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core::scoring::MinimizationNode Class Reference

#include <MinimizationGraph.hh>

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

typedef utility::graph::Node parent
 
typedef utility::vector1
< OneBodyEnergyCOP > 
OneBodyEnergies
 
typedef
OneBodyEnergies::const_iterator 
OneBodyEnergiesIterator
 
typedef utility::vector1
< TwoBodyEnergyCOP > 
TwoBodyEnergies
 
typedef
TwoBodyEnergies::const_iterator 
TwoBodyEnergiesIterator
 
typedef utility::vector1
< EnergyMethodCOP > 
EnergyMethods
 
typedef
EnergyMethods::const_iterator 
EnergyMethodsIterator
 
typedef conformation::Residue Residue
 
typedef pose::Pose Pose
 

Public Member Functions

 MinimizationNode (utility::graph::Graph *owner, Size index)
 
 ~MinimizationNode () override
 
void copy_from (parent const *source) override
 copy mmember data from source node More...
 
void print () const override
 
Size count_static_memory () const override
 
Size count_dynamic_memory () const override
 
ResSingleMinimizationData const & res_min_data () const
 
ResSingleMinimizationDatares_min_data ()
 
bool add_onebody_enmeth (OneBodyEnergyCOP enmeth, Residue const &rsd, Pose const &pose, int domain_map_color)
 
bool add_twobody_enmeth (TwoBodyEnergyCOP enmeth, Residue const &rsd, Pose const &pose, EnergyMap const &weights, int domain_map_color)
 
void setup_for_minimizing (Residue const &rsd, Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map, basic::datacache::BasicDataCache &res_data_cache)
 
void setup_for_scoring (Residue const &rsd, basic::datacache::BasicDataCache &residue_data_cache, Pose const &pose, ScoreFunction const &sfxn)
 
void setup_for_derivatives (Residue const &rsd, basic::datacache::BasicDataCache &residue_data_cache, pose::Pose const &pose, ScoreFunction const &sfxn)
 
void update_active_enmeths_for_residue (Residue const &rsd, pose::Pose const &pose, EnergyMap const &weights, int domain_map_color)
 
Real weight () const
 
void weight (Real setting)
 
Real dweight () const
 
void dweight (Real setting)
 
void add_sfs_drs_enmeth (EnergyMethodCOP enmeth)
 This method is not meant for general use; it's only to be called by the MinimizationNode and the MinimizationGraph. More...
 
OneBodyEnergiesIterator active_1benmeths_begin () const
 
OneBodyEnergiesIterator active_1benmeths_end () const
 
OneBodyEnergiesIterator active_1benmeths_std_begin () const
 
OneBodyEnergiesIterator active_1benmeths_std_end () const
 
OneBodyEnergiesIterator active_1benmeths_ext_begin () const
 
OneBodyEnergiesIterator active_1benmeths_ext_end () const
 
OneBodyEnergiesIterator dof_deriv_1benmeths_begin () const
 
OneBodyEnergiesIterator dof_deriv_1benmeths_end () const
 
OneBodyEnergiesIterator sfs_dm_req_1benmeths_begin () const
 
OneBodyEnergiesIterator sfs_dm_req_1benmeths_end () const
 
OneBodyEnergiesIterator sfd_req_1benmeths_begin () const
 
OneBodyEnergiesIterator sfd_req_1benmeths_end () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_begin () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_end () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_std_begin () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_std_end () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_ext_begin () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_ext_end () const
 
TwoBodyEnergiesIterator dof_deriv_2benmeths_begin () const
 
TwoBodyEnergiesIterator dof_deriv_2benmeths_end () const
 
TwoBodyEnergiesIterator sfs_dm_req_2benmeths_begin () const
 
TwoBodyEnergiesIterator sfs_dm_req_2benmeths_end () const
 
TwoBodyEnergiesIterator sfd_req_2benmeths_begin () const
 
TwoBodyEnergiesIterator sfd_req_2benmeths_end () const
 
EnergyMethodsIterator sfs_drs_req_enmeths_begin () const
 
EnergyMethodsIterator sfs_drs_req_enmeths_end () const
 

Public Attributes

 __pad0__:EnergyMethodCOP EnergyMethodCOP
 
 __pad1__:OneBodyEnergyCOP OneBodyEnergyCOP
 
 __pad2__:TwoBodyEnergyCOP TwoBodyEnergyCOP
 

Protected Member Functions

MinimizationGraph const * get_mingraph_owner () const
 
MinimizationGraphget_mingraph_owner ()
 

