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

#include <GenBornEnergy.hh>

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List of all members.

Public Types

typedef
ContextDependentLRTwoBodyEnergy 
parent

Public Member Functions

 GenBornEnergy (EnergyMethodOptions const &options)
 for use by ScoringManager
 GenBornEnergy (GenBornEnergy const &src)
LongRangeEnergyType long_range_type () const
virtual bool defines_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const
virtual EnergyMethodOP clone () const
 clone
virtual void setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &residues_repacking, utility::vector1< bool > const &) 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 DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
virtual void prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const
virtual void update_residue_for_packing (pose::Pose &, Size resid) const
 ensure this function gets called. The default behavior is to do nothing.
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 void evaluate_rotamer_intrares_energies (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const
 Batch computation of rotamer intrares energies. Need not be overriden in derived class -- by default, iterates over all rotamers, and calls derived class's intrares _energy method.
virtual void evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const
 Batch computation of rotamer intrares energy map. Need not be overriden in derived class -- by default, iterates over all rotamers, and calls derived class's intrares _energy method.
virtual void evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const
 Batch computation of rotamer pair energies. Need not be overriden in derived class -- by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
virtual void evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const
 Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
virtual void evaluate_rotamer_background_energy_maps (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< EnergyMap > &emaps) const
 Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
virtual void eval_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const
 Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative.
virtual void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
 GenBornEnergy distance cutoff set to the same cutoff used by EtableEnergy, for now.
virtual bool defines_intrares_energy (EnergyMap const &) const
 GenBornEnergy does define intraresidue interactions.
virtual void eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the intra-residue energy for a given residue.
Real packing_interaction_cutoff () const
 this is our own special function

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::methods::GenBornEnergy::GenBornEnergy ( EnergyMethodOptions const &  options)

for use by ScoringManager

Referenced by clone().

core::scoring::methods::GenBornEnergy::GenBornEnergy ( GenBornEnergy const &  src)

Member Function Documentation

EnergyMethodOP core::scoring::methods::GenBornEnergy::clone ( ) const [virtual]
bool core::scoring::methods::GenBornEnergy::defines_intrares_energy ( EnergyMap const &  ) const [virtual]

GenBornEnergy does define intraresidue interactions.

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

bool core::scoring::methods::GenBornEnergy::defines_residue_pair_energy ( pose::Pose const &  pose,
Size  res1,
Size  res2 
) const [virtual]
void core::scoring::methods::GenBornEnergy::eval_atom_derivative ( id::AtomID const &  id,
pose::Pose const &  pose,
kinematics::DomainMap const &  domain_map,
ScoreFunction const &  sfxn,
EnergyMap const &  emap,
Vector F1,
Vector F2 
) const [virtual]

Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative.

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) "Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations" Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

default implementation does not alter either the F1 or F2 vectors.

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

References core::scoring::gb_elec.

void core::scoring::methods::GenBornEnergy::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
void core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies ( conformation::RotamerSetBase const &  set,
conformation::Residue const &  residue,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap const &  weights,
utility::vector1< core::PackerEnergy > &  energy_vector 
) const [virtual]

Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::pose::Pose::data(), core::scoring::gb_elec, core::pose::datacache::CacheableDataType::GEN_BORN_POSE_INFO, core::conformation::RotamerSetCacheableDataType::GEN_BORN_ROTAMER_SET_INFO, core::conformation::Residue::is_DNA(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Residue::nbr_radius(), packing_interaction_cutoff(), core::scoring::GenBornRotamerSetInfo::residue_info(), and core::conformation::Residue::seqpos().

void core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps ( conformation::RotamerSetBase const &  set,
conformation::Residue const &  residue,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap const &  weights,
utility::vector1< EnergyMap > &  emaps 
) const [virtual]

Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::pose::Pose::data(), core::scoring::gb_elec, core::pose::datacache::CacheableDataType::GEN_BORN_POSE_INFO, core::conformation::RotamerSetCacheableDataType::GEN_BORN_ROTAMER_SET_INFO, core::conformation::Residue::is_DNA(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Residue::nbr_radius(), packing_interaction_cutoff(), core::scoring::GenBornRotamerSetInfo::residue_info(), and core::conformation::Residue::seqpos().

void core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energies ( conformation::RotamerSetBase const &  set,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
utility::vector1< core::PackerEnergy > &  energies 
) const [virtual]

Batch computation of rotamer intrares energies. Need not be overriden in derived class -- by default, iterates over all rotamers, and calls derived class's intrares _energy method.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::scoring::gb_elec, core::conformation::RotamerSetCacheableDataType::GEN_BORN_ROTAMER_SET_INFO, core::pose::Pose::residue(), and core::scoring::GenBornRotamerSetInfo::residue_info().

void core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energy_maps ( conformation::RotamerSetBase const &  set,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
utility::vector1< EnergyMap > &  emaps 
) const [virtual]

Batch computation of rotamer intrares energy map. Need not be overriden in derived class -- by default, iterates over all rotamers, and calls derived class's intrares _energy method.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::scoring::gb_elec, core::conformation::RotamerSetCacheableDataType::GEN_BORN_ROTAMER_SET_INFO, core::pose::Pose::residue(), and core::scoring::GenBornRotamerSetInfo::residue_info().

void core::scoring::methods::GenBornEnergy::evaluate_rotamer_pair_energies ( conformation::RotamerSetBase const &  set1,
conformation::RotamerSetBase const &  set2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap const &  weights,
ObjexxFCL::FArray2D< core::PackerEnergy > &  energy_table 
) const [virtual]

Batch computation of rotamer pair energies. Need not be overriden in derived class -- by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::conformation::RotamerSetBase::data(), core::scoring::gb_elec, core::conformation::RotamerSetCacheableDataType::GEN_BORN_ROTAMER_SET_INFO, core::conformation::RotamerSetBase::get_n_residue_types(), core::conformation::RotamerSetBase::get_n_rotamers_for_residue_type(), core::conformation::RotamerSetBase::get_residue_type_begin(), packing_interaction_cutoff(), core::conformation::RotamerSetBase::resid(), core::pose::Pose::residue(), core::scoring::GenBornRotamerSetInfo::residue_info(), and core::conformation::RotamerSetBase::rotamer().

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

GenBornEnergy distance cutoff set to the same cutoff used by EtableEnergy, for now.

GenBornEnergy requires no context graphs

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

LongRangeEnergyType core::scoring::methods::GenBornEnergy::long_range_type ( ) const [inline, virtual]
Real core::scoring::methods::GenBornEnergy::packing_interaction_cutoff ( ) const [inline]
void core::scoring::methods::GenBornEnergy::prepare_rotamers_for_packing ( pose::Pose const &  ,
conformation::RotamerSetBase  
) const [virtual]

default implementation noop

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

References core::scoring::GenBornPotential::get_rotamers_born_radii().

void core::scoring::methods::GenBornEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
void core::scoring::methods::GenBornEnergy::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::GenBornPotential::get_all_born_radii().

void core::scoring::methods::GenBornEnergy::setup_for_packing ( pose::Pose ,
utility::vector1< bool > const &  ,
utility::vector1< bool > const &   
) const [virtual]
void core::scoring::methods::GenBornEnergy::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &   
) const [virtual]
void core::scoring::methods::GenBornEnergy::update_residue_for_packing ( pose::Pose ,
Size  resid 
) const [virtual]

ensure this function gets called. The default behavior is to do nothing.

default implementation noop

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

References core::scoring::GenBornPotential::update_residue_for_packing().


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