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core::scoring::MultipoleElecPotential Class Reference

#include <MultipoleElecPotential.hh>

Inheritance diagram for core::scoring::MultipoleElecPotential:
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Public Types

typedef core::conformation::Residue Residue
 

Public Member Functions

 MultipoleElecPotential ()
 ctor More...
 
 MultipoleElecPotential (methods::EnergyMethodOptions const &options)
 Options constructor. More...
 
void read_in_amoeba_parameters ()
 
void read_in_multipole_parameters ()
 read in multipole parameters for amoeba types More...
 
void find_params_and_neighbors (core::pose::Pose const &pose, MultipoleParameterOP &mp_param, MultipoleElecResidueInfo &mp, core::conformation::Residue const &rsd, Size const j, Size const this_type) const
 Find the appropriate multipole params and axis atoms. More...
 
void build_frame_and_rotate (core::pose::Pose const &pose, MultipoleParameterOP &mp_param, Size orig_atom, MultipoleElecResidueInfo &mp, core::conformation::Residue const &rsd) const
 
core::Size amoeba_type_lookup (std::string const &atomname, std::string const &resname, std::string const &variantname, std::string const &variantname2) const
 Look up Amoeba type by resname/atomname/variant name. More...
 
void align_residue_multipole_axes (core::pose::Pose const &pose, Residue const &rsd, MultipoleElecResidueInfo &mp) const
 called prior to scoring, eg More...
 
void align_multipole_axes (pose::Pose &pose) const
 called prior to scoring, eg More...
 
void assign_residue_amoeba_type (Residue const &rsd, MultipoleElecResidueInfo &mp) const
 called prior to scoring, eg More...
 
void assign_all_amoeba_types (pose::Pose &pose) const
 called prior to scoring, eg More...
 
void determine_polarization_groups (pose::Pose &pose) const
 called prior to scoring, eg More...
 
void induce_polarizable_dipoles (pose::Pose &pose) const
 called prior to scoring, eg More...
 
void store_induced_dipoles (pose::Pose &pose) const
 Copies over induced dipoles to storage. More...
 
core::Real relax_induced_dipoles (pose::Pose &pose, Real relax) const
 Copies over induced dipoles to storage. More...
 
void calculate_fixed_fields_for_polarization (pose::Pose &pose) const
 Get the electric field due to permanent multipoles. More...
 
void clear_induced_fields (pose::Pose &pose) const
 Zero out the fields due to induced dipoles. More...
 
void calculate_induced_fields_for_polarization (pose::Pose &pose) const
 Get the electric field due to permanent multipoles. More...
 
void get_polarization_from_fields (pose::Pose &pose) const
 Get the electric field due to permanent multipoles. More...
 
void get_effective_radii (pose::Pose &pose) const
 Get the effective radii for Generalized Kirkwood. More...
 
void get_rotamers_multipole_info (pose::Pose const &pose, conformation::RotamerSetBase &) const
 Get the amoeba info for rotamers. More...
 
void get_rotamers_effective_radii (pose::Pose const &pose, conformation::RotamerSetBase &) const
 Get the effective radii for Generalized Kirkwood. More...
 
void get_single_rotamer_effective_radii (Residue const &rsd1, pose::Pose const &pose, MultipoleElecPoseInfoCOP mp_info, MultipoleElecResidueInfo &mp1) const
 Get the effective radii for Generalized Kirkwood. More...
 
void setup_for_scoring (pose::Pose &pose) const
 
void setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &repacking_residues) const
 Note: when called at the beginning of rotamer_trials, task.being_packed(i) will be false for all i this ensures that we use all the information we have to compute the current set of radii. More...
 
void update_residue_for_packing (pose::Pose &pose, Size const seqpos) const
 called eg after a rotamer substitution is accepted during rotamer trials More...
 
