info(), core::conformation::Conformation::detect_bonds(), protocols::loops::loop_closure::ccd::get_deviation(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Conformation::insert_ideal_geometry_at_residue_connection(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close(), core::conformation::orient_residue_for_ideal_bond(), protocols::simple_moves::CyclizationMover::setup_constraints(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().

icoor() [2/2]

void core::chemical::ResidueConnection::icoor ( AtomICoor const &  ic )

inline

set atom's AtomICoor

References icoor_.

index() [1/2]

int core::chemical::ResidueConnection::index ( ) const

inline

References index_.

Referenced by protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), core::chemical::compare_residue_connection(), core::energy_methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::methods::determine_lo_and_hi_residues(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), core::conformation::insert_partial_atom_ids_for_mainchain_torsion(), core::energy_methods::ProClosureEnergy::measure_chi4(), and core::energy_methods::ProClosureEnergy::residue_pair_energy().

index() [2/2]

void core::chemical::ResidueConnection::index ( int  index_in )

inline

References index_.

Member Data Documentation

atomno_

int core::chemical::ResidueConnection::atomno_

private

atom index number

Referenced by atomno().

icoor_

AtomICoor core::chemical::ResidueConnection::icoor_

private

atom AtomICoor

Referenced by icoor().

index_

int core::chemical::ResidueConnection::index_

private

Which residue connection # am I in my owners list of residue connections?

Referenced by index().

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

• src/core/chemical/ResidueConnection.hh