#include <SequenceConstraint.hh>
Inheritance diagram for core::scoring::aa_composition_energy::SequenceConstraint:
Public Member Functions | |
| SequenceConstraint (core::scoring::ScoreType const &t) | |
| Constructor. More... | |
| SequenceConstraint (SequenceConstraint const &src) | |
| Copy constructor. More... | |
| ~SequenceConstraint () override | |
| Destructor. More... | |
| void | score (core::scoring::func::XYZ_Func const &, EnergyMap const &, EnergyMap &) const override |
| Implemented because the base class requires it; not used by a sequence constraint. More... | |
| core::Real | dist (core::scoring::func::XYZ_Func const &) const override |
| Implemented because the base class requires it; not used by a sequence constraint. More... | |
| void | fill_f1_f2 (core::id::AtomID const &, core::scoring::func::XYZ_Func const &, Vector &, Vector &, EnergyMap const &) const override |
| Implemented because the base class requires it; not used by a sequence constraint. More... | |
| core::Size | natoms () const override |
| Implemented because the base class requires it; not used by a sequence constraint. More... | |
| core::id::AtomID const & | atom (core::Size const) const override |
| Implemented because the base class requires it; not used by a sequence constraint. More... | |
 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 () const =0 |
| 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... | |
| virtual ConstraintOP | clone (func::FuncOP) const |
| Clone the constraint, but where a new Func object is to be used instead. More... | |
| virtual ConstraintOP | remapped_clone (pose::Pose const &, pose::Pose const &, id::SequenceMappingCOP map) 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... | |
| 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 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 ConstraintOP | remap_resid (core::id::SequenceMapping const &) 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 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 std::string | type () const |
| Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More... | |
| virtual void | setup_for_scoring (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const |
| virtual void | setup_for_derivatives (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const |
| virtual void | show (std::ostream &) 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 &, pose::Pose const &) const |
| 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... | |
| virtual void | read_def (std::istream &, pose::Pose const &, core::scoring::func::FuncFactory const &) |
| Reads the definition of a Constraint from the given std::istream, 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. More... | |
| 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 Size | show_violations (std::ostream &out, pose::Pose const &, Size, 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 core::scoring::func::Func const & | get_func () const |
| Returns the func::Func object associated with this Constraint object. More... | |
| virtual bool | operator== (Constraint const &) const =0 |
| Equality operator to test whether two constraints are functionally identical. More... | |
| bool | operator!= (Constraint const &other) const |
| Inequality operator to test whether two constraints are not functionally identical. More... | |
| virtual bool | same_type_as_me (Constraint const &other) const =0 |
| 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... | |
| 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 |
Private Attributes | |
| core::id::AtomID | dummy_atomid_ |
| Silly fake atomID necessary for the atom() function that all Constraints have to implement. More... | |
Additional Inherited Members | |
| Public Types inherited from core::scoring::constraints::Constraint | |
| typedef id::AtomID | AtomID |
Constructor & Destructor Documentation
◆ SequenceConstraint() [1/2]
| core::scoring::aa_composition_energy::SequenceConstraint::SequenceConstraint | ( | core::scoring::ScoreType const & | t | ) |
Constructor.
◆ SequenceConstraint() [2/2]
| core::scoring::aa_composition_energy::SequenceConstraint::SequenceConstraint | ( | SequenceConstraint const & | src | ) |
Copy constructor.
◆ ~SequenceConstraint()
|
overridedefault |
Destructor.
Member Function Documentation
◆ atom()
|
inlineoverridevirtual |
Implemented because the base class requires it; not used by a sequence constraint.
Always returns AtomID(0,0).
Implements core::scoring::constraints::Constraint.
References dummy_atomid_.
◆ dist()
|
inlineoverridevirtual |
Implemented because the base class requires it; not used by a sequence constraint.
Implements core::scoring::constraints::Constraint.
◆ fill_f1_f2()
|
inlineoverridevirtual |
Implemented because the base class requires it; not used by a sequence constraint.
Implements core::scoring::constraints::Constraint.
◆ natoms()
|
inlineoverridevirtual |
Implemented because the base class requires it; not used by a sequence constraint.
Always returns zero.
Implements core::scoring::constraints::Constraint.
◆ score()
|
inlineoverridevirtual |
Implemented because the base class requires it; not used by a sequence constraint.
Implements core::scoring::constraints::Constraint.
Member Data Documentation
◆ dummy_atomid_
|
private |
The documentation for this class was generated from the following files:
- src/core/scoring/aa_composition_energy/SequenceConstraint.hh
- src/core/scoring/aa_composition_energy/SequenceConstraint.cc
