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core::scoring::constraints::MultiConstraint Class Reference

#include <MultiConstraint.hh>

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Public Member Functions

 MultiConstraint (ScoreType const &t=dof_constraint)
 default Constructor More...
 
 MultiConstraint (const ConstraintCOPs &cst_in, ScoreType const &t=dof_constraint)
 Constructor. More...
 
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 MultiConstraintOP empty_clone () const
 
Size natoms () const
 number of atoms involved in this MultiConstraint container More...
 
Size size () const
 number of constraints data More...
 
virtual std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
virtual void read_def (std::istream &data, pose::Pose const &pose, FuncFactory const &func_factory)
 read in constraint defiinition More...
 
virtual bool operator== (Constraint const &other) const
 possibility to compare constraint according to data and not just pointers More...
 
virtual void score (XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const
 compute score More...
 
virtual AtomID const & atom (Size const n) const
 Returns the AtomID referred to by index. 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 setup_for_scoring (XYZ_Func const &, ScoreFunction const &) const
 
virtual void add_individual_constraint (ConstraintCOP cst_in)
 add individual constraint into MultiConstraint 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...
 
virtual void fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
 compute atom deriv More...
 
virtual 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...
 
virtual 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...
 
virtual Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, 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 ... More...
 
ConstraintCOPs const & member_constraints () const
 
virtual ConstraintOP remapped_clone (pose::Pose const &, pose::Pose const &, 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...
 
void set_effective_sequence_separation (core::Size setting)
 
virtual core::Size choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, numeric::random::RandomGenerator &)
 
virtual core::Size effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &) 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 ConstraintOP clone (FuncOP) const
 
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 core::Real dist (core::pose::Pose const &) const
 return the "raw" distance before handed to the FUNC object More...
 
virtual core::Real dist (XYZ_Func 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 Func const & get_func () const
 Returns the Func object associated with this Constraint object. More...
 
bool operator!= (Constraint const &other) const
 possibility to do object comparison instead of pointer comparison More...
 

Protected Attributes

ConstraintCOPs member_constraints_
 

Private Attributes

utility::vector1< core::Sizemember_residues_
 
utility::vector1< AtomIDmember_atoms_
 
std::map< AtomID, ConstraintCOPsAtomID_to_Csts_
 
core::Size report_this_as_effective_sequence_separation_
 

Additional Inherited Members

- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 

Constructor & Destructor Documentation

core::scoring::constraints::MultiConstraint::MultiConstraint ( ScoreType const &  t = dof_constraint)
inline

default Constructor

Referenced by clone(), empty_clone(), and remap_resid().

core::scoring::constraints::MultiConstraint::MultiConstraint ( const ConstraintCOPs cst_in,
ScoreType const &  t = dof_constraint 
)

Constructor.

References add_individual_constraint().

Member Function Documentation

void core::scoring::constraints::MultiConstraint::add_individual_constraint ( ConstraintCOP  cst_in)
virtual
virtual AtomID const& core::scoring::constraints::MultiConstraint::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 member_atoms_.

core::Size core::scoring::constraints::MultiConstraint::choose_effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const &  sp,
numeric::random::RandomGenerator &  RG 
)
virtual
virtual ConstraintOP core::scoring::constraints::MultiConstraint::clone ( ) const
inlinevirtual
virtual core::Size core::scoring::constraints::MultiConstraint::effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const &  ) const
inlinevirtual
virtual MultiConstraintOP core::scoring::constraints::MultiConstraint::empty_clone ( ) const
inlinevirtual
void core::scoring::constraints::MultiConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const
virtual

compute atom deriv

function that figures out what constraints this atom is part of and calculates the derivative for those

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

Reimplemented in core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::AmbiguousConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

References AtomID_to_Csts_.

ConstraintCOPs const& core::scoring::constraints::MultiConstraint::member_constraints ( ) const
inline
Size core::scoring::constraints::MultiConstraint::natoms ( ) const
inlinevirtual

number of atoms involved in this MultiConstraint container

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

References member_atoms_.

bool core::scoring::constraints::MultiConstraint::operator== ( Constraint const &  other_cst) const
virtual

possibility to compare constraint according to data and not just pointers

this function only checks whether the member_constraints_ are identical. should mean by inference that the member_residues_, member_atoms_ and AtomID_to_Csts_ are also identical

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

Reimplemented in core::scoring::constraints::AmbiguousConstraint.

References member_constraints_, report_this_as_effective_sequence_separation_, and core::scoring::constraints::Constraint::score_type().

Referenced by core::scoring::constraints::AmbiguousConstraint::operator==().

void core::scoring::constraints::MultiConstraint::read_def ( std::istream &  data,
pose::Pose const &  pose,
FuncFactory const &  func_factory 
)
virtual
ConstraintOP core::scoring::constraints::MultiConstraint::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.

Reimplemented in core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::AmbiguousConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

References member_constraints_, and MultiConstraint().

ConstraintOP core::scoring::constraints::MultiConstraint::remapped_clone ( pose::Pose const &  ,
pose::Pose const &  ,
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 empty_clone(), and member_constraints_.

virtual utility::vector1< core::Size > core::scoring::constraints::MultiConstraint::residues ( ) const
inlinevirtual

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

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

References member_residues_.

void core::scoring::constraints::MultiConstraint::score ( XYZ_Func const &  xyz_func,
EnergyMap const &  weights,
EnergyMap emap 
) const
virtual
void core::scoring::constraints::MultiConstraint::set_effective_sequence_separation ( core::Size  setting)
inline
void core::scoring::constraints::MultiConstraint::setup_for_scoring ( XYZ_Func const &  xyz,
ScoreFunction const &  scfxn 
) const
virtual
void core::scoring::constraints::MultiConstraint::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.

Reimplemented in core::scoring::constraints::KofNConstraint, core::scoring::constraints::AmbiguousConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::SiteConstraint, core::scoring::constraints::SiteConstraintResidues, and core::scoring::constraints::FabConstraint.

References member_constraints_.

void core::scoring::constraints::MultiConstraint::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.

Reimplemented in core::scoring::constraints::AmbiguousNMRConstraint.

References member_constraints(), and type().

Referenced by read_def().

Size core::scoring::constraints::MultiConstraint::show_violations ( std::ostream &  out,
pose::Pose const &  ,
Size  ,
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.

Reimplemented in core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::AmbiguousConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

References member_constraints_.

Size core::scoring::constraints::MultiConstraint::size ( ) const
inline
virtual std::string core::scoring::constraints::MultiConstraint::type ( ) const
inlinevirtual

Member Data Documentation

std::map< AtomID, ConstraintCOPs > core::scoring::constraints::MultiConstraint::AtomID_to_Csts_
private
utility::vector1< AtomID > core::scoring::constraints::MultiConstraint::member_atoms_
private
ConstraintCOPs core::scoring::constraints::MultiConstraint::member_constraints_
protected
utility::vector1< core::Size > core::scoring::constraints::MultiConstraint::member_residues_
private
core::Size core::scoring::constraints::MultiConstraint::report_this_as_effective_sequence_separation_
private

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