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core::scoring::constraints::FabConstraint Class Reference

#include <FabConstraint.hh>

Inheritance diagram for core::scoring::constraints::FabConstraint:
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Public Member Functions

 FabConstraint ()
 Constructor. More...
 
 FabConstraint (ConstraintCOPs const &cst_in)
 Constructor. More...
 
ConstraintOP clone () const override
 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. This function must return a deep copy of itself – meaning that if this Constraint holds pointers to other Constraints that it must invoke clone on those Constraints as well. If the Constraint holds a FuncOP, then the Func should also be cloned. More...
 
std::string type () const override
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
void show (std::ostream &out) const override
 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 read_def (std::istream &data, pose::Pose const &pose, func::FuncFactory const &func_factory) override
 read in constraint definition More...
 
Size pose_res_no (core::pose::Pose const &pose, std::string tempres)
 
utility::vector1< Realcalc_penalty_vec (Size start_res, Size stop_res, utility::vector1< Size > res1, utility::vector1< Size > res2)
 
void setup_csts (core::pose::Pose const &pose, utility::vector1< Size > res1, utility::vector1< Size > res2, std::string antchains)
 
bool operator== (Constraint const &rhs) const override
 Equality operator to test whether two constraints are functionally identical. More...
 
bool same_type_as_me (Constraint const &other) const override
 Determine if the calling class has the same type as the input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it. More...
 
- Public Member Functions inherited from core::scoring::constraints::MultiConstraint
 MultiConstraint (ScoreType const &t=dof_constraint)
 default Constructor More...
 
 MultiConstraint (ConstraintCOPs const &cst_in, ScoreType const &t=dof_constraint)
 Constructor – performs a shallow copy of the input ConstraintCOPs. More...
 
ConstraintOP clone () const override
 Creates a deep copy of this MultiConstaint, cloning all constraints that it holds. More...
 
virtual MultiConstraintOP empty_clone () const
 
Size natoms () const override
 number of atoms involved in this MultiConstraint container More...
 
Size size () const
 number of constraints that are held by this MultiConstraint More...
 
std::string type () const override
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
void read_def (std::istream &data, pose::Pose const &pose, func::FuncFactory const &func_factory) override
 read in constraint defiinition More...
 
bool operator== (Constraint const &other) const override
 possibility to compare constraint according to data and not just pointers More...
 
bool same_type_as_me (Constraint const &other) const override
 Determine if the calling class has the same type as the input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it. More...
 
void score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const override
 compute score More...
 
core::Real dist (core::scoring::func::XYZ_Func const &) const override
 
AtomID const & atom (Size const n) const override
 Returns the AtomID referred to by index. More...
 
utility::vector1< core::Sizeresidues () const override
 Returns the pose numbers of the residues involved in this constraint, in no particular order. More...
 
void setup_for_scoring (func::XYZ_Func const &, ScoreFunction const &) const override
 
virtual void add_individual_constraint (ConstraintCOP cst_in)
 add individual constraint into MultiConstraint More...
 
ConstraintOP remap_resid (core::id::SequenceMapping const &seqmap) const override
 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 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override
 compute atom deriv More...
 
void show (std::ostream &out) const override
 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 override
 Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given func::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...
 
Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1.0) const override
 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
 
ConstraintOP remapped_clone (pose::Pose const &, pose::Pose const &, id::SequenceMappingCOP map=nullptr) const override
 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)
 
core::Size choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, numeric::random::RandomGenerator &) override
 
core::Size effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &) const override
 
- Public Member Functions inherited from core::scoring::constraints::Constraint
 Constraint (ScoreType const &t)
 Constructor for Constraint class. More...
 
