Rosetta 3.4
Public Member Functions | Static Public Attributes | Protected Member Functions | Protected Attributes
core::scoring::saxs::SAXSEnergy Class Reference

#include <SAXSEnergy.hh>

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List of all members.

Public Member Functions

 SAXSEnergy (std::string &, core::chemical::ResidueTypeSetCAP, ScoreType, SAXSEnergyCreator *)
 c-tor
 SAXSEnergy (const std::string &, const utility::vector1< Real > &, const utility::vector1< Real > &, ScoreType, SAXSEnergyCreator *)
 c-tor
virtual ~SAXSEnergy ()
virtual methods::EnergyMethodOP clone () const
virtual void finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) 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.
virtual void indicate_required_context_graphs (utility::vector1< bool > &) 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.
methods::EnergyMethodOP create_energy_method (methods::EnergyMethodOptions const &) const
utility::vector1< Real > & get_reference_intensities ()
utility::vector1< Real > & get_pose_intensities ()
utility::vector1< Real > & get_q ()
Size count_scoring_atoms ()
Real total_energy (const pose::Pose &pose) const
Real compute_zero_intensity () const

Static Public Attributes

static std::string fa_cfg_file_
static std::string cen_cfg_file_

Protected Member Functions

void init_ff (const std::string &)
void set_up_q (const utility::vector1< Real > &)
 Sets a vector of q arguments to be used by this class in all SAXS-related calculations.
void set_up_q ()
 Sets a vector of q arguments using the command-line flags to be used by this class in all SAXS-related calculations.
void read_spectrum (std::string &, utility::vector1< Real > &, utility::vector1< Real > &) const
 Reads two vectors from a file: q and I(q) (meant to be experimental values)
void fit_intensities (const utility::vector1< Real > &, const utility::vector1< Real > &, utility::vector1< Real > &) const
 Takes two vectors: q and I(q) and returns a SAXS spectrum as a function of Q as defined in this class.
void read_intensities (std::string &, utility::vector1< Real > &) const
 A shortcut that calls read_spectrum() and then fit_intensities()
void compute_intensities (const core::pose::Pose &, utility::vector1< Real > &) const
 computes I(q) from a pose
void rehash_form_factors (const core::pose::Pose &pose) const
 ce-calculates form factors

Protected Attributes

ScoreType saxs_score_variant_
std::string the_config_file_

Constructor & Destructor Documentation

core::scoring::saxs::SAXSEnergy::SAXSEnergy ( std::string &  config_file,
core::chemical::ResidueTypeSetCAP  rsd_set,
ScoreType  the_variant,
SAXSEnergyCreator creator 
)
core::scoring::saxs::SAXSEnergy::SAXSEnergy ( const std::string &  config_file,
const utility::vector1< Real > &  source_q,
const utility::vector1< Real > &  reference_spectrum,
ScoreType  score_variant,
SAXSEnergyCreator the_creator 
)
virtual core::scoring::saxs::SAXSEnergy::~SAXSEnergy ( ) [inline, virtual]

Member Function Documentation

virtual methods::EnergyMethodOP core::scoring::saxs::SAXSEnergy::clone ( ) const [inline, virtual]
void core::scoring::saxs::SAXSEnergy::compute_intensities ( const core::pose::Pose pose,
utility::vector1< Real > &  result 
) const [protected]
Real core::scoring::saxs::SAXSEnergy::compute_zero_intensity ( ) const
Size core::scoring::saxs::SAXSEnergy::count_scoring_atoms ( ) [inline]
methods::EnergyMethodOP core::scoring::saxs::SAXSEnergy::create_energy_method ( methods::EnergyMethodOptions const &  ) const [inline]
void core::scoring::saxs::SAXSEnergy::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.

References compute_intensities(), and saxs_score_variant_.

void core::scoring::saxs::SAXSEnergy::fit_intensities ( const utility::vector1< Real > &  q,
const utility::vector1< Real > &  I,
utility::vector1< Real > &  result 
) const [protected]

Takes two vectors: q and I(q) and returns a SAXS spectrum as a function of Q as defined in this class.

Detailed: This is basically done by fiting a spline and re-evaluating I(q) at different q values

Referenced by read_intensities(), and SAXSEnergy().

utility::vector1<Real>& core::scoring::saxs::SAXSEnergy::get_pose_intensities ( ) [inline]
utility::vector1<Real>& core::scoring::saxs::SAXSEnergy::get_q ( ) [inline]
utility::vector1<Real>& core::scoring::saxs::SAXSEnergy::get_reference_intensities ( ) [inline]
virtual void core::scoring::saxs::SAXSEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const [inline, 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.

void core::scoring::saxs::SAXSEnergy::init_ff ( const std::string &  config_file) [protected]
void core::scoring::saxs::SAXSEnergy::read_intensities ( std::string &  file_name,
utility::vector1< Real > &  result 
) const [protected]

A shortcut that calls read_spectrum() and then fit_intensities()

References fit_intensities(), and read_spectrum().

Referenced by SAXSEnergy().

void core::scoring::saxs::SAXSEnergy::read_spectrum ( std::string &  file_name,
utility::vector1< Real > &  q,
utility::vector1< Real > &  I 
) const [protected]

Reads two vectors from a file: q and I(q) (meant to be experimental values)

References core::scoring::saxs::trSAXSEnergy().

Referenced by read_intensities().

void core::scoring::saxs::SAXSEnergy::rehash_form_factors ( const core::pose::Pose pose) const [protected]

ce-calculates form factors

Detailed: This is necessary when :
  • this is the first time
  • an amino acid sequence within the scored pose has been changed
  • teh q-value set has been affected

References core::conformation::Residue::atom_type(), compute_zero_intensity(), core::chemical::AtomType::is_hydrogen(), core::chemical::AtomType::name(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::scoring::saxs::trSAXSEnergy().

Referenced by compute_intensities().

void core::scoring::saxs::SAXSEnergy::set_up_q ( ) [protected]

Sets a vector of q arguments using the command-line flags to be used by this class in all SAXS-related calculations.

References core::scoring::saxs::trSAXSEnergy().

Referenced by SAXSEnergy().

void core::scoring::saxs::SAXSEnergy::set_up_q ( const utility::vector1< Real > &  source_q) [protected]

Sets a vector of q arguments to be used by this class in all SAXS-related calculations.

References core::scoring::saxs::trSAXSEnergy().

Real core::scoring::saxs::SAXSEnergy::total_energy ( const pose::Pose pose) const

References compute_intensities().


Member Data Documentation


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