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Rosetta 3.5
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Rosetta 3.5
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#include <SiteConstraint.hh>
Public Member Functions | |
| SiteConstraint () | |
| Constructor. More... | |
| SiteConstraint (ConstraintCOPs &cst_in) | |
| Constructor. More... | |
| virtual ConstraintOP | clone () const |
| 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. More... | |
| 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, 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 res, std::string name, std::string chain, core::pose::Pose const &pose, FuncOP const &func) |
 Public Member Functions inherited from core::scoring::constraints::AmbiguousConstraint | |
| AmbiguousConstraint () | |
| Constructor. More... | |
| AmbiguousConstraint (ConstraintCOPs &cst_in) | |
| Constructor. More... | |
| virtual MultiConstraintOP | empty_clone () const |
| void | init_cst_score_types () |
| bool | operator== (Constraint const &other) const |
| possibility to compare constraint according to data and not just pointers More... | |
| void | score (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, 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 (const ConstraintCOPs &cst_in, ScoreType const &t=dof_constraint) | |
| Constructor. More... | |
| Size | natoms () const |
| number of atoms involved in this MultiConstraint container More... | |
| Size | size () const |
| number of constraints data 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 (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 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 (FuncOP) const |
| virtual void | read_constraint (std::istream &, core::pose::Pose const &) |
| This method is totally redundant with read_def YAY. 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 core::Real | dist (core::pose::Pose const &) const |
| return the "raw" distance before handed to the FUNC object More... | |
| virtual core::Real | dist (XYZ_Func const &) const |
| virtual void | setup_for_derivatives (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 &) |
| std::string | to_string () const |
| Convenience function, returns the results of show() as a string. Not to be overriden by derived classes. More... | |
| virtual Func const & | get_func () const |
| Returns the Func object associated with this Constraint object. More... | |
| bool | operator!= (Constraint const &other) const |
| possibility to do object comparison instead of pointer comparison More... | |
Additional Inherited Members | |
| Public Types inherited from core::scoring::constraints::Constraint | |
| typedef id::AtomID | AtomID |
| Protected Attributes inherited from core::scoring::constraints::MultiConstraint | |
| ConstraintCOPs | member_constraints_ |
Definition at line 46 of file SiteConstraint.hh.
| core::scoring::constraints::SiteConstraint::SiteConstraint | ( | ) |
| core::scoring::constraints::SiteConstraint::SiteConstraint | ( | ConstraintCOPs & | cst_in) |
Constructor.
Definition at line 47 of file SiteConstraint.cc.
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inlinevirtual |
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.
Reimplemented from core::scoring::constraints::AmbiguousConstraint.
Definition at line 57 of file SiteConstraint.hh.
References SiteConstraint().
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virtual |
read in constraint defiinition
Reimplemented from core::scoring::constraints::AmbiguousConstraint.
Definition at line 67 of file SiteConstraint.cc.
References core::scoring::constraints::FuncFactory::new_func(), core::scoring::constraints::ConstraintIO::parse_residue(), setup_csts(), core::scoring::constraints::TR(), and type().
| void core::scoring::constraints::SiteConstraint::setup_csts | ( | Size | res, |
| std::string | name, | ||
| std::string | chain, | ||
| core::pose::Pose const & | pose, | ||
| FuncOP const & | func | ||
| ) |
Definition at line 107 of file SiteConstraint.cc.
References core::scoring::constraints::MultiConstraint::add_individual_constraint(), core::chemical::ResidueType::atom_index(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::get_chain_id_from_chain(), and core::pose::Pose::residue_type().
Referenced by read_def().
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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.
Definition at line 52 of file SiteConstraint.cc.
References core::scoring::constraints::MultiConstraint::member_constraints().
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inlinevirtual |
Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
Reimplemented from core::scoring::constraints::AmbiguousConstraint.
Definition at line 61 of file SiteConstraint.hh.
Referenced by read_def().
1.8.4