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core::scoring::constraints::AmbiguousNMRDistanceConstraint Class Reference

#include <AmbiguousNMRDistanceConstraint.hh>

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Public Types

typedef utility::vector1< AtomIDAtoms
 
- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 

Public Member Functions

 AmbiguousNMRDistanceConstraint (Atoms const &a1, Atoms const &a2, FuncOP func, ScoreType scoretype=atom_pair_constraint)
 c-tor More...
 
 AmbiguousNMRDistanceConstraint (id::NamedAtomID const &a1, id::NamedAtomID const &a2, core::pose::Pose const &, FuncOP func, ScoreType scoretype=atom_pair_constraint)
 
 AmbiguousNMRDistanceConstraint ()
 
virtual 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. More...
 
virtual ConstraintOP clone (FuncOP func) const
 
virtual ConstraintOP remapped_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP map=NULL) const
 Copies the data from this Constraint into a new object and returns an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes. More...
 
ConstraintOP map_to_CEN (pose::Pose const &src, pose::Pose const &centroid, core::Size &nr_mapped, std::string const &map_atom) const
 returns AtomPairConstraint or AmbigousNMRDistanceConstraint (e.g. for GLY HA1-HA2 ... ) More...
 
void score (XYZ_Func const &xyz, EnergyMap const &, 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. More...
 
core::Real inv_dist6 (XYZ_Func const &xyz) const
 
virtual void fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
 Fill the f1 and f2 vectors, necessary for considering the derivative this constraint during minimization. (someone please reference Bill Wedermeyer's paper here, as I'm in an airport and can't fill it in myself!) More...
 
std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
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. More...
 
Size natoms (core::Size i) const
 
Size multiplicity () const
 
Size resid (core::Size i) const
 return residue number: i=1,2 More...
 
virtual 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. More...
 
AtomID const & atom (Size const n) const
 Returns the AtomID referred to by index. More...
 
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. More...
 
void show_def (std::ostream &out, 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. More...
 
void read_def (std::istream &in, pose::Pose const &pose, FuncFactory const &func_factory)
 
Real dist (pose::Pose const &pose) const
 return the "raw" distance before handed to the FUNC object More...
 
Real dist (XYZ_Func const &xyz) const
 
Real score (pose::Pose const &pose) const
 
virtual Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1) 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 ... More...
 
virtual Func const & get_func () const
 Returns the Func object associated with this Constraint object. More...
 
virtual core::Size effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp) const
 
- Public Member Functions inherited from core::scoring::constraints::Constraint
 Constraint (ScoreType const &t)
 Constructor for Constraint class. More...
 
virtual ~Constraint ()
 Virtual destructor. More...
 
virtual utility::vector1
< core::Size
residues () const
 Returns the pose numbers of the residues involved in this constraint, in no particular order. More...
 
virtual void read_constraint (std::istream &, core::pose::Pose const &)
 This method is totally redundant with read_def YAY. More...
 
ScoreType const & score_type () const
 Returns the ScoreType that this Constraint object will use. More...
 
virtual void read_data (std::istream &)
 initialize this Constraint from the given std::istream. It's amazing that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint, More...
 
virtual void setup_for_scoring (XYZ_Func const &, ScoreFunction const &) const
 
virtual void setup_for_derivatives (XYZ_Func const &, ScoreFunction const &) const
 
virtual Real score (conformation::Conformation const &) const
 Returns the score of this constraint computed over the given conformation. Not necessarily implemented in all derived classes, as it's redundant with the score( XYZ_Func, EnergyMap, EnergyMap ) method defined above. Returns 0.0 if not implemented. More...
 
virtual void steal_def (pose::Pose const &)
 
std::string to_string () const
 Convenience function, returns the results of show() as a string. Not to be overriden by derived classes. More...
 
virtual bool operator== (Constraint const &) const
 possibility to do object comparison instead of pointer comparison More...
 
bool operator!= (Constraint const &other) const
 possibility to do object comparison instead of pointer comparison More...
 
virtual core::Size choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, numeric::random::RandomGenerator &)
 

Protected Attributes

Atoms atoms1_
 
Atoms atoms2_
 
FuncOP func_
 

Private Member Functions

Real func (Real const theta) const
 
Real dfunc (Real const theta) const
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::constraints::AmbiguousNMRDistanceConstraint::AmbiguousNMRDistanceConstraint ( Atoms const &  a1,
Atoms const &  a2,
FuncOP  func,
ScoreType  scoretype = atom_pair_constraint 
)
inline

c-tor

core::scoring::constraints::AmbiguousNMRDistanceConstraint::AmbiguousNMRDistanceConstraint ( id::NamedAtomID const &  a1,
id::NamedAtomID const &  a2,
core::pose::Pose const &  pose,
FuncOP  func,
ScoreType  scoretype = atom_pair_constraint 
)
core::scoring::constraints::AmbiguousNMRDistanceConstraint::AmbiguousNMRDistanceConstraint ( )
inline

Member Function Documentation

AtomID const& core::scoring::constraints::AmbiguousNMRDistanceConstraint::atom ( Size const  index) const
inlinevirtual

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.

References atoms1_, atoms2_, and natoms().

Referenced by fill_f1_f2(), remap_resid(), and remapped_clone().

virtual ConstraintOP core::scoring::constraints::AmbiguousNMRDistanceConstraint::clone ( ) const
inlinevirtual

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 AmbiguousNMRDistanceConstraint(), atoms1_, atoms2_, func_, and core::scoring::constraints::Constraint::score_type().

virtual ConstraintOP core::scoring::constraints::AmbiguousNMRDistanceConstraint::clone ( FuncOP  func) const
inlinevirtual
Real core::scoring::constraints::AmbiguousNMRDistanceConstraint::dfunc ( Real const  theta) const
inlineprivate

References func_.

Referenced by fill_f1_f2().

Real core::scoring::constraints::AmbiguousNMRDistanceConstraint::dist ( pose::Pose const &  ) const
virtual

return the "raw" distance before handed to the FUNC object

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

References core::pose::Pose::conformation().

Referenced by fill_f1_f2(), inv_dist6(), score(), and show_violations().

Real core::scoring::constraints::AmbiguousNMRDistanceConstraint::dist ( XYZ_Func const &  xyz) const
virtual

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

References inv_dist6().

core::Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const &  sp) const
virtual
void core::scoring::constraints::AmbiguousNMRDistanceConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz_func,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const
virtual

Fill the f1 and f2 vectors, necessary for considering the derivative this constraint during minimization. (someone please reference Bill Wedermeyer's paper here, as I'm in an airport and can't fill it in myself!)

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

References atom(), atoms1_, atoms2_, dfunc(), dist(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

Real core::scoring::constraints::AmbiguousNMRDistanceConstraint::func ( Real const  theta) const
inlineprivate

References func_.

Referenced by score().

virtual Func const& core::scoring::constraints::AmbiguousNMRDistanceConstraint::get_func ( ) const
inlinevirtual

Returns the Func object associated with this Constraint object.

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

References func_.

Real core::scoring::constraints::AmbiguousNMRDistanceConstraint::inv_dist6 ( XYZ_Func const &  xyz) const

References atoms1_, atoms2_, dist(), and protocols::kinmatch::xyz().

Referenced by dist(), and score().

ConstraintOP core::scoring::constraints::AmbiguousNMRDistanceConstraint::map_to_CEN ( pose::Pose const &  src,
pose::Pose const &  centroid,
core::Size nr_mapped,
std::string const &  map_atom 
) const
Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::multiplicity ( ) const
inline

References atoms1_, and atoms2_.

Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::natoms ( ) const
inlinevirtual

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.

References atoms1_, and atoms2_.

Referenced by atom().

Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::natoms ( core::Size  i) const
inline

References atoms1_, and atoms2_.

void core::scoring::constraints::AmbiguousNMRDistanceConstraint::read_def ( std::istream &  data,
pose::Pose const &  pose,
FuncFactory const &  func_factory 
)
virtual
ConstraintOP core::scoring::constraints::AmbiguousNMRDistanceConstraint::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 AmbiguousNMRDistanceConstraint(), atom(), atoms1_, atoms2_, func_, core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().

ConstraintOP core::scoring::constraints::AmbiguousNMRDistanceConstraint::remapped_clone ( pose::Pose const &  src,
pose::Pose const &  dest,
id::SequenceMappingCOP  map = NULL 
) const
virtual

Copies the data from this Constraint into a new object and returns an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.

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

References AmbiguousNMRDistanceConstraint(), atom(), core::pose::atom_id_to_named_atom_id(), core::conformation::atom_id_to_named_atom_id(), atoms1_, atoms2_, func_, core::pose::named_atom_id_to_atom_id(), core::id::NamedAtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().

Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::resid ( core::Size  i) const
inline

return residue number: i=1,2

References atoms1_, and atoms2_.

Referenced by effective_sequence_separation(), and map_to_CEN().

void core::scoring::constraints::AmbiguousNMRDistanceConstraint::score ( XYZ_Func const &  xyz_func,
EnergyMap const &  weights,
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 func(), inv_dist6(), and core::scoring::constraints::Constraint::score_type().

Real core::scoring::constraints::AmbiguousNMRDistanceConstraint::score ( pose::Pose const &  pose) const
inline

References dist(), and func_.

void core::scoring::constraints::AmbiguousNMRDistanceConstraint::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.

References atoms1_, atoms2_, and func_.

void core::scoring::constraints::AmbiguousNMRDistanceConstraint::show_def ( std::ostream &  ,
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.

References atoms1_, atoms2_, core::scoring::constraints::combine_NMR_atom_string(), func_, and type().

Size core::scoring::constraints::AmbiguousNMRDistanceConstraint::show_violations ( std::ostream &  out,
pose::Pose const &  ,
Size  ,
Real  threshold = 1 
) 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.

References atoms1_, atoms2_, dist(), func_, and core::pose::Pose::residue_type().

std::string core::scoring::constraints::AmbiguousNMRDistanceConstraint::type ( ) const
inlinevirtual

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

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

Referenced by read_def(), and show_def().

Member Data Documentation

Atoms core::scoring::constraints::AmbiguousNMRDistanceConstraint::atoms1_
protected
Atoms core::scoring::constraints::AmbiguousNMRDistanceConstraint::atoms2_
protected
FuncOP core::scoring::constraints::AmbiguousNMRDistanceConstraint::func_
protected

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