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protocols::constraints_additional::AmbiguousMultiConstraint Class Reference

#include <AmbiguousMultiConstraint.hh>

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Public Member Functions

 AmbiguousMultiConstraint (core::Size num_act_csts)
 Constructor. More...
 
 AmbiguousMultiConstraint (core::Size num_act_csts, core::scoring::constraints::ConstraintCOPs &cst_in)
 Constructor. More...
 
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. More...
 
std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
void score (core::scoring::constraints::XYZ_Func const &xyz_func, core::scoring::EnergyMap const &weights, core::scoring::EnergyMap &emap) const
 read in constraint defiinition More...
 
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. More...
 
void fill_f1_f2 (core::id::AtomID const &atom, core::scoring::constraints::XYZ_Func const &xyz, core::Vector &F1, core::Vector &F2, core::scoring::EnergyMap const &weights) const
 compute atom deriv 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...
 
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 ... More...
 
- Public Member Functions inherited from core::scoring::constraints::AmbiguousConstraint
 AmbiguousConstraint ()
 Constructor. More...
 
 AmbiguousConstraint (ConstraintCOPs &cst_in)
 Constructor. More...
 
virtual MultiConstraintOP empty_clone () const
 
void init_cst_score_types ()
 
void read_def (std::istream &data, pose::Pose const &pose, FuncFactory const &func_factory)
 read in constraint defiinition More...
 
bool operator== (Constraint const &other) const
 possibility to compare constraint according to data and not just pointers More...
 
core::Real calculate_total_cst_score (EnergyMap const &weights, EnergyMap &emap) const
 helper function to accumulate all constraint scores into one number More...
 
ConstraintCOP active_constraint () const
 
- Public Member Functions inherited from core::scoring::constraints::MultiConstraint
 MultiConstraint (ScoreType const &t=dof_constraint)
 default Constructor More...
 
 MultiConstraint (const ConstraintCOPs &cst_in, ScoreType const &t=dof_constraint)
 Constructor. More...
 
Size natoms () const
 number of atoms involved in this MultiConstraint container More...
 
Size size () const
 number of constraints data 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 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...
 
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...
 

Private Attributes

core::Size num_active_constraints_
 
core::scoring::constraints::ConstraintCOPs active_constraints_
 

Additional Inherited Members

- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 
- Protected Attributes inherited from core::scoring::constraints::MultiConstraint
ConstraintCOPs member_constraints_
 

Constructor & Destructor Documentation

protocols::constraints_additional::AmbiguousMultiConstraint::AmbiguousMultiConstraint ( core::Size  num_act_csts)

Constructor.

References active_constraints_.

Referenced by clone(), and remap_resid().

protocols::constraints_additional::AmbiguousMultiConstraint::AmbiguousMultiConstraint ( core::Size  num_act_csts,
core::scoring::constraints::ConstraintCOPs cst_in 
)

Constructor.

References active_constraints_.

Member Function Documentation

virtual core::scoring::constraints::ConstraintOP protocols::constraints_additional::AmbiguousMultiConstraint::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.

Reimplemented from core::scoring::constraints::AmbiguousConstraint.

References AmbiguousMultiConstraint().

void protocols::constraints_additional::AmbiguousMultiConstraint::fill_f1_f2 ( core::id::AtomID const &  atom,
core::scoring::constraints::XYZ_Func const &  xyz,
core::Vector F1,
core::Vector F2,
core::scoring::EnergyMap const &  weights 
) const
virtual

compute atom deriv

function to minimize the N lowest scoring member constraints

Reimplemented from core::scoring::constraints::AmbiguousConstraint.

References active_constraints_, and num_active_constraints_.

core::scoring::constraints::ConstraintOP protocols::constraints_additional::AmbiguousMultiConstraint::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::AmbiguousConstraint.

References AmbiguousMultiConstraint(), core::scoring::constraints::MultiConstraint::member_constraints_, and num_active_constraints_.

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

read in constraint defiinition

ScoreFunction, scores all member constraints but only reports the lowest N ones.

compute score

note: this could potentially be made faster if the cur_emap isn't copied, but instead pushed back right away into score_cst_pairs and then score_cst_pairs.last() is handed to the member_it->score() function

Reimplemented from core::scoring::constraints::AmbiguousConstraint.

References active_constraints_, core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::backbone_stub_constraint, core::scoring::constraints::AmbiguousConstraint::calculate_total_cst_score(), core::scoring::constant_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::scoring::constraints::MultiConstraint::member_constraints(), num_active_constraints_, and core::scoring::constraints::MultiConstraint::size().

void protocols::constraints_additional::AmbiguousMultiConstraint::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::AmbiguousConstraint.

References core::scoring::constraints::MultiConstraint::member_constraints().

core::Size protocols::constraints_additional::AmbiguousMultiConstraint::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::AmbiguousConstraint.

References active_constraints_, core::scoring::constraints::MultiConstraint::member_constraints(), and type().

std::string protocols::constraints_additional::AmbiguousMultiConstraint::type ( ) const
inlinevirtual

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

Reimplemented from core::scoring::constraints::AmbiguousConstraint.

Referenced by show_violations().

Member Data Documentation

core::scoring::constraints::ConstraintCOPs protocols::constraints_additional::AmbiguousMultiConstraint::active_constraints_
mutableprivate
core::Size protocols::constraints_additional::AmbiguousMultiConstraint::num_active_constraints_
private

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


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