Rosetta 3.4

#include <OccludedHbondSolEnergy.hh>
Public Member Functions  
OccludedHbondSolEnergy (methods::EnergyMethodOptions const &options, bool const verbose=false)  
OccludedHbondSolEnergy (OccludedHbondSolEnergy const &src)  
virtual methods::EnergyMethodOP  clone () const 
virtual void  setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const 
virtual void  setup_for_derivatives (pose::Pose &pose, ScoreFunction const &) const 
Called immediately before atom and DOFderivatives are calculated allowing the derived class a chance to prepare for future calls.  
virtual void  residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &, ScoreFunction const &, EnergyMap &emap) const 
Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.  
virtual void  eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const 
Evaluate the intraresidue energy for a given residue.  
virtual bool  minimize_in_whole_structure_context (pose::Pose const &) const 
Inform inquiring algorithms that this energy method will optin to the residuepair decomposable derivative evaluation scheme.  
virtual bool  defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const 
virtual void  eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const 
Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fastrelax runs by ~40%.  
virtual void  eval_intrares_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const 
Evaluate the derivative for the intraresidue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.  
virtual bool  defines_intrares_energy (EnergyMap const &) const 
Two body energies are able to define intraresidue energies, and to do so only in the presence of certain nonzero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.  
virtual Distance  atomic_interaction_cutoff () const 
how far apart must two heavy atoms be to have a zero interaction energy?  
virtual void  indicate_required_context_graphs (utility::vector1< bool > &) const 
Indicate in the contextgraphsrequired list which contextgraphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.  
Public Attributes  
__pad0__:ContextIndependentTwoBodyEnergy parent 
core::scoring::geometric_solvation::OccludedHbondSolEnergy::OccludedHbondSolEnergy  (  methods::EnergyMethodOptions const &  options, 
bool const  verbose = false 

) 
References core::scoring::geometric_solvation::tr().
Referenced by clone().
core::scoring::geometric_solvation::OccludedHbondSolEnergy::OccludedHbondSolEnergy  (  OccludedHbondSolEnergy const &  src  ) 
References core::scoring::geometric_solvation::tr().
Distance core::scoring::geometric_solvation::OccludedHbondSolEnergy::atomic_interaction_cutoff  (  )  const [virtual] 
how far apart must two heavy atoms be to have a zero interaction energy?
If hydrogen atoms interact at the same range as heavy atoms, then this distance should buildin a 2 * maxboundhdistancecutoff buffer. There is an improper mixing here between runtime aquired chemical knowledge (maxboundhdistancecutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().
Implements core::scoring::methods::ShortRangeTwoBodyEnergy.
References core::scoring::geometric_solvation::DatabaseOccSolEne::atomic_interaction_cutoff().
methods::EnergyMethodOP core::scoring::geometric_solvation::OccludedHbondSolEnergy::clone  (  )  const [virtual] 
Implements core::scoring::methods::EnergyMethod.
References OccludedHbondSolEnergy().
virtual bool core::scoring::geometric_solvation::OccludedHbondSolEnergy::defines_intrares_energy  (  EnergyMap const &  weights  )  const [inline, virtual] 
Two body energies are able to define intraresidue energies, and to do so only in the presence of certain nonzero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.
For example, the Etable method defines intraresidue energies only when one or more of the fa_intra_{atr,rep,sol} weights are nonzero.
Implements core::scoring::methods::TwoBodyEnergy.
bool core::scoring::geometric_solvation::OccludedHbondSolEnergy::defines_score_for_residue_pair  (  conformation::Residue const &  res1, 
conformation::Residue const &  res2,  
bool  res_moving_wrt_eachother  
)  const [virtual] 
return true if the two residues are moving with respect to each other.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
void core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_intrares_derivatives  (  conformation::Residue const &  rsd, 
ResSingleMinimizationData const &  min_data,  
pose::Pose const &  pose,  
EnergyMap const &  weights,  
utility::vector1< DerivVectorPair > &  atom_derivs  
)  const [virtual] 
Evaluate the derivative for the intraresidue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
void core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_intrares_energy  (  conformation::Residue const &  rsd, 
pose::Pose const &  pose,  
ScoreFunction const &  sfxn,  
EnergyMap &  emap  
)  const [virtual] 
Evaluate the intraresidue energy for a given residue.
Implements core::scoring::methods::TwoBodyEnergy.
References core::scoring::occ_sol_fitted, and core::scoring::geometric_solvation::tr().
void core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives  (  conformation::Residue const &  rsd1, 
conformation::Residue const &  rsd2,  
ResSingleMinimizationData const &  ,  
ResSingleMinimizationData const &  ,  
ResPairMinimizationData const &  min_data,  
pose::Pose const &  pose,  
EnergyMap const &  weights,  
utility::vector1< DerivVectorPair > &  r1_atom_derivs,  
utility::vector1< DerivVectorPair > &  r2_atom_derivs  
)  const [virtual] 
Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fastrelax runs by ~40%.
Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect to each other and increment the derivatives in atomderivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
virtual void core::scoring::geometric_solvation::OccludedHbondSolEnergy::indicate_required_context_graphs  (  utility::vector1< bool > &  context_graphs_required  )  const [inline, virtual] 
Indicate in the contextgraphsrequired list which contextgraphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Implements core::scoring::methods::EnergyMethod.
virtual bool core::scoring::geometric_solvation::OccludedHbondSolEnergy::minimize_in_whole_structure_context  (  pose::Pose const &  )  const [inline, virtual] 
Inform inquiring algorithms that this energy method will optin to the residuepair decomposable derivative evaluation scheme.
Reimplemented from core::scoring::methods::EnergyMethod.
void core::scoring::geometric_solvation::OccludedHbondSolEnergy::residue_pair_energy  (  conformation::Residue const &  rsd1, 
conformation::Residue const &  rsd2,  
pose::Pose const &  pose,  
ScoreFunction const &  sfxn,  
EnergyMap &  emap  
)  const [virtual] 
Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
Implements core::scoring::methods::TwoBodyEnergy.
References core::scoring::occ_sol_fitted, core::conformation::Residue::seqpos(), and core::scoring::geometric_solvation::tr().
void core::scoring::geometric_solvation::OccludedHbondSolEnergy::setup_for_derivatives  (  pose::Pose &  pose, 
ScoreFunction const &  sfxn  
)  const [virtual] 
Called immediately before atom and DOFderivatives are calculated allowing the derived class a chance to prepare for future calls.
default implementation noop
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::update_residue_neighbors().
void core::scoring::geometric_solvation::OccludedHbondSolEnergy::setup_for_scoring  (  pose::Pose &  pose, 
ScoreFunction const &  
)  const [virtual] 
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::update_residue_neighbors().