Rosetta

This class favors a particular residue identity at a particular position by reducing its res_type energy. More...
#include <MembraneSpanTermZConstraint.hh>
Public Types  
typedef core::Real  Real 
Public Types inherited from core::scoring::constraints::Constraint  
typedef id::AtomID  AtomID 
Public Member Functions  
MembraneSpanTermZConstraint ()  
MembraneSpanTermZConstraint (pose::Pose const &pose)  
~MembraneSpanTermZConstraint () override  
Size  natoms () const override 
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...  
AtomID const &  atom (Size const) const override 
Returns the AtomID referred to by index. More...  
utility::vector1< core::Size >  residues () const override 
Returns the pose numbers of the residues involved in this constraint, in no particular order. 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...  
ConstraintOP  remap_resid (core::id::SequenceMapping const &) 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...  
bool  operator== (Constraint const &other) 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...  
ConstraintOP  remapped_clone (pose::Pose const &src, pose::Pose const &dest, 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  score (func::XYZ_Func const &, EnergyMap const &, EnergyMap &emap) const override 
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  calc_score () const 
core::Real  score_delta (core::Real a, core::Real b) const 
core::Real  dist (core::scoring::func::XYZ_Func const &xyz) const override 
void  fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override 
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...  
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...  
virtual void  score (core::scoring::func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const=0 
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...  
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 core::Real  dist (core::scoring::func::XYZ_Func const &) const=0 
return the raw "distance" before that distance is handed to the FUNC object More...  
virtual Real  dist (core::pose::Pose const &) const 
return the raw "distance" before that distance is handed to the FUNC object 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 (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 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_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...  
bool  operator!= (Constraint const &other) const 
Inequality operator to test whether two constraints are not functionally identical. 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  
utility::vector1< core::conformation::ResidueCOP >  in_res_ 
utility::vector1< core::conformation::ResidueCOP >  out_res_ 
This class favors a particular residue identity at a particular position by reducing its res_type energy.
core::scoring::constraints::MembraneSpanTermZConstraint::MembraneSpanTermZConstraint  (  ) 
Referenced by clone().
core::scoring::constraints::MembraneSpanTermZConstraint::MembraneSpanTermZConstraint  (  pose::Pose const &  pose  ) 

override 

inlineoverridevirtual 
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 core::id::GLOBAL_BOGUS_ATOM_ID.
core::Real core::scoring::constraints::MembraneSpanTermZConstraint::calc_score  (  )  const 
References in_res_, out_res_, score(), and score_delta().
Referenced by score().

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 MembraneSpanTermZConstraint().
Real core::scoring::constraints::Constraint::dist 
return the raw "distance" before that distance is handed to the FUNC object
virtual core::Real core::scoring::constraints::Constraint::dist 
return the raw "distance" before that distance is handed to the FUNC object

overridevirtual 
Return 1.0 if constraint will get a bonus, 0.0 if not
Implements core::scoring::constraints::Constraint.

overridevirtual 
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.

inlineoverridevirtual 
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.

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 in_res_, out_res_, core::scoring::constraints::Constraint::same_type_as_me(), same_type_as_me(), and core::scoring::constraints::Constraint::score_type().

overridevirtual 
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.

overridevirtual 
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.

overridevirtual 
Returns the pose numbers of the residues involved in this constraint, in no particular order.
Used in determining onebody/twobody/multibody 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.

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.
Referenced by operator==().
virtual void core::scoring::constraints::Constraint::score 
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.
Referenced by calc_score().

overridevirtual 
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 calc_score(), and core::scoring::constraints::Constraint::score_type().
Real core::scoring::constraints::Constraint::score 
Returns the unweighted score of this constraint computed over the given pose.
Real core::scoring::constraints::Constraint::score 
Returns the weighted score of this constraint computed over the given pose.
core::Real core::scoring::constraints::MembraneSpanTermZConstraint::score_delta  (  core::Real  a, 
core::Real  b  
)  const 
References core::pose::motif::a(), and protocols::match::upstream::b.
Referenced by calc_score(), and show().

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 in_res_, core::conformation::membrane::out, out_res_, and score_delta().

private 
Referenced by calc_score(), MembraneSpanTermZConstraint(), operator==(), residues(), and show().

private 
Referenced by calc_score(), MembraneSpanTermZConstraint(), operator==(), residues(), and show().