Real get_res_res_elecE (Residue const &rsd1, MultipoleElecResidueInfo const &mp1, Residue const &rsd2, MultipoleElecResidueInfo const &mp2) const
 
void calculate_res_res_fixed_fields_for_polarization (Residue const &rsd1, MultipoleElecResidueInfo &mp1, Residue const &rsd2, MultipoleElecResidueInfo &mp2) const
 
void calculate_res_res_induced_fields_for_polarization (Residue const &rsd1, MultipoleElecResidueInfo &mp1, Residue const &rsd2, MultipoleElecResidueInfo &mp2) const
 
void calculate_and_store_all_derivs (pose::Pose const &pose) const
 
void eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, MultipoleElecResidueInfo const &mp1, MultipoleElecResidueInfo const &mp2, pose::Pose const &pose, Real const &factor, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const
 

Private Attributes

Real Ep
 
Real Ew
 
Real const bohr
 
bool use_polarization
 
bool use_gen_kirkwood
 
std::map< std::string, Sizetype_lookup_
 
std::string const default_variant_
 
std::multimap< Size,
MultipoleParameter::MultipoleParameterOP
multipole_info_
 
utility::vector1
< utility::vector1
< DerivVectorPair > > 
cached_atom_derivs_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::MultipoleElecPotential::MultipoleElecPotential ( )
inline
core::scoring::MultipoleElecPotential::MultipoleElecPotential ( methods::EnergyMethodOptions const &  options)

Options constructor.

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

References read_in_amoeba_parameters(), and read_in_multipole_parameters().

Member Function Documentation

void core::scoring::MultipoleElecPotential::align_multipole_axes ( pose::Pose pose) const
void core::scoring::MultipoleElecPotential::align_residue_multipole_axes ( core::pose::Pose const &  pose,
Residue const &  rsd,
MultipoleElecResidueInfo mp 
) const
core::Size core::scoring::MultipoleElecPotential::amoeba_type_lookup ( std::string const &  atomname,
std::string const &  resname,
std::string const &  variantname,
std::string const &  variantname2 
) const

Look up Amoeba type by resname/atomname/variant name.

References core::scoring::TR(), and type_lookup_.

Referenced by assign_residue_amoeba_type().

void core::scoring::MultipoleElecPotential::assign_all_amoeba_types ( pose::Pose pose) const
void core::scoring::MultipoleElecPotential::assign_residue_amoeba_type ( Residue const &  rsd,
MultipoleElecResidueInfo mp 
) const
void core::scoring::MultipoleElecPotential::build_frame_and_rotate ( core::pose::Pose const &  pose,
MultipoleParameterOP mp_param,
Size  orig_atom,
MultipoleElecResidueInfo mp,
core::conformation::Residue const &  rsd 
) const
void core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs ( pose::Pose const &  pose) const
void core::scoring::MultipoleElecPotential::calculate_fixed_fields_for_polarization ( pose::Pose pose) const
void core::scoring::MultipoleElecPotential::calculate_induced_fields_for_polarization ( pose::Pose pose) const
void core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization ( Residue const &  rsd1,
MultipoleElecResidueInfo mp1,
Residue const &  rsd2,
MultipoleElecResidueInfo mp2 
) const
void core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization ( Residue const &  rsd1,
MultipoleElecResidueInfo mp1,
Residue const &  rsd2,
MultipoleElecResidueInfo mp2 
) const
void core::scoring::MultipoleElecPotential::clear_induced_fields ( pose::Pose pose) const
void core::scoring::MultipoleElecPotential::determine_polarization_groups ( pose::Pose pose) const
void core::scoring::MultipoleElecPotential::eval_residue_pair_derivatives ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
MultipoleElecResidueInfo const &  mp1,
MultipoleElecResidueInfo const &  mp2,
pose::Pose const &  pose,
Real const &  factor,
utility::vector1< DerivVectorPair > &  r1_atom_derivs,
utility::vector1< DerivVectorPair > &  r2_atom_derivs 
) const
void core::scoring::MultipoleElecPotential::find_params_and_neighbors ( core::pose::Pose const &  pose,
MultipoleParameterOP mp_param,
MultipoleElecResidueInfo mp,
core::conformation::Residue const &  rsd,
Size const  j,
Size const  this_type 
) const
void core::scoring::MultipoleElecPotential::get_effective_radii ( pose::Pose pose) const
void core::scoring::MultipoleElecPotential::get_polarization_from_fields ( pose::Pose pose) const
Real core::scoring::MultipoleElecPotential::get_res_res_elecE ( Residue const &  rsd1,
MultipoleElecResidueInfo const &  mp1,
Residue const &  rsd2,
MultipoleElecResidueInfo const &  mp2 
) const