Private Member Functions

void add_active_1benmeth_std (OneBodyEnergyCOP enmeth)
 
void add_active_1benmeth_ext (OneBodyEnergyCOP enmeth)
 
void add_dof_deriv_1benmeth (OneBodyEnergyCOP enmeth)
 
void add_sfs_dm_1benmeth (OneBodyEnergyCOP enmeth)
 
void add_sfd_1benmeth (OneBodyEnergyCOP enmeth)
 
void add_active_2benmeth_std (TwoBodyEnergyCOP enmeth)
 
void add_active_2benmeth_ext (TwoBodyEnergyCOP enmeth)
 
void add_dof_deriv_2benmeth (TwoBodyEnergyCOP enmeth)
 
void add_sfs_dm_2benmeth (TwoBodyEnergyCOP enmeth)
 
void add_sfd_2benmeth (TwoBodyEnergyCOP enmeth)
 
bool classify_onebody_enmeth (OneBodyEnergyCOP enmeth, Residue const &rsd, Pose const &pose, int domain_map_color)
 
bool classify_twobody_enmeth (TwoBodyEnergyCOP enmeth, Residue const &rsd, Pose const &pose, EnergyMap const &weights, int domain_map_color)
 

Private Attributes

ResSingleMinimizationData res_min_data_
 
OneBodyEnergies onebody_enmeths_
 
OneBodyEnergies active_1benmeths_
 
OneBodyEnergies active_1benmeths_std_
 
OneBodyEnergies active_1benmeths_ext_
 
OneBodyEnergies dof_deriv_1benmeths_
 
OneBodyEnergies sfs_dm_req_1benmeths_
 
OneBodyEnergies sfd_req_1benmeths_
 
TwoBodyEnergies twobody_enmeths_
 
TwoBodyEnergies active_intrares2benmeths_
 
TwoBodyEnergies active_intrares2benmeths_std_
 
TwoBodyEnergies active_intrares2benmeths_ext_
 
TwoBodyEnergies dof_deriv_2benmeths_
 
TwoBodyEnergies sfs_dm_req_2benmeths_
 
TwoBodyEnergies sfd_req_2benmeths_
 
EnergyMethods sfs_drs_req_enmeths_
 
Real weight_
 
Real dweight_
 

Detailed Description

Class MinimizationNode holds the ResSingleMinimizationData information for a single residue in a Pose which is being minimized. The data held in this node will be used in both scoring the residue one-body energies and evaluating atom derivatives during minimization.

Member Typedef Documentation

typedef utility::vector1< EnergyMethodCOP > core::scoring::MinimizationNode::EnergyMethods
typedef EnergyMethods::const_iterator core::scoring::MinimizationNode::EnergyMethodsIterator
typedef utility::vector1< OneBodyEnergyCOP > core::scoring::MinimizationNode::OneBodyEnergies
typedef OneBodyEnergies::const_iterator core::scoring::MinimizationNode::OneBodyEnergiesIterator
typedef utility::graph::Node core::scoring::MinimizationNode::parent
typedef utility::vector1< TwoBodyEnergyCOP > core::scoring::MinimizationNode::TwoBodyEnergies
typedef TwoBodyEnergies::const_iterator core::scoring::MinimizationNode::TwoBodyEnergiesIterator

Constructor & Destructor Documentation

core::scoring::MinimizationNode::MinimizationNode ( utility::graph::Graph *  owner,
Size  index 
)

Referenced by count_static_memory().

