Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Private Attributes | Static Private Attributes | List of all members
protocols::constraints_additional::BindingSiteConstraint Class Reference

#include <BindingSiteConstraint.hh>

Public Member Functions

 BindingSiteConstraint ()
 null constructor More...
 
 BindingSiteConstraint (utility::vector1< AtomID > const &atms, core::pose::Pose const &start_pose, core::scoring::ScoreType scoretype=core::scoring::atom_pair_constraint)
 ctor from atom list + input pose More...
 
 BindingSiteConstraint (utility::vector1< AtomID > const &atms, ObjexxFCL::FArray2D< core::Real > tgt_pos, ObjexxFCL::FArray2D< core::Real > tgt_pos_centroid, core::scoring::ScoreType scoretype=core::scoring::atom_pair_constraint)
 ctor from a vector of atom positions (in lieu of a pose) More...
 
virtual
core::scoring::constraints::ConstraintOP 
clone () const
 
void score (core::scoring::func::XYZ_Func const &xyz, core::scoring::EnergyMap const &, core::scoring::EnergyMap &emap) const
 
void setup_for_scoring (core::scoring::func::XYZ_Func const &xyz, core::scoring::ScoreFunction const &scfxn) const
 
void pre_align (utility::vector1< numeric::xyzVector< core::Real > > const &templ_atms, utility::vector1< bool > const &) const
 
void setup_for_derivatives (core::scoring::func::XYZ_Func const &xyz, core::scoring::ScoreFunction const &scfxn) const
 
virtual void fill_f1_f2 (AtomID const &atom, core::scoring::func::XYZ_Func const &xyz, core::Vector &F1, core::Vector &F2, core::scoring::EnergyMap const &weights) const
 
std::string type () const
 
Size natoms () const
 
virtual
core::scoring::constraints::ConstraintOP 
remap_resid (core::id::SequenceMapping const &seqmap) const
 
AtomID const & atom (Size const n) const
 
void show (std::ostream &out) const
 
void show_def (std::ostream &out, core::pose::Pose const &pose) const
 
void read_def (std::istream &in, core::pose::Pose const &pose, core::scoring::func::FuncFactory const &func_factory)
 Format should look like: Dunbrack seqpos_ rot_vec_pos_ rot_bin_ bonus_. More...
 
Size show_violations (std::ostream &out, core::pose::Pose const &pose, core::Size verbose_level, core::Real threshold=1.0) const
 

Protected Member Functions

void init (core::pose::Pose const &start_pose)
 

Private Attributes

utility::vector1< AtomID > atms_
 
ObjexxFCL::FArray2D< core::Realtgt_pos_
 
ObjexxFCL::FArray2D< core::Realtgt_pos_centroid_
 

Static Private Attributes

static std::map< AtomID,
numeric::xyzVector< core::Real > > 
rot_db
 

Constructor & Destructor Documentation

protocols::constraints_additional::BindingSiteConstraint::BindingSiteConstraint ( )
inline

null constructor

References atom_pair_constraint, constraints, and scoring.

Referenced by clone(), and remap_resid().

protocols::constraints_additional::BindingSiteConstraint::BindingSiteConstraint ( utility::vector1< AtomID > const &  atms,
core::pose::Pose const &  start_pose,
core::scoring::ScoreType  scoretype = core::scoring::atom_pair_constraint 
)

ctor from atom list + input pose

c-tor

Parameters
scoretype? TO DO – give own scoretype

References init().

protocols::constraints_additional::BindingSiteConstraint::BindingSiteConstraint ( utility::vector1< AtomID > const &  atms,
ObjexxFCL::FArray2D< core::Real tgt_pos,
ObjexxFCL::FArray2D< core::Real tgt_pos_centroid,
core::scoring::ScoreType  scoretype = core::scoring::atom_pair_constraint 
)

ctor from a vector of atom positions (in lieu of a pose)

Parameters
scoretype? TO DO – give own scoretype

Member Function Documentation

core::id::AtomID const & protocols::constraints_additional::BindingSiteConstraint::atom ( core::Size const  n) const
virtual
virtual core::scoring::constraints::ConstraintOP protocols::constraints_additional::BindingSiteConstraint::clone ( ) const
inlinevirtual
void protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2 ( AtomID const &  atom,
core::scoring::func::XYZ_Func const &  xyz,
core::Vector F1,
core::Vector F2,
core::scoring::EnergyMap const &  weights 
) const
virtual
void protocols::constraints_additional::BindingSiteConstraint::init ( core::pose::Pose const &  start_pose)
protected
core::Size protocols::constraints_additional::BindingSiteConstraint::natoms ( ) const
virtual
void protocols::constraints_additional::BindingSiteConstraint::pre_align ( utility::vector1< numeric::xyzVector< core::Real > > const &  templ_atms,
utility::vector1< bool > const &  align_centroid 
) const
void protocols::constraints_additional::BindingSiteConstraint::read_def ( std::istream &  in,
core::pose::Pose const &  pose,
core::scoring::func::FuncFactory const &  func_factory 
)

Format should look like: Dunbrack seqpos_ rot_vec_pos_ rot_bin_ bonus_.

References atms_, core::chemical::ResidueType::atom_index(), init(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and tr.

core::scoring::constraints::ConstraintOP protocols::constraints_additional::BindingSiteConstraint::remap_resid ( core::id::SequenceMapping const &  seqmap) const
virtual
void protocols::constraints_additional::BindingSiteConstraint::score ( core::scoring::func::XYZ_Func const &  xyz,
core::scoring::EnergyMap const &  ,
core::scoring::EnergyMap emap 
) const
virtual
void protocols::constraints_additional::BindingSiteConstraint::setup_for_derivatives ( core::scoring::func::XYZ_Func const &  xyz,
core::scoring::ScoreFunction const &  scfxn 
) const

References setup_for_scoring().

void protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring ( core::scoring::func::XYZ_Func const &  xyz,
core::scoring::ScoreFunction const &  scfxn 
) const
void protocols::constraints_additional::BindingSiteConstraint::show ( std::ostream &  out) const
virtual
void protocols::constraints_additional::BindingSiteConstraint::show_def ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
core::Size protocols::constraints_additional::BindingSiteConstraint::show_violations ( std::ostream &  out,
core::pose::Pose const &  pose,
core::Size  verbose_level,
core::Real  threshold = 1.0 
) const
std::string protocols::constraints_additional::BindingSiteConstraint::type ( ) const
virtual

Member Data Documentation

utility::vector1< AtomID > protocols::constraints_additional::BindingSiteConstraint::atms_
private
std::map< core::id::AtomID, numeric::xyzVector< core::Real > > protocols::constraints_additional::BindingSiteConstraint::rot_db
staticprivate

Referenced by fill_f1_f2(), pre_align(), and score().

ObjexxFCL::FArray2D< core::Real > protocols::constraints_additional::BindingSiteConstraint::tgt_pos_
private

Referenced by clone(), init(), pre_align(), and remap_resid().

ObjexxFCL::FArray2D< core::Real > protocols::constraints_additional::BindingSiteConstraint::tgt_pos_centroid_
private

Referenced by clone(), init(), pre_align(), and remap_resid().


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