References core::scoring::etable::count_pair::CP_CROSSOVER_34, core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_intrares_count_pair_function(), core::scoring::MultipoleElecResidueInfo::dipole(), Ep, Ew, core::scoring::get_damped_scale_factors(), core::scoring::MultipoleElecResidueInfo::induced_dipole(), core::conformation::Residue::is_virtual(), core::scoring::MultipoleElecResidueInfo::monopole(), core::scoring::MultipoleElecResidueInfo::mp_param(), core::conformation::Residue::natoms(), core::scoring::MultipoleElecResidueInfo::quadrupole(), core::scoring::MultipoleElecResidueInfo::rKirkwood(), core::scoring::same_polarization_group(), core::conformation::Residue::seqpos(), use_gen_kirkwood, and core::conformation::Residue::xyz().

Referenced by core::scoring::methods::MultipoleElecEnergy::eval_intrares_energy(), core::scoring::methods::MultipoleElecEnergy::eval_intrares_energy_ext(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::MultipoleElecEnergy::residue_pair_energy(), and core::scoring::methods::MultipoleElecEnergy::residue_pair_energy_ext().

void core::scoring::MultipoleElecPotential::get_rotamers_effective_radii ( pose::Pose const &  pose,
conformation::RotamerSetBase rotamer_set 
) const
void core::scoring::MultipoleElecPotential::get_rotamers_multipole_info ( pose::Pose const &  pose,
conformation::RotamerSetBase rotamer_set 
) const
void core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii ( Residue const &  rsd1,
pose::Pose const &  pose,
MultipoleElecPoseInfoCOP  mp_info,
MultipoleElecResidueInfo mp1 
) const
void core::scoring::MultipoleElecPotential::induce_polarizable_dipoles ( pose::Pose pose) const
void core::scoring::MultipoleElecPotential::read_in_amoeba_parameters ( )

read in parameters for amoeba and mappings between Rosetta residues/atoms and Amoeba types

References type_lookup_.

Referenced by MultipoleElecPotential().

void core::scoring::MultipoleElecPotential::read_in_multipole_parameters ( )
core::Real core::scoring::MultipoleElecPotential::relax_induced_dipoles ( pose::Pose pose,
Real  relax 
) const
void core::scoring::MultipoleElecPotential::setup_for_packing ( pose::Pose pose,
utility::vector1< bool > const &  repacking_residues 
) const

Note: when called at the beginning of rotamer_trials, task.being_packed(i) will be false for all i this ensures that we use all the information we have to compute the current set of radii.

References core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO.

void core::scoring::MultipoleElecPotential::setup_for_scoring ( pose::Pose pose) const
void core::scoring::MultipoleElecPotential::store_induced_dipoles ( pose::Pose pose) const
void core::scoring::MultipoleElecPotential::update_residue_for_packing ( pose::Pose pose,
Size const  seqpos 
) const

Member Data Documentation

Real const core::scoring::MultipoleElecPotential::bohr
private
utility::vector1< utility::vector1< DerivVectorPair > > core::scoring::MultipoleElecPotential::cached_atom_derivs_
mutableprivate
std::string const core::scoring::MultipoleElecPotential::default_variant_
private
Real core::scoring::MultipoleElecPotential::Ep
private
Real core::scoring::MultipoleElecPotential::Ew
private
std::multimap< Size, MultipoleParameter::MultipoleParameterOP > core::scoring::MultipoleElecPotential::multipole_info_
private
std::map< std::string, Size > core::scoring::MultipoleElecPotential::type_lookup_
private
bool core::scoring::MultipoleElecPotential::use_gen_kirkwood
private
bool core::scoring::MultipoleElecPotential::use_polarization
private

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