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Rosetta
2020.50
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#include <MMBondAngleResidueTypeParam.hh>
Public Member Functions | |
MMBondAngleResidueTypeParam () | |
Default ctor. More... | |
void | init (core::chemical::ResidueType const &residue_type, MMBondAngleLibrary const &mm_bondangle_library, bool use_residue_type_theta0, utility::vector1< std::string > const ¢ral_atoms_to_score) |
initialize the parameters More... | |
Size | num_bondangles () const |
get number of intraresidue bond angles More... | |
three_atom_set const & | bondangle (Size const bondang) const |
Return the indices for the set of atoms that define a particular intraresidue angle. More... | |
core::Real | Ktheta (Size const bondang) const |
get Ktheta for a particular intraresidue angle More... | |
core::Real | theta0 (Size const bondang) const |
get Ktheta for a particular intraresidue angle More... | |
utility::vector1< Size > const & | bondangles_for_atom (Size atomno) const |
Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom. More... | |
core::Size | bondangle_index (three_atom_set const &atom_set) const |
Returns the index of the intraresidue bond angle, 0 if not found. More... | |
Size | n_possible_residue_connections () const |
number of ResidueConnections, counting polymeric residue connections More... | |
Size | n_connection_pairs (Size const connection) const |
number of ResidueConnections, counting polymeric residue connections More... | |
two_atom_set const & | connection_pair (Size const connection, Size const bondang) const |
Return the indices for the set of two atoms that form part of a interresidue bond angle. More... | |
core::Real | connection_theta0 (Size const connection, Size const bondang) const |
Return ResidueType derived theta0 for a interresidue bond angle. More... | |
bool | connection_use_theta0 (Size const connection, Size const bondang) const |
Return whether to use ResidueType derived theta0 for a interresidue bond angle. More... | |
core::Size | connection_index (Size const connection, two_atom_set const &atom_set) const |
Returns the index of the interresidue bond angle, 0 if not found. More... | |
Private Attributes | |
utility::vector1< three_atom_set > | bondangle_atom_sets_ |
vector of sets of atoms that make up bond angles in the residue More... | |
utility::vector1< core::Real > | Ktheta_ |
vector of Ktheta values for each set More... | |
utility::vector1< core::Real > | theta0_ |
vector of theta0 values for each set More... | |
utility::vector1 < utility::vector1< Size > > | bondangles_for_atom_ |
all intra-residue bond angles that each atom "participates" in. More... | |
std::map< three_atom_set, core::Size > | bondangle_index_ |
map to lookup a bondangle given its three atoms More... | |
utility::vector1 < utility::vector1 < two_atom_set > > | connection_atom_sets_ |
vector of vector of pairs of atoms that take part in interresidue bond angles More... | |
utility::vector1 < utility::vector1< core::Real > > | connection_theta0_ |
vector of vector of theta0 values for pairs of atoms that take part in interresidue bond angles More... | |
utility::vector1 < utility::vector1< bool > > | connection_use_theta0_ |
vector of vector of booleans indicating whether to use theta0_ or lookup on the fly More... | |
utility::vector1< std::map < two_atom_set, core::Size > > | connection_index_ |
vector of maps for lookup of interresidue theta0 parameters More... | |
Friends | |
std::ostream & | operator<< (std::ostream &os, MMBondAngleResidueTypeParam const &residue_type_param) |
stream << MMBondAngleResidueTypeParam More... | |
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Default ctor.
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Return the indices for the set of atoms that define a particular intraresidue angle.
References bondangle_atom_sets_.
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Returns the index of the intraresidue bond angle, 0 if not found.
References bondangle_index_.
Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().
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Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom.
References bondangles_for_atom_.
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Returns the index of the interresidue bond angle, 0 if not found.
References connection_index_, and core::sequence::end.
Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().
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Return the indices for the set of two atoms that form part of a interresidue bond angle.
References connection_atom_sets_.
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Return ResidueType derived theta0 for a interresidue bond angle.
References connection_theta0_.
Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().
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Return whether to use ResidueType derived theta0 for a interresidue bond angle.
References connection_use_theta0_.
Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().
void core::scoring::mm::MMBondAngleResidueTypeParam::init | ( | core::chemical::ResidueType const & | residue_type, |
MMBondAngleLibrary const & | mm_bondangle_library, | ||
bool | use_residue_type_theta0, | ||
utility::vector1< std::string > const & | central_atoms_to_score | ||
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initialize the parameters
References core::chemical::ResidueType::bondangle(), bondangle_atom_sets_, bondangle_index_, bondangles_for_atom_, core::chemical::ResidueType::bonded_neighbor(), connection_atom_sets_, connection_index_, connection_theta0_, connection_use_theta0_, core::chemical::ResidueType::ideal_xyz(), Ktheta_, core::scoring::mm::MMBondAngleLibrary::lookup(), core::chemical::ResidueType::mm_name(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::num_bondangles(), core::chemical::ResidueType::residue_connection(), core::scoring::mm::score_atom_centrally(), and theta0_.
Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::get(), and core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().
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get Ktheta for a particular intraresidue angle
References Ktheta_.
Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().
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number of ResidueConnections, counting polymeric residue connections
References connection_atom_sets_.
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number of ResidueConnections, counting polymeric residue connections
References connection_atom_sets_.
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get number of intraresidue bond angles
References bondangle_atom_sets_.
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get Ktheta for a particular intraresidue angle
References theta0_.
Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().
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stream << MMBondAngleResidueTypeParam
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vector of sets of atoms that make up bond angles in the residue
Referenced by bondangle(), init(), num_bondangles(), and core::scoring::mm::operator<<().
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map to lookup a bondangle given its three atoms
Referenced by bondangle_index(), and init().
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all intra-residue bond angles that each atom "participates" in.
Referenced by bondangles_for_atom(), and init().
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vector of vector of pairs of atoms that take part in interresidue bond angles
Referenced by connection_pair(), init(), n_connection_pairs(), n_possible_residue_connections(), and core::scoring::mm::operator<<().
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vector of maps for lookup of interresidue theta0 parameters
Referenced by connection_index(), and init().
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vector of vector of theta0 values for pairs of atoms that take part in interresidue bond angles
Referenced by connection_theta0(), init(), and core::scoring::mm::operator<<().
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vector of vector of booleans indicating whether to use theta0_ or lookup on the fly
Referenced by connection_use_theta0(), init(), and core::scoring::mm::operator<<().
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vector of Ktheta values for each set
Referenced by init(), Ktheta(), and core::scoring::mm::operator<<().
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vector of theta0 values for each set
Referenced by init(), core::scoring::mm::operator<<(), and theta0().