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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 activate_dof_deriv_one_body_method (OneBodyEnergyCOP enmeth, pose::Pose const &pose)
 Energy methods that define DOF derivatives sometimes have to be activated for residues that are not having internal-DOF changes because the DOFs they rely on extend into residues whose coordinates are changing. The code constructing the MinimizationGraph has to have already decided that the input energy method should be active. More...
 
void activate_dof_deriv_two_body_method (TwoBodyEnergyCOP enmeth, pose::Pose const &pose)
 Energy methods that define DOF derivatives sometimes have to be activated for residues that are not having internal-DOF changes because the DOFs they rely on extend into residues whose coordinates are changing. The code constructing the MinimizationGraph has to have already decided that the input energy method should be active. More...
 
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)
 
void _activate_1benmeth (OneBodyEnergyCOP enmeth)
 invoked when classify_onebody_enmeth decides an energy method should be activated; shuttles enmeth into either active_1benmeths_std_ or active_1benmeths_ext_ More...
 
void _check_sfs_and_sfd_for_1benmeth (OneBodyEnergyCOP enmeth, Pose const &pose)
 invoked when classify_onebody_enmeth decides an energy method should be activated; shuttles enmeth into sfs_dm_req_1benmeths_, sfs_dm_req_1benmeths_, and/or sfd_req_1benmeths_ as appropriate. More...
 
void _activate_2benmeth (TwoBodyEnergyCOP enmeth)
 invoked when classify_twobody_enmeth decides an energy method should be activated; shuttles enmeth into either active_2benmeths_std_ or active_2benmeths_ext_ More...
 
void _check_sfs_and_sfd_for_2benmeth (TwoBodyEnergyCOP enmeth, Pose const &pose)
 invoked when classify_twobody_enmeth decides an energy method should be activated; shuttles enmeth into sfs_dm_req_2benmeths_, sfd_req_2benmeths_, and sfs_drs_req_enmeths_ as appropriate. More...
 

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

void core::scoring::MinimizationNode::_activate_1benmeth ( OneBodyEnergyCOP  enmeth)
private

invoked when classify_onebody_enmeth decides an energy method should be activated; shuttles enmeth into either active_1benmeths_std_ or active_1benmeths_ext_

References add_active_1benmeth_ext(), and add_active_1benmeth_std().

Referenced by activate_dof_deriv_one_body_method(), and classify_onebody_enmeth().

void core::scoring::MinimizationNode::_activate_2benmeth ( TwoBodyEnergyCOP  enmeth)
private

invoked when classify_twobody_enmeth decides an energy method should be activated; shuttles enmeth into either active_2benmeths_std_ or active_2benmeths_ext_

References add_active_2benmeth_ext(), and add_active_2benmeth_std().

Referenced by activate_dof_deriv_two_body_method(), and classify_twobody_enmeth().

void core::scoring::MinimizationNode::_check_sfs_and_sfd_for_1benmeth ( OneBodyEnergyCOP  enmeth,
pose::Pose const &  pose 
)
private

invoked when classify_onebody_enmeth decides an energy method should be activated; shuttles enmeth into sfs_dm_req_1benmeths_, sfs_dm_req_1benmeths_, and/or sfd_req_1benmeths_ as appropriate.

References add_sfd_1benmeth(), add_sfs_dm_1benmeth(), and add_sfs_drs_enmeth().

Referenced by activate_dof_deriv_one_body_method(), and classify_onebody_enmeth().

void core::scoring::MinimizationNode::_check_sfs_and_sfd_for_2benmeth ( TwoBodyEnergyCOP  enmeth,
pose::Pose const &  pose 
)
private

invoked when classify_twobody_enmeth decides an energy method should be activated; shuttles enmeth into sfs_dm_req_2benmeths_, sfd_req_2benmeths_, and sfs_drs_req_enmeths_ as appropriate.

References add_sfd_2benmeth(), add_sfs_dm_2benmeth(), and add_sfs_drs_enmeth().

Referenced by activate_dof_deriv_two_body_method(), and classify_twobody_enmeth().

void core::scoring::MinimizationNode::activate_dof_deriv_one_body_method ( OneBodyEnergyCOP  enmeth,
pose::Pose const &  pose 
)

Energy methods that define DOF derivatives sometimes have to be activated for residues that are not having internal-DOF changes because the DOFs they rely on extend into residues whose coordinates are changing. The code constructing the MinimizationGraph has to have already decided that the input energy method should be active.

basically the logic of classify_onebody_enmeth without the decision of whether or not residue should be active

References _activate_1benmeth(), _check_sfs_and_sfd_for_1benmeth(), add_dof_deriv_1benmeth(), and dof_deriv_1benmeths_.

void core::scoring::MinimizationNode::activate_dof_deriv_two_body_method ( TwoBodyEnergyCOP  enmeth,
pose::Pose const &  pose 
)

Energy methods that define DOF derivatives sometimes have to be activated for residues that are not having internal-DOF changes because the DOFs they rely on extend into residues whose coordinates are changing. The code constructing the MinimizationGraph has to have already decided that the input energy method should be active.

References _activate_2benmeth(), _check_sfs_and_sfd_for_2benmeth(), add_dof_deriv_2benmeth(), and dof_deriv_2benmeths_.

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
void core::scoring::MinimizationNode::add_dof_deriv_2benmeth ( TwoBodyEnergyCOP  enmeth)
private
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
void core::scoring::MinimizationNode::add_sfd_2benmeth ( TwoBodyEnergyCOP  enmeth)
private
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: