#include <SiteConstraint.hh>
Inheritance diagram for core::scoring::constraints::SiteConstraint:
Public Member Functions | |
| SiteConstraint () | |
| Constructor. More... | |
| SiteConstraint (ConstraintCOPs const &cst_in) | |
| Constructor. More... | |
| ConstraintOP | clone () const override |
| bool | operator== (Constraint const &) const override |
| 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... | |
| std::string | type () const override |
| Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More... | |
| void | read_def (std::istream &data, pose::Pose const &pose, func::FuncFactory const &func_factory) override |
| read in constraint defiinition 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... | |
| void | setup_csts (Size res, std::string name, std::string chain, core::pose::Pose const &pose, func::FuncOP const &func) |
| Sets up SiteConstaint between the residue of interest and a chain. More... | |
| void | setup_csts (Size res, std::string name, utility::vector1< bool > const &residues, core::pose::Pose const &pose, func::FuncOP const &func) |
| Sets up SiteConstraint between the residue of interest and a subset of residues. More... | |
 Public Member Functions inherited from core::scoring::constraints::AmbiguousConstraint | |
| AmbiguousConstraint () | |
| Constructor. More... | |
| AmbiguousConstraint (ConstraintCOPs const &cst_in) | |
| Constructor. More... | |
| MultiConstraintOP | empty_clone () const override |
| void | init_cst_score_types () |
| void | score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const override |
| compute score More... | |
| core::Real | calculate_total_cst_score (EnergyMap const &weights, EnergyMap &emap) const |
| helper function to accumulate all constraint scores into one number More... | |
| ConstraintOP | remap_resid (core::id::SequenceMapping const &seqmap) 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... | |
| void | fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override |
| compute atom deriv More... | |
| ConstraintCOP | active_constraint () const |
| Size | show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1.0) 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... | |
| Public Member Functions inherited from core::scoring::constraints::MultiConstraint | |
| MultiConstraint (ScoreType const &t=dof_constraint) | |
| default Constructor More... | |
| MultiConstraint (ConstraintCOPs const &cst_in, ScoreType const &t=dof_constraint) | |
| Constructor – performs a shallow copy of the input ConstraintCOPs. More... | |
| Size | natoms () const override |
| number of atoms involved in this MultiConstraint container More... | |
| Size | size () const |
| number of constraints that are held by this MultiConstraint More... | |
| void | score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const override |
| compute score More... | |
| core::Real | dist (core::scoring::func::XYZ_Func const &) const override |
| AtomID const & | atom (Size const n) 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 | setup_for_scoring (func::XYZ_Func const &, ScoreFunction const &) const override |
| virtual void | add_individual_constraint (ConstraintCOP cst_in) |
| add individual constraint into MultiConstraint More... | |
| ConstraintOP | remap_resid (core::id::SequenceMapping const &seqmap) 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... | |
| void | fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override |
| compute atom deriv 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... | |
| Size | show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1.0) 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... | |
| ConstraintCOPs const & | member_constraints () const |
| ConstraintOP | remapped_clone (pose::Pose const &, pose::Pose const &, 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 | set_effective_sequence_separation (core::Size setting) |
| core::Size | choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, numeric::random::RandomGenerator &) override |
| core::Size | effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &) const override |
| 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 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... | |
| 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... | |
Additional Inherited Members | |
| Public Types inherited from core::scoring::constraints::Constraint | |
| typedef id::AtomID | AtomID |
| Protected Member Functions inherited from core::scoring::constraints::AmbiguousConstraint | |
| AmbiguousConstraint (AmbiguousConstraint const &src) | |
| Copy constructor for derived classes to ensure that they perform a deep copy on the approriate data members. More... | |
| Protected Member Functions inherited from core::scoring::constraints::MultiConstraint | |
| MultiConstraint (MultiConstraint const &src) | |
| Explicit copy constructor so that derived classes will recieve a deep copy of the member constraints held in this class. More... | |
| MultiConstraint (MultiConstraint const &src, dont_copy_constraints const &) | |
| non-public key for special constructor More... | |
| ConstraintCOPs | cloned_member_constraints () const |
| Return a vector of Constraints that are clones of the member constraints. More... | |
Constructor & Destructor Documentation
◆ SiteConstraint() [1/2]
| core::scoring::constraints::SiteConstraint::SiteConstraint | ( | ) |
Constructor.
Referenced by clone().
◆ SiteConstraint() [2/2]
| core::scoring::constraints::SiteConstraint::SiteConstraint | ( | ConstraintCOPs const & | cst_in | ) |
Constructor.
Member Function Documentation
◆ clone()
|
overridevirtual |
Clone into a vector all of the member constraints held in the base class and then invoke the copy constructor with this vector of clones
Reimplemented from core::scoring::constraints::AmbiguousConstraint.
References SiteConstraint().
◆ operator==()
|
overridevirtual |
@detail this function only checks whether the passed in cst is the same type and then hands off to the multi cst. probably overkill to also demand that the active cst is identical
Reimplemented from core::scoring::constraints::AmbiguousConstraint.
References core::scoring::constraints::AmbiguousConstraint::operator==().
◆ read_def()
|
overridevirtual |
read in constraint defiinition
Reimplemented from core::scoring::constraints::AmbiguousConstraint.
References core::scoring::func::FuncFactory::new_func(), core::scoring::constraints::ConstraintIO::parse_residue(), setup_csts(), core::pose::Pose::size(), and core::scoring::constraints::TR().
◆ 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::AmbiguousConstraint.
◆ setup_csts() [1/2]
| void core::scoring::constraints::SiteConstraint::setup_csts | ( | Size | res, |
| std::string | name, | ||
| std::string | chain, | ||
| core::pose::Pose const & | pose, | ||
| func::FuncOP const & | func | ||
| ) |
Sets up SiteConstaint between the residue of interest and a chain.
References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::get_chain_ids_from_chain(), core::scoring::constraints::MultiConstraint::residues(), and core::pose::Pose::size().
Referenced by read_def().
◆ setup_csts() [2/2]
| void core::scoring::constraints::SiteConstraint::setup_csts | ( | Size | res, |
| std::string | name, | ||
| utility::vector1< bool > const & | residues, | ||
| core::pose::Pose const & | pose, | ||
| func::FuncOP const & | func | ||
| ) |
Sets up SiteConstraint between the residue of interest and a subset of residues.
References core::scoring::constraints::MultiConstraint::add_individual_constraint(), core::chemical::ResidueType::atom_index(), core::conformation::Residue::carbohydrate_info(), core::conformation::Residue::is_carbohydrate(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::constraints::MultiConstraint::residues(), core::pose::Pose::size(), core::scoring::constraints::TR(), and core::id::AtomID::valid().
◆ 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::AmbiguousConstraint.
References core::scoring::constraints::MultiConstraint::member_constraints(), and core::conformation::membrane::out.
◆ type()
|
overridevirtual |
Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
Reimplemented from core::scoring::constraints::AmbiguousConstraint.
The documentation for this class was generated from the following files:
- src/core/scoring/constraints/SiteConstraint.hh
- src/core/scoring/constraints/SiteConstraint.cc
