Rosetta 3.4
Public Types | Public Member Functions
core::scoring::methods::Fa_MbsolvEnergy Class Reference

#include <Fa_MbsolvEnergy.hh>

Inheritance diagram for core::scoring::methods::Fa_MbsolvEnergy:
Inheritance graph
[legend]
Collaboration diagram for core::scoring::methods::Fa_MbsolvEnergy:
Collaboration graph
[legend]

List of all members.

Public Types

typedef
ContextDependentTwoBodyEnergy 
parent

Public Member Functions

 Fa_MbsolvEnergy (etable::Etable const &etable_in, etable::MembEtable const &memb_etable_in)
virtual EnergyMethodOP clone () const
 clone
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
virtual void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
 called during gradient-based minimization inside dfunc
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
 Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
virtual bool defines_intrares_energy (EnergyMap const &) const
 Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.
virtual void eval_intrares_energy (conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &emap) const
 Evaluate the intra-residue energy for a given residue.
virtual Distance atomic_interaction_cutoff () const
 how far apart must two heavy atoms be to have a zero interaction energy?
void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
 Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
MembraneTopology const & MembraneTopology_from_pose (pose::Pose const &pose) const
Membrane_FAEmbed const & Membrane_FAEmbed_from_pose (pose::Pose const &pose) const
void setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
virtual void finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &emap) const
 called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::methods::Fa_MbsolvEnergy::Fa_MbsolvEnergy ( etable::Etable const &  etable_in,
etable::MembEtable const &  memb_etable_in 
)

Referenced by clone().


Member Function Documentation

Distance core::scoring::methods::Fa_MbsolvEnergy::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 build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) 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::etable::Etable::max_dis().

EnergyMethodOP core::scoring::methods::Fa_MbsolvEnergy::clone ( ) const [virtual]
virtual bool core::scoring::methods::Fa_MbsolvEnergy::defines_intrares_energy ( EnergyMap const &  weights) const [inline, virtual]

Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero 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 intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.

Implements core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative ( id::AtomID const &  id,
pose::Pose const &  pose,
kinematics::DomainMap const &  domain_map,
ScoreFunction const &  sfxn,
EnergyMap const &  weights,
Vector F1,
Vector F2 
) const [virtual]
void core::scoring::methods::Fa_MbsolvEnergy::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluate the intra-residue energy for a given residue.

Implements core::scoring::methods::TwoBodyEnergy.

References core::scoring::fa_mbsolv.

void core::scoring::methods::Fa_MbsolvEnergy::finalize_total_energy ( pose::Pose pose,
ScoreFunction const &  sfxn,
EnergyMap total_energy 
) const [virtual]

called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

called at the end of energy evaluation

Reimplemented from core::scoring::methods::EnergyMethod.

void core::scoring::methods::Fa_MbsolvEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const [virtual]

Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.

Implements core::scoring::methods::EnergyMethod.

Membrane_FAEmbed const & core::scoring::methods::Fa_MbsolvEnergy::Membrane_FAEmbed_from_pose ( pose::Pose const &  pose) const

Pose must already contain a cenlist object or this method will fail.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_FAEMBED.

Referenced by eval_atom_derivative().

MembraneTopology const & core::scoring::methods::Fa_MbsolvEnergy::MembraneTopology_from_pose ( pose::Pose const &  pose) const
void core::scoring::methods::Fa_MbsolvEnergy::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::fa_mbsolv.

void core::scoring::methods::Fa_MbsolvEnergy::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  sfxn 
) const [virtual]

Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

References core::scoring::fa_mbsolv, core::pose::Pose::update_residue_neighbors(), and core::scoring::ScoreFunction::weights().

void core::scoring::methods::Fa_MbsolvEnergy::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &   
) const [virtual]

The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines