#include <NamedAngleConstraint.hh>
Public Member Functions | |
| NamedAngleConstraint (id::NamedAtomID const &a1, id::NamedAtomID const &a2, id::NamedAtomID const &a3, func::FuncOP func, ScoreType scoretype=angle_constraint) | |
| std::string | type () const override |
| Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. 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... | |
| 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 .. nullptr = identity mapping to the new object. Intended to be implemented by derived classes. More... | |
| ConstraintOP | remap_resid (core::id::SequenceMapping const &seqmap) const override |
| This overrride updates the sequence numbering but not the atom names. More... | |
| bool | operator== (Constraint const &rhs) 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 | 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... | |
| void | show_def_nopose (std::ostream &out) const |
| void | read_def (std::istream &in, pose::Pose const &pose, func::FuncFactory const &func_factory) override |
| void | score (func::XYZ_Func const &xyz, EnergyMap const &, EnergyMap &emap) const override |
| compute score More... | |
| void | setup_for_scoring (func::XYZ_Func const &, ScoreFunction const &) const override |
| core::Real | dist (core::scoring::func::XYZ_Func const &xyz) const override |
| return the raw "distance" before that distance is handed to the FUNC object 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::AngleConstraint | |
| AngleConstraint (AtomID const &a1, AtomID const &a2, AtomID const &a3, core::scoring::func::FuncOP func_in, ScoreType scotype=angle_constraint) | |
| Constructor. More... | |
| AngleConstraint (core::scoring::func::FuncOP func_in, ScoreType scoretype=angle_constraint) | |
| Constructor without atom IDs – if you create an AngleConstraint with this constructor, you must never call its score( XYZFunc ) method! Dangerous and stupid! More... | |
| Real | score (Vector const &xyz1, Vector const &xyz2, Vector const &xyz3) const |
| compute score More... | |
| virtual core::Real | score (conformation::Conformation const &) const |
| Real | angle (Vector const &xyz1, Vector const &xyz2, Vector const &xyz3) const |
| compute More... | |
| void | fill_f1_f2 (AtomID const &atom, core::scoring::func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override |
| compute atom deriv More... | |
| Size | natoms () const override |
| number of atoms — always 3 for angles More... | |
| AtomID const & | atom (Size const n) const override |
| return AtomID for atom 1,2,3 More... | |
| Size | show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, core::Real threshold=1) const override |
| output violation of constraint to out - returns 1 if violated ( i.e., func.show_violations() > 0 ) 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... | |
| core::scoring::func::Func const & | get_func () const override |
| Returns the func::Func object associated with this Constraint object. More... | |
| Real | func (Real const theta) const |
| evaluate func at theta More... | |
| Real | dfunc (Real const theta) const |
| evaluate dfunc at theta More... | |
| void | p1_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &F1, Vector &F2) const |
| void | p2_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &F1, Vector &F2) const |
| AtomID const & | atom1 () const |
| AtomID const & | atom2 () const |
| AtomID const & | atom3 () const |
| 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 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 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... | |
| 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 |
Protected Member Functions | |
| NamedAngleConstraint (NamedAngleConstraint const &src) | |
| Protected Member Functions inherited from core::scoring::constraints::AngleConstraint | |
| AngleConstraint (AngleConstraint const &src) | |
| Explicit copy constructor so that derived classes will recieve a deep copy of the Func this class contains. More... | |
| func::FuncCOP | func () const |
| const access to func More... | |
| void | set_func (func::FuncOP f) |
| set func More... | |
| void | atom1 (AtomID newid) const |
| void | atom2 (AtomID newid) const |
| void | atom3 (AtomID newid) const |
Private Attributes | |
| id::NamedAtomID | named_atom1_ |
| id::NamedAtomID | named_atom2_ |
| id::NamedAtomID | named_atom3_ |
| core::Size | type1_id_ |
| core::Size | type2_id_ |
| core::Size | type3_id_ |
Additional Inherited Members | |
| Public Types inherited from core::scoring::constraints::Constraint | |
| typedef id::AtomID | AtomID |
| Static Public Member Functions inherited from core::scoring::constraints::AngleConstraint | |
| static void | p1_theta_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &f1, Vector &f2) |
| static void | helper (Vector const &M, Vector const &w, Vector &F1, Vector &F2) |
Constructor & Destructor Documentation
◆ NamedAngleConstraint() [1/2]
| core::scoring::constraints::NamedAngleConstraint::NamedAngleConstraint | ( | id::NamedAtomID const & | a1, |
| id::NamedAtomID const & | a2, | ||
| id::NamedAtomID const & | a3, | ||
| func::FuncOP | func, | ||
| ScoreType | scoretype = angle_constraint |
||
| ) |
Referenced by clone(), and remap_resid().
◆ NamedAngleConstraint() [2/2]
|
protecteddefault |
Member Function Documentation
◆ 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.
Reimplemented from core::scoring::constraints::AngleConstraint.
References NamedAngleConstraint().
Referenced by remap_resid(), and remapped_clone().
