Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Attributes | Friends | List of all members
core::scoring::mm::MMBondAngleResidueTypeParam Class Reference

#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 &central_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_setbondangle_atom_sets_
 vector of sets of atoms that make up bond angles in the residue More...
 
utility::vector1< core::RealKtheta_
 vector of Ktheta values for each set More...
 
utility::vector1< core::Realtheta0_
 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...
 

Constructor & Destructor Documentation

core::scoring::mm::MMBondAngleResidueTypeParam::MMBondAngleResidueTypeParam ( )
default

Default ctor.

Member Function Documentation

three_atom_set const& core::scoring::mm::MMBondAngleResidueTypeParam::bondangle ( Size const  bondang) const
inline

Return the indices for the set of atoms that define a particular intraresidue angle.

References bondangle_atom_sets_.

core::Size core::scoring::mm::MMBondAngleResidueTypeParam::bondangle_index ( three_atom_set const &  atom_set) const
inline

Returns the index of the intraresidue bond angle, 0 if not found.

References bondangle_index_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().

utility::vector1< Size > const& core::scoring::mm::MMBondAngleResidueTypeParam::bondangles_for_atom ( Size  atomno) const
inline

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_.

core::Size core::scoring::mm::MMBondAngleResidueTypeParam::connection_index ( Size const  connection,
two_atom_set const &  atom_set 
) const
inline

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().

two_atom_set const& core::scoring::mm::MMBondAngleResidueTypeParam::connection_pair ( Size const  connection,
Size const  bondang 
) const
inline

Return the indices for the set of two atoms that form part of a interresidue bond angle.

References connection_atom_sets_.

core::Real core::scoring::mm::MMBondAngleResidueTypeParam::connection_theta0 ( Size const  connection,
Size const  bondang 
) const
inline

Return ResidueType derived theta0 for a interresidue bond angle.

References connection_theta0_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().

bool core::scoring::mm::MMBondAngleResidueTypeParam::connection_use_theta0 ( Size const  connection,
Size const  bondang 
) const
inline

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 
)
core::Real core::scoring::mm::MMBondAngleResidueTypeParam::Ktheta ( Size const  bondang) const
inline

get Ktheta for a particular intraresidue angle

References Ktheta_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().

Size core::scoring::mm::MMBondAngleResidueTypeParam::n_connection_pairs ( Size const  connection) const
inline

number of ResidueConnections, counting polymeric residue connections

References connection_atom_sets_.

Size core::scoring::mm::MMBondAngleResidueTypeParam::n_possible_residue_connections ( ) const
inline

number of ResidueConnections, counting polymeric residue connections

References connection_atom_sets_.

Size core::scoring::mm::MMBondAngleResidueTypeParam::num_bondangles ( ) const
inline

get number of intraresidue bond angles

References bondangle_atom_sets_.

core::Real core::scoring::mm::MMBondAngleResidueTypeParam::theta0 ( Size const  bondang) const
inline

get Ktheta for a particular intraresidue angle

References theta0_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
MMBondAngleResidueTypeParam const &  residue_type_param 
)
friend

Member Data Documentation

utility::vector1< three_atom_set > core::scoring::mm::MMBondAngleResidueTypeParam::bondangle_atom_sets_
private

vector of sets of atoms that make up bond angles in the residue

Referenced by bondangle(), init(), num_bondangles(), and core::scoring::mm::operator<<().

std::map< three_atom_set, core::Size > core::scoring::mm::MMBondAngleResidueTypeParam::bondangle_index_
private

map to lookup a bondangle given its three atoms

Referenced by bondangle_index(), and init().

utility::vector1< utility::vector1< Size > > core::scoring::mm::MMBondAngleResidueTypeParam::bondangles_for_atom_
private

all intra-residue bond angles that each atom "participates" in.

Referenced by bondangles_for_atom(), and init().

utility::vector1< utility::vector1< two_atom_set > > core::scoring::mm::MMBondAngleResidueTypeParam::connection_atom_sets_
private

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<<().

utility::vector1< std::map< two_atom_set, core::Size > > core::scoring::mm::MMBondAngleResidueTypeParam::connection_index_
private

vector of maps for lookup of interresidue theta0 parameters

Referenced by connection_index(), and init().

utility::vector1< utility::vector1< core::Real > > core::scoring::mm::MMBondAngleResidueTypeParam::connection_theta0_
private

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<<().

utility::vector1< utility::vector1< bool > > core::scoring::mm::MMBondAngleResidueTypeParam::connection_use_theta0_
private

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<<().

utility::vector1< core::Real > core::scoring::mm::MMBondAngleResidueTypeParam::Ktheta_
private

vector of Ktheta values for each set

Referenced by init(), Ktheta(), and core::scoring::mm::operator<<().

utility::vector1< core::Real > core::scoring::mm::MMBondAngleResidueTypeParam::theta0_
private

vector of theta0 values for each set

Referenced by init(), core::scoring::mm::operator<<(), and theta0().


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