core::scoring::MinimizationNode::~MinimizationNode ( )
overridedefault

Member Function Documentation

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_begin ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_end ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_ext_begin ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_ext_end ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_std_begin ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_std_end ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_begin ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_end ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_ext_begin ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_ext_end ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_std_begin ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_std_end ( ) const
void core::scoring::MinimizationNode::add_active_1benmeth_ext ( OneBodyEnergyCOP  enmeth)
private
void core::scoring::MinimizationNode::add_active_1benmeth_std ( OneBodyEnergyCOP  enmeth)
private
void core::scoring::MinimizationNode::add_active_2benmeth_ext ( TwoBodyEnergyCOP  enmeth)
private
void core::scoring::MinimizationNode::add_active_2benmeth_std ( TwoBodyEnergyCOP  enmeth)
private
void core::scoring::MinimizationNode::add_dof_deriv_1benmeth ( OneBodyEnergyCOP  enmeth)
private

References dof_deriv_1benmeths_.

Referenced by classify_onebody_enmeth().

void core::scoring::MinimizationNode::add_dof_deriv_2benmeth ( TwoBodyEnergyCOP  enmeth)
private

References dof_deriv_2benmeths_.

Referenced by classify_twobody_enmeth().

bool core::scoring::MinimizationNode::add_onebody_enmeth ( OneBodyEnergyCOP  enmeth,
Residue const &  rsd,
Pose const &  pose,
int  domain_map_color 
)
void core::scoring::MinimizationNode::add_sfd_1benmeth ( OneBodyEnergyCOP  enmeth)
private

References sfd_req_1benmeths_.

Referenced by classify_onebody_enmeth().

void core::scoring::MinimizationNode::add_sfd_2benmeth ( TwoBodyEnergyCOP  enmeth)
private

References sfd_req_2benmeths_.

Referenced by classify_twobody_enmeth().

void core::scoring::MinimizationNode::add_sfs_dm_1benmeth ( OneBodyEnergyCOP  enmeth)
private
void core::scoring::MinimizationNode::add_sfs_dm_2benmeth ( TwoBodyEnergyCOP  enmeth)
private
void core::scoring::MinimizationNode::add_sfs_drs_enmeth ( EnergyMethodCOP  enmeth)
bool core::scoring::MinimizationNode::add_twobody_enmeth ( TwoBodyEnergyCOP  enmeth,
Residue const &  rsd,
Pose const &  pose,
EnergyMap const &  weights,
int  domain_map_color 
)

Note that the minimization graph is used both to evaluate the scores for both the "modern" EnergyMethods and the "old" energy methods (those which still define eval_atom_derivative instead of the pairwise-decomposable derivative evaluation methods) so when these older energy methods are added to the minimization graph, they should not simply be rejected.

References classify_twobody_enmeth(), and twobody_enmeths_.

Referenced by core::scoring::ScoreFunction::setup_for_minimizing_for_node().

bool core::scoring::MinimizationNode::classify_onebody_enmeth ( OneBodyEnergyCOP  enmeth,
Residue const &  rsd,
Pose const &  pose,
int  domain_map_color 
)
private
bool core::scoring::MinimizationNode::classify_twobody_enmeth ( TwoBodyEnergyCOP  enmeth,
Residue const &  rsd,
Pose const &  pose,
EnergyMap const &  weights,
int  domain_map_color 
)
private
void core::scoring::MinimizationNode::copy_from ( parent const *  source)
override
Size core::scoring::MinimizationNode::count_dynamic_memory ( ) const
override
Size core::scoring::MinimizationNode::count_static_memory ( ) const
override

References MinimizationNode().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_1benmeths_begin ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_1benmeths_end ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_2benmeths_begin ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_2benmeths_end ( ) const
Real core::scoring::MinimizationNode::dweight ( ) const
inline

References dweight_.

void core::scoring::MinimizationNode::dweight ( Real  setting)
inline

References dweight_.

MinimizationGraph const * core::scoring::MinimizationNode::get_mingraph_owner ( ) const
protected
MinimizationGraph * core::scoring::MinimizationNode::get_mingraph_owner ( )
protected
void core::scoring::MinimizationNode::print ( ) const
override
ResSingleMinimizationData const& core::scoring::MinimizationNode::res_min_data ( ) const
inline
ResSingleMinimizationData& core::scoring::MinimizationNode::res_min_data ( )
inline

References res_min_data_.

void core::scoring::MinimizationNode::setup_for_derivatives ( Residue const &  rsd,
basic::datacache::BasicDataCache &  residue_data_cache,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
)
void core::scoring::MinimizationNode::setup_for_minimizing ( Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
kinematics::MinimizerMapBase const &  min_map,
basic::datacache::BasicDataCache &  res_data_cache 
)
void core::scoring::MinimizationNode::setup_for_scoring ( Residue const &  rsd,
basic::datacache::BasicDataCache &  residue_data_cache,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
)
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_1benmeths_begin ( ) const

References sfd_req_1benmeths_.

Referenced by setup_for_derivatives().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_1benmeths_end ( ) const

References sfd_req_1benmeths_.

Referenced by setup_for_derivatives().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_2benmeths_begin ( ) const

References sfd_req_2benmeths_.

Referenced by setup_for_derivatives().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_2benmeths_end ( ) const

References sfd_req_2benmeths_.

Referenced by setup_for_derivatives().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfs_dm_req_1benmeths_begin ( ) const

References sfs_dm_req_1benmeths_.

Referenced by setup_for_scoring().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfs_dm_req_1benmeths_end ( ) const

References sfs_dm_req_1benmeths_.

Referenced by setup_for_scoring().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfs_dm_req_2benmeths_begin ( ) const

References sfs_dm_req_2benmeths_.

Referenced by setup_for_scoring().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfs_dm_req_2benmeths_end ( ) const

References sfs_dm_req_2benmeths_.

Referenced by setup_for_scoring().

MinimizationNode::EnergyMethodsIterator core::scoring::MinimizationNode::sfs_drs_req_enmeths_begin ( ) const

References sfs_drs_req_enmeths_.

Referenced by setup_for_scoring().

MinimizationNode::EnergyMethodsIterator core::scoring::MinimizationNode::sfs_drs_req_enmeths_end ( ) const

References sfs_drs_req_enmeths_.

Referenced by setup_for_scoring().

void core::scoring::MinimizationNode::update_active_enmeths_for_residue ( Residue const &  rsd,
pose::Pose const &  pose,
EnergyMap const &  weights,
int  domain_map_color 
)
Real core::scoring::MinimizationNode::weight ( ) const
inline
void core::scoring::MinimizationNode::weight ( Real  setting)
inline

References weight_.

Member Data Documentation

core::scoring::MinimizationNode::__pad0__
core::scoring::MinimizationNode::__pad1__
core::scoring::MinimizationNode::__pad2__
OneBodyEnergies core::scoring::MinimizationNode::active_1benmeths_
private
OneBodyEnergies core::scoring::MinimizationNode::active_1benmeths_ext_
private
OneBodyEnergies core::scoring::MinimizationNode::active_1benmeths_std_
private
TwoBodyEnergies core::scoring::MinimizationNode::active_intrares2benmeths_
private
TwoBodyEnergies core::scoring::MinimizationNode::active_intrares2benmeths_ext_
private
TwoBodyEnergies core::scoring::MinimizationNode::active_intrares2benmeths_std_
private
OneBodyEnergies core::scoring::MinimizationNode::dof_deriv_1benmeths_
private
TwoBodyEnergies core::scoring::MinimizationNode::dof_deriv_2benmeths_
private
Real core::scoring::MinimizationNode::dweight_
private

Referenced by copy_from(), and dweight().

OneBodyEnergies core::scoring::MinimizationNode::onebody_enmeths_
private
ResSingleMinimizationData core::scoring::MinimizationNode::res_min_data_
private
OneBodyEnergies core::scoring::MinimizationNode::sfd_req_1benmeths_
private
TwoBodyEnergies core::scoring::MinimizationNode::sfd_req_2benmeths_
private
OneBodyEnergies core::scoring::MinimizationNode::sfs_dm_req_1benmeths_
private
TwoBodyEnergies core::scoring::MinimizationNode::sfs_dm_req_2benmeths_
private
EnergyMethods core::scoring::MinimizationNode::sfs_drs_req_enmeths_
private
TwoBodyEnergies core::scoring::MinimizationNode::twobody_enmeths_
private
Real core::scoring::MinimizationNode::weight_
private

Referenced by copy_from(), and weight().


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