◆ 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 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
Reimplemented from core::scoring::constraints::AngleConstraint.
References core::scoring::constraints::AngleConstraint::angle(), core::id::NamedAtomID::atom(), named_atom1_, named_atom2_, named_atom3_, core::id::NamedAtomID::rsd(), and protocols::kinmatch::xyz().
◆ operator==()
|
overridevirtual |
possibility to compare constraint according to data and not just pointers
Reimplemented from core::scoring::constraints::AngleConstraint.
References named_atom1_, named_atom2_, named_atom3_, type1_id_, type2_id_, and type3_id_.
◆ read_def()
|
overridevirtual |
one line definition "AngleConstraint atom1 res1 atom2 res2 atom3 res3 function_type function_definition"
Reimplemented from core::scoring::constraints::AngleConstraint.
References core::id::AtomID::atomno(), core::scoring::constraints::AngleConstraint::func(), named_atom1_, named_atom2_, named_atom3_, core::pose::named_atom_id_to_atom_id(), core::scoring::func::FuncFactory::new_func(), core::scoring::constraints::ConstraintIO::parse_residue(), core::scoring::constraints::AngleConstraint::set_func(), core::pose::Pose::size(), and core::scoring::constraints::TR().
◆ remap_resid()
|
overridevirtual |
This overrride updates the sequence numbering but not the atom names.
Reimplemented from core::scoring::constraints::AngleConstraint.
References core::id::NamedAtomID::atom(), clone(), core::scoring::constraints::AngleConstraint::func(), named_atom1_, named_atom2_, named_atom3_, NamedAngleConstraint(), core::id::NamedAtomID::rsd(), and core::scoring::constraints::Constraint::score_type().
◆ remapped_clone()
|
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 .. nullptr = identity mapping to the new object. Intended to be implemented by derived classes.
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::AngleConstraint.
References core::scoring::constraints::AngleConstraint::atom1(), core::scoring::constraints::AngleConstraint::atom2(), core::scoring::constraints::AngleConstraint::atom3(), clone(), core::scoring::constraints::AngleConstraint::func(), named_atom1_, named_atom2_, named_atom3_, core::pose::named_atom_id_to_atom_id(), core::id::AtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().
◆ 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.
Reimplemented from core::scoring::constraints::AngleConstraint.
◆ 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 |
compute score
Reimplemented from core::scoring::constraints::AngleConstraint.
References core::id::NamedAtomID::atom(), named_atom1_, named_atom2_, named_atom3_, core::scoring::func::XYZ_Func::residue(), core::id::NamedAtomID::rsd(), core::scoring::constraints::AngleConstraint::score(), core::scoring::constraints::Constraint::score_type(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().
◆ 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.
◆ setup_for_scoring()
|
overridevirtual |
Reimplemented from core::scoring::constraints::AngleConstraint.
References core::id::NamedAtomID::atom(), core::scoring::constraints::AngleConstraint::atom1(), core::scoring::constraints::AngleConstraint::atom2(), core::scoring::constraints::AngleConstraint::atom3(), named_atom1_, named_atom2_, named_atom3_, core::id::NamedAtomID::rsd(), show_def_nopose(), core::scoring::constraints::TR(), type(), type1_id_, type2_id_, type3_id_, and protocols::kinmatch::xyz().
◆ show_def()
|
overridevirtual |
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.
Reimplemented from core::scoring::constraints::AngleConstraint.
References core::conformation::membrane::out, and show_def_nopose().
◆ show_def_nopose()
| void core::scoring::constraints::NamedAngleConstraint::show_def_nopose | ( | std::ostream & | out | ) | const |
References core::scoring::constraints::AngleConstraint::func(), named_atom1_, named_atom2_, named_atom3_, core::conformation::membrane::out, and type().
Referenced by setup_for_scoring(), and show_def().
◆ type()
|
overridevirtual |
Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
Reimplemented from core::scoring::constraints::AngleConstraint.
Referenced by setup_for_scoring(), and show_def_nopose().
Member Data Documentation
◆ named_atom1_
|
private |
Referenced by dist(), operator==(), read_def(), remap_resid(), remapped_clone(), score(), setup_for_scoring(), and show_def_nopose().
◆ named_atom2_
|
private |
Referenced by dist(), operator==(), read_def(), remap_resid(), remapped_clone(), score(), setup_for_scoring(), and show_def_nopose().
◆ named_atom3_
|
private |
Referenced by dist(), operator==(), read_def(), remap_resid(), remapped_clone(), score(), setup_for_scoring(), and show_def_nopose().
◆ type1_id_
|
private |
Referenced by operator==(), and setup_for_scoring().
◆ type2_id_
|
private |
Referenced by operator==(), and setup_for_scoring().
◆ type3_id_
|
private |
Referenced by operator==(), and setup_for_scoring().
The documentation for this class was generated from the following files:
- src/core/scoring/constraints/NamedAngleConstraint.hh
- src/core/scoring/constraints/NamedAngleConstraint.cc
