Rosetta 3.4
Public Member Functions | Protected Member Functions
protocols::constraints_additional::BindingSiteConstraint Class Reference

#include <BindingSiteConstraint.hh>

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List of all members.

Public Member Functions

 BindingSiteConstraint ()
 null constructor
 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
 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)
virtual
core::scoring::constraints::ConstraintOP 
clone () const
 Copies the data from this Constraint into a new object and returns an OP to the new object. Intended to be implemented by derived classes and used by pose.add_constraint.
void score (core::scoring::constraints::XYZ_Func const &xyz, core::scoring::EnergyMap const &, core::scoring::EnergyMap &emap) const
 Calculates a score for this constraint using XYZ_Func, and puts the UNWEIGHTED score into emap. Although the current set of weights currently is provided, Constraint objects should put unweighted scores into emap because the ScoreFunction will do the weighting itself.
void setup_for_scoring (core::scoring::constraints::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::constraints::XYZ_Func const &xyz, core::scoring::ScoreFunction const &scfxn) const
virtual void fill_f1_f2 (AtomID const &atom, core::scoring::constraints::XYZ_Func const &xyz, core::Vector &F1, core::Vector &F2, core::scoring::EnergyMap const &weights) const
std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
Size natoms () const
 Returns the number of atoms involved in defining this constraint. If the constraint doesn't depend on particular atoms (e.g. a residue type constraint) this function can return zero.
virtual
core::scoring::constraints::ConstraintOP 
remap_resid (core::id::SequenceMapping const &seqmap) const
 apply a resid remapping to this constraint, returns the remapped constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice.
AtomID const & atom (Size const n) const
 Returns the AtomID referred to by index.
void show (std::ostream &out) const
 This method is intended to show the value of the Constraint function evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms.
void show_def (std::ostream &out, core::pose::Pose const &pose) const
 Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given FuncFactory. This method is intended to be overridden by derived classes if they'd like to use the ConstraintIO machinery. It's also not clear why this method takes a Pose, other than to be symmetric with read_def.
void read_def (std::istream &in, core::pose::Pose const &pose, core::scoring::constraints::FuncFactory const &func_factory)
 Format should look like: Dunbrack seqpos_ rot_vec_pos_ rot_bin_ bonus_.
Size show_violations (std::ostream &out, core::pose::Pose const &pose, core::Size verbose_level, core::Real threshold=1.0) const
 Prints the violations of this constraint to the given std::ostream. What are violations? It's not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don't know which definition is the right one. Documentation would be nice ...

Protected Member Functions

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

Constructor & Destructor Documentation

protocols::constraints_additional::BindingSiteConstraint::BindingSiteConstraint ( ) [inline]

null constructor

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 ( Size const  index) const [virtual]

Returns the AtomID referred to by index.

Note that this function isn't actually used by the constraint scoring machenery. If you're calling it on a generic Constraint (as opposed to specifically on a derived class) you're probably doing something wrong.

Implements core::scoring::constraints::Constraint.

Referenced by fill_f1_f2().

virtual core::scoring::constraints::ConstraintOP protocols::constraints_additional::BindingSiteConstraint::clone ( ) const [inline, virtual]

Copies the data from this Constraint into a new object and returns an OP to the new object. Intended to be implemented by derived classes and used by pose.add_constraint.

Implements core::scoring::constraints::Constraint.

References BindingSiteConstraint().

void protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2 ( AtomID const &  atom,
core::scoring::constraints::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]

Returns the number of atoms involved in defining this constraint. If the constraint doesn't depend on particular atoms (e.g. a residue type constraint) this function can return zero.

Note that this function isn't actually used by the constraint scoring machenery. If you're calling it on a generic Constraint (as opposed to specifically on a derived class) you're probably doing something wrong.

Implements core::scoring::constraints::Constraint.

Referenced by init(), pre_align(), and setup_for_scoring().

void protocols::constraints_additional::BindingSiteConstraint::pre_align ( utility::vector1< numeric::xyzVector< core::Real > > const &  templ_atms,
utility::vector1< bool > const &  align_centroid 
) const

References natoms().

Referenced by setup_for_scoring().

void protocols::constraints_additional::BindingSiteConstraint::read_def ( std::istream &  in,
core::pose::Pose const &  pose,
core::scoring::constraints::FuncFactory const &  func_factory 
) [virtual]

Format should look like: Dunbrack seqpos_ rot_vec_pos_ rot_bin_ bonus_.

Reimplemented from core::scoring::constraints::Constraint.

References init(), make_table_of_pilot_apps::name, 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 &  ) const [virtual]

apply a resid remapping to this constraint, returns the remapped constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice.

Reimplemented from core::scoring::constraints::Constraint.

References BindingSiteConstraint().

void protocols::constraints_additional::BindingSiteConstraint::score ( core::scoring::constraints::XYZ_Func const &  xyz_func,
core::scoring::EnergyMap const &  weights,
core::scoring::EnergyMap emap 
) const [virtual]

Calculates a score for this constraint using XYZ_Func, and puts the UNWEIGHTED score into emap. Although the current set of weights currently is provided, Constraint objects should put unweighted scores into emap because the ScoreFunction will do the weighting itself.

Implements core::scoring::constraints::Constraint.

References core::scoring::constraints::Constraint::score_type().

void protocols::constraints_additional::BindingSiteConstraint::setup_for_derivatives ( core::scoring::constraints::XYZ_Func const &  xyz,
core::scoring::ScoreFunction const &  scfxn 
) const [virtual]
void protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring ( core::scoring::constraints::XYZ_Func const &  xyz,
core::scoring::ScoreFunction const &  scfxn 
) const [virtual]
void protocols::constraints_additional::BindingSiteConstraint::show ( std::ostream &  ) const [virtual]

This method is intended to show the value of the Constraint function evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms.

Reimplemented from core::scoring::constraints::Constraint.

void protocols::constraints_additional::BindingSiteConstraint::show_def ( std::ostream &  ,
core::pose::Pose const &   
) const [virtual]

Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given FuncFactory. This method is intended to be overridden by derived classes if they'd like to use the ConstraintIO machinery. It's also not clear why this method takes a Pose, other than to be symmetric with read_def.

Reimplemented from core::scoring::constraints::Constraint.

core::Size protocols::constraints_additional::BindingSiteConstraint::show_violations ( std::ostream &  out,
core::pose::Pose const &  ,
core::Size  ,
core::Real  threshold = 1.0 
) const [virtual]

Prints the violations of this constraint to the given std::ostream. What are violations? It's not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don't know which definition is the right one. Documentation would be nice ...

Reimplemented from core::scoring::constraints::Constraint.

std::string protocols::constraints_additional::BindingSiteConstraint::type ( ) const [virtual]

Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.

Reimplemented from core::scoring::constraints::Constraint.


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