CapriTotalEnergy Class Reference

#include <capri15_scoring.hh>

Inheritance diagram for CapriTotalEnergy:

Public Member Functions
	CapriTotalEnergy ()
	C-tor. More...
virtual scoring::methods::EnergyMethodOP	clone () const
	clone More...
	CapriTotalEnergy (CapriTotalEnergy const &src)
virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &emap) const
virtual Distance	atomic_interaction_cutoff () const
virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const

Private Member Functions
void	add_score_types ()
void	read_datafile ()
void	score_experimental_constraints (pose::Pose const &pose, EnergyMap &emap) const
void	setup_rna_atoms_for_pose (pose::Pose const &pose, utility::vector1< utility::vector1< AtomID > > &rna_atoms) const

Private Attributes
utility::vector1< utility::vector1< std::pair< std::string, Size > > >	rna_atoms_

Detailed Description

Updated version of experimental constraints scoring, plus distance score between SAM CE and rGU N1 and conservation scoring.

Color code:

Blue == "must" make an atomic contact with protein Cyan == would be nice to hace protein nearby (say within 8-10 Angstroms) Pink == no protein within 8-10 A Red == no protein in atomic contact.

Constructor & Destructor Documentation

CapriTotalEnergy() [1/2]

CapriTotalEnergy::CapriTotalEnergy ( )

inline

C-tor.

CapriTotalEnergy() [2/2]

CapriTotalEnergy::CapriTotalEnergy ( CapriTotalEnergy const &  src )

inline

Member Function Documentation

add_score_types()

void CapriTotalEnergy::add_score_types ( )

inlineprivate

atomic_interaction_cutoff()

virtual Distance CapriTotalEnergy::atomic_interaction_cutoff ( ) const

inlinevirtual

clone()

virtual scoring::methods::EnergyMethodOP CapriTotalEnergy::clone ( ) const

inlinevirtual

clone

finalize_total_energy()

void CapriTotalEnergy::finalize_total_energy ( pose::Pose &  pose, ScoreFunction const &  , EnergyMap &  emap  ) const

virtual

Calculates the cyan score and the conservation score

References CapriData::conserved_residues, utility::graph::Node::const_edge_list_end(), test.T200_Scoring::emap, utility::graph::Edge::get_node(), create_a3b_hbs::i, min(), beta_nonlocal::pose, retrieve_capri_data_from_pose(), numeric::square(), and utility_exit_with_message.

indicate_required_context_graphs()

virtual void CapriTotalEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  ) const

inlinevirtual

read_datafile()

void CapriTotalEnergy::read_datafile ( )

private

References BLUE, CYAN, data, getline(), extract_by_sidechain_sasa_score::l, line, n_experimental_constraint_scores, PINK, RED, and utility_exit_with_message.

score_experimental_constraints()

void CapriTotalEnergy::score_experimental_constraints ( pose::Pose const &  pose, EnergyMap &  emap  ) const

private

References begin, BLUE, CYAN, numeric::xyzVector< T >::distance_squared(), test.T200_Scoring::emap, end, create_a3b_hbs::i, max(), min(), n_experimental_constraint_scores, PINK, beta_nonlocal::pose, RED, reverse(), create_a3b_hbs::score, numeric::square(), and predPRE::t.

setup_rna_atoms_for_pose()

void CapriTotalEnergy::setup_rna_atoms_for_pose ( pose::Pose const &  pose, utility::vector1< utility::vector1< AtomID > > &  rna_atoms  ) const

private

References create_a3b_hbs::first, create_a3b_hbs::i, n_experimental_constraint_scores, pid(), beta_nonlocal::pose, and predPRE::t.

Member Data Documentation

rna_atoms_

utility::vector1< utility::vector1< std::pair< std::string, Size > > > CapriTotalEnergy::rna_atoms_

private

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

• src/apps/pilot/phil/capri15_scoring.hh