 ~Constraint () override
 Virtual destructor. More...
 
virtual ConstraintOP clone (func::FuncOP) const
 Clone the constraint, but where a new Func object is to be used instead. More...
 
virtual void read_constraint (std::istream &, core::pose::Pose const &)
 This method is totally redundant with read_def YAY DON'T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL. 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 Real score (pose::Pose const &pose) const
 Returns the unweighted score of this constraint computed over the given pose. More...
 
virtual Real score (pose::Pose const &pose, EnergyMap const &weights) const
 Returns the weighted score of this constraint computed over the given pose. More...
 
virtual Real dist (core::pose::Pose const &) const
 return the raw "distance" before that distance is handed to the FUNC object More...
 
virtual void setup_for_derivatives (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const
 
virtual void steal_def (pose::Pose const &)
 take coordinates, distances, angles, etc from given pose More...
 
std::string to_string () const
 Convenience function, returns the results of show() as a string. Not to be overriden by derived classes. More...
 
virtual
core::scoring::func::Func
const & 
get_func () const
 Returns the func::Func object associated with this Constraint object. More...
 
bool operator!= (Constraint const &other) const
 Inequality operator to test whether two constraints are not functionally identical. More...
 

Additional Inherited Members

- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 
- Protected Member Functions inherited from core::scoring::constraints::MultiConstraint
 MultiConstraint (MultiConstraint const &src)
 Explicit copy constructor so that derived classes will recieve a deep copy of the member constraints held in this class. More...
 
 MultiConstraint (MultiConstraint const &src, dont_copy_constraints const &)
 non-public key for special constructor More...
 
ConstraintCOPs cloned_member_constraints () const
 Return a vector of Constraints that are clones of the member constraints. More...
 

Constructor & Destructor Documentation

core::scoring::constraints::FabConstraint::FabConstraint ( )

Constructor.

Referenced by clone().

core::scoring::constraints::FabConstraint::FabConstraint ( ConstraintCOPs const &  cst_in)

Constructor.

Member Function Documentation

utility::vector1< Real > core::scoring::constraints::FabConstraint::calc_penalty_vec ( Size  start_res,
Size  stop_res,
utility::vector1< Size res1,
utility::vector1< Size res2 
)

Referenced by setup_csts().

ConstraintOP core::scoring::constraints::FabConstraint::clone ( ) const
overridevirtual

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. This function must return a deep copy of itself – meaning that if this Constraint holds pointers to other Constraints that it must invoke clone on those Constraints as well. If the Constraint holds a FuncOP, then the Func should also be cloned.

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

References FabConstraint().

bool core::scoring::constraints::FabConstraint::operator== ( Constraint const &  ) const
overridevirtual

Equality operator to test whether two constraints are functionally identical.

This operator should use floating point comparison and should not decide that two floats are identical if they are within some epsilon > 0. This method allows developes to remove specific constraints from Poses, even if the constraints have been cloned. Remapped constraints should not be considered identical – i.e., if cst1 is between residues i and j and cst2 is between residues i+1 and j+1. All subclasses of Constraint must implement this method.

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

References core::scoring::constraints::MultiConstraint::operator==().

Size core::scoring::constraints::FabConstraint::pose_res_no ( core::pose::Pose const &  pose,
std::string  tempres 
)

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

Referenced by read_def().

void core::scoring::constraints::FabConstraint::read_def ( std::istream &  data,
pose::Pose const &  pose,
func::FuncFactory const &  func_factory 
)
overridevirtual

read in constraint definition

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

References pose_res_no(), setup_csts(), and core::scoring::constraints::TR().

bool core::scoring::constraints::FabConstraint::same_type_as_me ( Constraint const &  other) const
overridevirtual

Determine if the calling class has the same type as the input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it.

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

void core::scoring::constraints::FabConstraint::setup_csts ( core::pose::Pose const &  pose,
utility::vector1< Size res1,
utility::vector1< Size res2,
std::string  antchains 
)
void core::scoring::constraints::FabConstraint::show ( std::ostream &  ) const
overridevirtual

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

std::string core::scoring::constraints::FabConstraint::type ( ) const
overridevirtual

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: