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core::scoring::VdWTinkerPotential Class Reference

#include <VdWTinkerPotential.hh>

Inheritance diagram for core::scoring::VdWTinkerPotential:
Inheritance graph
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Public Types

typedef core::conformation::Residue Residue
 

Public Member Functions

 VdWTinkerPotential ()
 ctor More...
 
void read_in_amoeba_parameters ()
 
void read_in_vdw_tinker_parameters ()
 read in vdw parameters for amoeba types More...
 
core::Size amoeba_type_lookup (std::string const &atomname, std::string const &resname, std::string const &variantname) const
 Look up Amoeba type by resname/atomname/variant name. More...
 
void assign_residue_amoeba_type (Residue const &rsd, VdWTinkerResidueInfo &mp) const
 called prior to scoring, eg More...
 
void assign_all_amoeba_types (pose::Pose &pose) const
 called prior to scoring, eg More...
 
void get_rotamers_vdw_info (pose::Pose const &pose, conformation::RotamerSetBase &) const
 Get the amoeba info for rotamers. 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_vdw (Residue const &rsd1, VdWTinkerResidueInfo const &mp1, Residue const &rsd2, VdWTinkerResidueInfo const &mp2) const
 
void eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, VdWTinkerResidueInfo const &mp1, VdWTinkerResidueInfo const &mp2, pose::Pose const &pose, Real const &factor, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const
 

Private Attributes

std::map< std::string, Sizetype_lookup_
 
std::string const default_variant_
 
utility::vector1< Realvdw_radius_
 
utility::vector1< Realvdw_depth_
 
utility::vector1< Realvdw_reduce_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::VdWTinkerPotential::VdWTinkerPotential ( )
inline

Member Function Documentation

core::Size core::scoring::VdWTinkerPotential::amoeba_type_lookup ( std::string const &  atomname,
std::string const &  resname,
std::string const &  variantname 
) 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::VdWTinkerPotential::assign_all_amoeba_types ( pose::Pose pose) const
void core::scoring::VdWTinkerPotential::assign_residue_amoeba_type ( Residue const &  rsd,
VdWTinkerResidueInfo mp 
) const
void core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
VdWTinkerResidueInfo const &  mp1,
VdWTinkerResidueInfo const &  mp2,
pose::Pose const &  pose,
Real const &  factor,
utility::vector1< DerivVectorPair > &  r1_atom_derivs,
utility::vector1< DerivVectorPair > &  r2_atom_derivs 
) const
Real core::scoring::VdWTinkerPotential::get_res_res_vdw ( Residue const &  rsd1,
VdWTinkerResidueInfo const &  mp1,
Residue const &  rsd2,
VdWTinkerResidueInfo const &  mp2 
) const
void core::scoring::VdWTinkerPotential::get_rotamers_vdw_info ( pose::Pose const &  pose,
conformation::RotamerSetBase rotamer_set 
) const
void core::scoring::VdWTinkerPotential::read_in_amoeba_parameters ( )

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

References type_lookup_.

Referenced by VdWTinkerPotential().

void core::scoring::VdWTinkerPotential::read_in_vdw_tinker_parameters ( )

read in vdw parameters for amoeba types

References vdw_depth_, vdw_radius_, and vdw_reduce_.

Referenced by VdWTinkerPotential().

void core::scoring::VdWTinkerPotential::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::VDWTINKER_POSE_INFO.

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

Member Data Documentation

std::string const core::scoring::VdWTinkerPotential::default_variant_
private
std::map< std::string, Size > core::scoring::VdWTinkerPotential::type_lookup_
private
utility::vector1< Real > core::scoring::VdWTinkerPotential::vdw_depth_
private
utility::vector1< Real > core::scoring::VdWTinkerPotential::vdw_radius_
private
utility::vector1< Real > core::scoring::VdWTinkerPotential::vdw_reduce_
private

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