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Rosetta 3.5
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Rosetta 3.5
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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) | |
| constructor with atom index number and AtomICoor 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... | |
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 fullfilled 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.
Definition at line 59 of file ResidueConnection.hh.
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default constructor
Definition at line 62 of file ResidueConnection.hh.
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constructor with atom index number
Definition at line 68 of file ResidueConnection.hh.
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constructor with atom index number and AtomICoor
Definition at line 76 of file ResidueConnection.hh.
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constructor with atom index number, AtomICoor, and connection index
Definition at line 86 of file ResidueConnection.hh.
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get atom index number
Definition at line 98 of file ResidueConnection.hh.
References atomno_.
Referenced by core::conformation::Conformation::append_residue_by_bond(), core::scoring::mm::connection_indices(), core::conformation::Residue::copy_residue_connections(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::conformation::Conformation::declare_chemical_bond(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::conformation::disulfide_bonds(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::conformation::Conformation::inter_residue_connection_partner(), core::conformation::is_disulfide_bond(), core::conformation::orient_residue_for_ideal_bond(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::conformation::setup_corresponding_atoms(), and core::chemical::write_topology_file().
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get atom's AtomICoor
Definition at line 112 of file ResidueConnection.hh.
References icoor_.
Referenced by protocols::ligand_docking::AddHydrogen::apply(), protocols::loops::loop_closure::ccd::ccd_moves(), core::conformation::Residue::connection_distance(), core::conformation::Conformation::detect_bonds(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), protocols::swa::protein::StepWiseProteinLoopBridger::KIC_loop_close(), core::conformation::orient_residue_for_ideal_bond(), and core::chemical::ICoorAtomID::xyz().
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Definition at line 124 of file ResidueConnection.hh.
References index_.
Referenced by core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), and core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs().
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Definition at line 125 of file ResidueConnection.hh.
References index_.
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Which residue connection # am I in my owners list of residue connections?
Definition at line 145 of file ResidueConnection.hh.
Referenced by index().
1.8.4