#include <NamedDihedralConstraint.hh>
Public Member Functions | |
| NamedDihedralConstraint (id::NamedAtomID const &a1, id::NamedAtomID const &a2, id::NamedAtomID const &a3, id::NamedAtomID const &a4, func::FuncOP func, ScoreType scoretype=dihedral_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 |
| @breif Perform a deep clone by cloning the func_ pointer held by this DihedralConstraint 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 |
| 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 |
| 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::DihedralConstraint | |
| Size | show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1) 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... | |
| Real | score (Vector const &xyz1, Vector const &xyz2, Vector const &xyz3, Vector const &xyz4) const |
| Real | score (conformation::Conformation const &conformation) const |
| 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... | |
| DihedralConstraint (AtomID const &a1, AtomID const &a2, AtomID const &a3, AtomID const &a4, func::FuncOP func, ScoreType scotype=dihedral_constraint) | |
| c-tor More... | |
| 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 n) const override |
| Returns the AtomID referred to by index. 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... | |
| func::Func const & | get_func () const override |
| Returns the func::Func object associated with this Constraint 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::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_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 | 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 | |
| NamedDihedralConstraint (NamedDihedralConstraint const &src) | |
| Protected Member Functions inherited from core::scoring::constraints::DihedralConstraint | |
| DihedralConstraint (DihedralConstraint 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... | |
Private Attributes | |
| id::NamedAtomID | named_atom1_ |
| id::NamedAtomID | named_atom2_ |
| id::NamedAtomID | named_atom3_ |
| id::NamedAtomID | named_atom4_ |
Additional Inherited Members | |
| Public Types inherited from core::scoring::constraints::Constraint | |
| typedef id::AtomID | AtomID |
Constructor & Destructor Documentation
◆ NamedDihedralConstraint() [1/2]
| core::scoring::constraints::NamedDihedralConstraint::NamedDihedralConstraint | ( | id::NamedAtomID const & | a1, |
| id::NamedAtomID const & | a2, | ||
| id::NamedAtomID const & | a3, | ||
| id::NamedAtomID const & | a4, | ||
| func::FuncOP | func, | ||
| ScoreType | scoretype = dihedral_constraint |
||
| ) |
Referenced by clone(), and remap_resid().
◆ NamedDihedralConstraint() [2/2]
|
protecteddefault |
Member Function Documentation
◆ clone()
|
overridevirtual |
@breif Perform a deep clone by cloning the func_ pointer held by this DihedralConstraint
Reimplemented from core::scoring::constraints::DihedralConstraint.
References NamedDihedralConstraint().
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::DihedralConstraint.
References core::id::NamedAtomID::atom(), named_atom1_, named_atom2_, named_atom3_, named_atom4_, 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::DihedralConstraint.
References named_atom1_, named_atom2_, named_atom3_, and named_atom4_.
◆ read_def()
|
overridevirtual |
one line definition "DihedralConstraint atom1 res1 atom2 res2 atom3 res3 function_type function_definition"
Reimplemented from core::scoring::constraints::DihedralConstraint.
References core::id::AtomID::atomno(), core::scoring::constraints::DihedralConstraint::func(), named_atom1_, named_atom2_, named_atom3_, named_atom4_, core::pose::named_atom_id_to_atom_id(), core::scoring::func::FuncFactory::new_func(), core::scoring::constraints::ConstraintIO::parse_residue(), core::scoring::constraints::DihedralConstraint::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::DihedralConstraint.
References core::id::NamedAtomID::atom(), clone(), core::scoring::constraints::DihedralConstraint::func(), named_atom1_, named_atom2_, named_atom3_, named_atom4_, NamedDihedralConstraint(), 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::DihedralConstraint.
References clone(), core::scoring::constraints::DihedralConstraint::func(), named_atom1_, named_atom2_, named_atom3_, named_atom4_, core::pose::named_atom_id_to_atom_id(), core::id::NamedAtomID::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::DihedralConstraint.
◆ 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.
Reimplemented from core::scoring::constraints::DihedralConstraint.
References core::id::NamedAtomID::atom(), named_atom1_, named_atom2_, named_atom3_, named_atom4_, core::scoring::func::XYZ_Func::residue(), core::id::NamedAtomID::rsd(), core::scoring::constraints::DihedralConstraint::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.
◆ 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::DihedralConstraint.
References core::conformation::membrane::out, and show_def_nopose().
◆ show_def_nopose()
| void core::scoring::constraints::NamedDihedralConstraint::show_def_nopose | ( | std::ostream & | out | ) | const |
References core::scoring::constraints::DihedralConstraint::func(), named_atom1_, named_atom2_, named_atom3_, core::conformation::membrane::out, and type().
Referenced by 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::DihedralConstraint.
Referenced by show_def_nopose().
Member Data Documentation
◆ named_atom1_
|
private |
Referenced by dist(), operator==(), read_def(), remap_resid(), remapped_clone(), score(), and show_def_nopose().
◆ named_atom2_
|
private |
Referenced by dist(), operator==(), read_def(), remap_resid(), remapped_clone(), score(), and show_def_nopose().
◆ named_atom3_
|
private |
Referenced by dist(), operator==(), read_def(), remap_resid(), remapped_clone(), score(), and show_def_nopose().
◆ named_atom4_
|
private |
Referenced by dist(), operator==(), read_def(), remap_resid(), remapped_clone(), and score().
The documentation for this class was generated from the following files:
- src/core/scoring/constraints/NamedDihedralConstraint.hh
- src/core/scoring/constraints/NamedDihedralConstraint.cc
