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Rosetta
2016.11
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Rosetta
2016.11
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#include <SiteConstraintResidues.hh>
Public Member Functions | |
| SiteConstraintResidues () | |
| Constructor. More... | |
| SiteConstraintResidues (ConstraintCOPs const &cst_in) | |
| Constructor. More... | |
| virtual ConstraintOP | clone () const |
| virtual bool | operator== (Constraint const &) const |
| virtual bool | same_type_as_me (Constraint const &) const |
| 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... | |
| virtual std::string | type () const |
| 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) |
| read in constraint defiinition More... | |
| void | show (std::ostream &out) const |
| 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 res1, std::string name, Size res2, Size res3, core::pose::Pose const &pose, func::FuncOP const &func) |
 Public Member Functions inherited from core::scoring::constraints::AmbiguousConstraint | |
| AmbiguousConstraint () | |
| Constructor. More... | |
| AmbiguousConstraint (ConstraintCOPs const &cst_in) | |
| Constructor. More... | |
| virtual MultiConstraintOP | empty_clone () const |
| void | init_cst_score_types () |
| void | score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const |
| 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... | |
| virtual ConstraintOP | remap_resid (core::id::SequenceMapping const &seqmap) 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... | |
| void | fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const |
| 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 |
| 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 |
| number of atoms involved in this MultiConstraint container More... | |
| Size | size () const |
| number of constraints that are held by this MultiConstraint More... | |
| virtual AtomID const & | atom (Size const n) const |
| Returns the AtomID referred to by index. 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 | setup_for_scoring (func::XYZ_Func const &, ScoreFunction const &) const |
| virtual void | add_individual_constraint (ConstraintCOP cst_in) |
| add individual constraint into MultiConstraint More... | |
| virtual void | show_def (std::ostream &out, pose::Pose const &pose) 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... | |
| ConstraintCOPs const & | member_constraints () const |
| virtual ConstraintOP | remapped_clone (pose::Pose const &, pose::Pose const &, id::SequenceMappingCOP map=NULL) 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... | |
| void | set_effective_sequence_separation (core::Size setting) |
| 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 |
| Public Member Functions inherited from core::scoring::constraints::Constraint | |
| Constraint (ScoreType const &t) | |
| Constructor for Constraint class. More... | |
| virtual | ~Constraint () |
| 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 &) const |
| virtual core::Real | dist (core::pose::Pose const &) const |
| return the raw "distance" before that distance is handed to the FUNC object More... | |
| virtual core::Real | dist (core::scoring::func::XYZ_Func const &) const |
| virtual void | setup_for_derivatives (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const |
| virtual Real | score (conformation::Conformation const &) const |
| Returns the score of this constraint computed over the given conformation. Not necessarily implemented in all derived classes, as it's redundant with the score( XYZ_Func, EnergyMap, EnergyMap ) method defined above. Returns 0.0 if not implemented. 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 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... | |
| ConstraintCOPs | cloned_member_constraints () const |
| Return a vector of Constraints that are clones of the member constraints. More... | |
| core::scoring::constraints::SiteConstraintResidues::SiteConstraintResidues | ( | ) |
Constructor.
Referenced by clone().
| core::scoring::constraints::SiteConstraintResidues::SiteConstraintResidues | ( | ConstraintCOPs const & | cst_in | ) |
Constructor.
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virtual |
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 SiteConstraintResidues().
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virtual |
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==().
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virtual |
read in constraint defiinition
Reimplemented from core::scoring::constraints::AmbiguousConstraint.
References core::scoring::func::FuncFactory::new_func(), setup_csts(), and core::scoring::constraints::TR().
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virtual |
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.
| void core::scoring::constraints::SiteConstraintResidues::setup_csts | ( | Size | res1, |
| std::string | name, | ||
| Size | res2, | ||
| Size | res3, | ||
| core::pose::Pose const & | pose, | ||
| func::FuncOP const & | func | ||
| ) |
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virtual |
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::sequence::end, and core::scoring::constraints::MultiConstraint::member_constraints().
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virtual |
Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
Reimplemented from core::scoring::constraints::AmbiguousConstraint.
1.8.7