This class favors a particular residue identity at two particular positions by adding the scaled tensor value to the energy map. More...
#include <ResidueCouplingConstraint.hh>
Public Types | |
| typedef core::Real | Real |
 Public Types inherited from core::scoring::constraints::Constraint | |
| typedef id::AtomID | AtomID |
Public Member Functions | |
| ResidueCouplingConstraint () | |
| ResidueCouplingConstraint (pose::Pose const &pose, Size const &seqpos1, Size const &seqpos2, Size const &tensor_index1, Size const &tensor_index2, CouplingTensorCOP const &tensor_const, Real const &strength, std::string const &alphabet) | |
| ~ResidueCouplingConstraint () 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 | set_alphabet (std::string const &alphabet) |
| std::string | get_alphabet () const |
| 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... | |
| bool | operator== (Constraint const &other) const override |
| and not just pointers More... | |
| bool | same_type_as_me (Constraint const &) 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 |
| 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 | 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 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 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_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 | |
| Size | seqpos1_ |
| Size | seqpos2_ |
| Size | tensor_index1_ |
| Size | tensor_index2_ |
| CouplingTensorCOP | tensor_const_ |
| Real | strength_ |
| std::string | alphabet_ |
| std::map< char, long unsigned int > | amino_acids_ |
Detailed Description
This class favors a particular residue identity at two particular positions by adding the scaled tensor value to the energy map.
Member Typedef Documentation
◆ Real
Constructor & Destructor Documentation
◆ ResidueCouplingConstraint() [1/2]
| core::scoring::constraints::ResidueCouplingConstraint::ResidueCouplingConstraint | ( | ) |
◆ ResidueCouplingConstraint() [2/2]
| core::scoring::constraints::ResidueCouplingConstraint::ResidueCouplingConstraint | ( | pose::Pose const & | pose, |
| Size const & | seqpos1, | ||
| Size const & | seqpos2, | ||
| Size const & | tensor_index1, | ||
| Size const & | tensor_index2, | ||
| CouplingTensorCOP const & | tensor_const, | ||
| Real const & | strength, | ||
| std::string const & | alphabet | ||
| ) |
References protocols::cluster::calibur::aa, amino_acids_, and get_alphabet().
◆ ~ResidueCouplingConstraint()
|
overridedefault |
Member Function Documentation
◆ atom()
|
overridevirtual |
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.
◆ clone()
|
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.
◆ dist() [1/3]
| Real core::scoring::constraints::Constraint::dist |
return the raw "distance" before that distance is handed to the FUNC object
- If such a distance doesn't make sense for this constraint, just return 0
◆ dist() [2/3]
| virtual core::Real core::scoring::constraints::Constraint::dist |
return the raw "distance" before that distance is handed to the FUNC object
- If such a distance doesn't make sense for this constraint, just return 0
◆ dist() [3/3]
|
overridevirtual |
Return 1.0 if constraint will get a bonus/penalty, 0.0 if not
Implements core::scoring::constraints::Constraint.
References core::conformation::Residue::aa(), core::scoring::func::XYZ_Func::residue(), seqpos1_, and seqpos2_.
◆ fill_f1_f2()
|
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.
◆ get_alphabet()
| std::string core::scoring::constraints::ResidueCouplingConstraint::get_alphabet | ( | ) | const |
References alphabet_.
Referenced by ResidueCouplingConstraint().
◆ natoms()
|
overridevirtual |
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.
◆ operator==()
|
overridevirtual |
and not just pointers
Implements core::scoring::constraints::Constraint.
References same_type_as_me(), core::scoring::constraints::Constraint::same_type_as_me(), seqpos1_, and seqpos2_.
◆ residues()
|
overridevirtual |
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.
◆ same_type_as_me()
|
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==().
◆ score() [1/4]
| 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.
◆ score() [2/4]
|
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 amino_acids_, core::chemical::ResidueTypeBase::name1(), core::scoring::func::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), seqpos1_, seqpos2_, strength_, tensor_const_, tensor_index1_, tensor_index2_, and core::conformation::Residue::type().
◆ score() [3/4]
| Real core::scoring::constraints::Constraint::score |
Returns the unweighted score of this constraint computed over the given pose.
◆ score() [4/4]
| Real core::scoring::constraints::Constraint::score |
Returns the weighted score of this constraint computed over the given pose.
◆ set_alphabet()
| void core::scoring::constraints::ResidueCouplingConstraint::set_alphabet | ( | std::string const & | alphabet | ) |
References alphabet_.
◆ 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 core::conformation::membrane::out, seqpos1_, and seqpos2_.
Member Data Documentation
◆ alphabet_
|
private |
Referenced by get_alphabet(), and set_alphabet().
◆ amino_acids_
|
private |
Referenced by ResidueCouplingConstraint(), and score().
◆ seqpos1_
|
private |
Referenced by dist(), operator==(), residues(), score(), and show().
◆ seqpos2_
|
private |
Referenced by dist(), operator==(), residues(), score(), and show().
◆ strength_
|
private |
Referenced by score().
◆ tensor_const_
|
private |
Referenced by score().
◆ tensor_index1_
|
private |
Referenced by score().
◆ tensor_index2_
|
private |
Referenced by score().
The documentation for this class was generated from the following files:
- src/core/scoring/constraints/ResidueCouplingConstraint.hh
- src/core/scoring/constraints/ResidueCouplingConstraint.cc
