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Rosetta 3.5
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Rosetta 3.5
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#include <SequenceCouplingConstraint.hh>
Public Types | |
| typedef core::sequence::SequenceCoupling | SequenceCoupling |
| typedef core::sequence::SequenceCouplingOP | SequenceCouplingOP |
| typedef core::sequence::SequenceCouplingCOP | SequenceCouplingCOP |
| typedef core::id::SequenceMapping | SequenceMapping |
| typedef core::pose::Pose | Pose |
| typedef core::conformation::Conformation | Conformation |
| typedef core::scoring::EnergyMap | EnergyMap |
| typedef core::scoring::constraints::FuncFactory | FuncFactory |
| typedef core::scoring::constraints::XYZ_Func | XYZ_Func |
| typedef core::scoring::constraints::ConstraintOP | ConstraintOP |
 Public Types inherited from core::scoring::constraints::Constraint | |
| typedef id::AtomID | AtomID |
Public Member Functions | |
| SequenceCouplingConstraint () | |
| SequenceCouplingConstraint (Pose const &, core::Size, core::Size, SequenceCouplingOP profile=NULL) | |
| SequenceCouplingConstraint (core::Size, core::Size, SequenceCouplingOP profile=NULL) | |
| virtual | ~SequenceCouplingConstraint () |
| 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... | |
| virtual std::string | type () const |
| Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More... | |
| virtual void | read_def (std::istream &, Pose const &, FuncFactory const &) |
| used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file) More... | |
| virtual void | show_def (std::ostream &, Pose const &) 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... | |
| virtual 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... | |
| core::Size | seqpos1 () const |
| core::Size | seqpos2 () const |
| void | set_sequence_coupling (SequenceCouplingOP) |
| SequenceCouplingOP | sequence_coupling () |
| SequenceCouplingCOP | sequence_coupling () const |
| virtual core::Size | natoms () const |
| 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... | |
| virtual AtomID const & | atom (Size const ) 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 | score (XYZ_Func const &, EnergyMap const &, EnergyMap &) const |
| 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 void | fill_f1_f2 (AtomID const &, XYZ_Func const &, core::Vector &, core::Vector &, EnergyMap const &) const |
| 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... | |
| 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 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... | |
| 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 ConstraintOP | remap_resid (core::id::SequenceMapping const &) 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... | |
| 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_scoring (XYZ_Func const &, ScoreFunction 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 Size | show_violations (std::ostream &out, pose::Pose const &, Size, Real threshold=1) 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... | |
| virtual Func const & | get_func () const |
| Returns the Func object associated with this Constraint object. More... | |
| virtual bool | operator== (Constraint const &) const |
| possibility to do object comparison instead of pointer comparison More... | |
| bool | operator!= (Constraint const &other) const |
| possibility to do object comparison instead of pointer comparison 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 |
Private Attributes | |
| core::Size | seqpos1_ |
| core::Size | seqpos2_ |
| SequenceCouplingOP | sequence_coupling_ |
Definition at line 34 of file SequenceCouplingConstraint.hh.
| typedef core::conformation::Conformation protocols::constraints_additional::SequenceCouplingConstraint::Conformation |
Definition at line 41 of file SequenceCouplingConstraint.hh.
| typedef core::scoring::constraints::ConstraintOP protocols::constraints_additional::SequenceCouplingConstraint::ConstraintOP |
Definition at line 45 of file SequenceCouplingConstraint.hh.
| typedef core::scoring::EnergyMap protocols::constraints_additional::SequenceCouplingConstraint::EnergyMap |
Definition at line 42 of file SequenceCouplingConstraint.hh.
| typedef core::scoring::constraints::FuncFactory protocols::constraints_additional::SequenceCouplingConstraint::FuncFactory |
Definition at line 43 of file SequenceCouplingConstraint.hh.
Definition at line 40 of file SequenceCouplingConstraint.hh.
| typedef core::sequence::SequenceCoupling protocols::constraints_additional::SequenceCouplingConstraint::SequenceCoupling |
Definition at line 36 of file SequenceCouplingConstraint.hh.
| typedef core::sequence::SequenceCouplingCOP protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingCOP |
Definition at line 38 of file SequenceCouplingConstraint.hh.
| typedef core::sequence::SequenceCouplingOP protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingOP |
Definition at line 37 of file SequenceCouplingConstraint.hh.
| typedef core::id::SequenceMapping protocols::constraints_additional::SequenceCouplingConstraint::SequenceMapping |
Definition at line 39 of file SequenceCouplingConstraint.hh.
| typedef core::scoring::constraints::XYZ_Func protocols::constraints_additional::SequenceCouplingConstraint::XYZ_Func |
Definition at line 44 of file SequenceCouplingConstraint.hh.
| protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingConstraint | ( | ) |
Definition at line 57 of file SequenceCouplingConstraint.cc.
Referenced by clone().
| protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingConstraint | ( | Pose const & | , |
| core::Size | seqpos1, | ||
| core::Size | seqpos2, | ||
| SequenceCouplingOP | profile = NULL |
||
| ) |
Definition at line 64 of file SequenceCouplingConstraint.cc.
| protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingConstraint | ( | core::Size | seqpos1, |
| core::Size | seqpos2, | ||
| SequenceCouplingOP | profile = NULL |
||
| ) |
Definition at line 76 of file SequenceCouplingConstraint.cc.
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virtual |
Definition at line 87 of file SequenceCouplingConstraint.cc.
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inlinevirtual |
Returns the AtomID referred to by index.
Note that this function isn't actually used by the constraint scoring machenery. If you're calling it on a generic Constraint (as opposed to specifically on a derived class) you're probably doing something wrong.
Implements core::scoring::constraints::Constraint.
Definition at line 90 of file SequenceCouplingConstraint.hh.
References core::id::BOGUS_ATOM_ID.
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virtual |
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.
Implements core::scoring::constraints::Constraint.
Definition at line 90 of file SequenceCouplingConstraint.cc.
References SequenceCouplingConstraint().
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virtual |
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!)
Implements core::scoring::constraints::Constraint.
Definition at line 246 of file SequenceCouplingConstraint.cc.
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inlinevirtual |
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.
Note that this function isn't actually used by the constraint scoring machenery. If you're calling it on a generic Constraint (as opposed to specifically on a derived class) you're probably doing something wrong.
Implements core::scoring::constraints::Constraint.
Definition at line 89 of file SequenceCouplingConstraint.hh.
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virtual |
used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file)
one line definition "SequenceProfile resindex profilefilename" (profilefilename can also be set to "none" in the constraints file, and specified by -in::file::pssm)
Reimplemented from core::scoring::constraints::Constraint.
Definition at line 96 of file SequenceCouplingConstraint.cc.
References protocols::swa::rna::file_exists(), seqpos1_, seqpos2_, sequence_coupling_, core::pose::Pose::total_residue(), and protocols::constraints_additional::TR().
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virtual |
Returns the pose numbers of the residues involved in this constraint, in no particular order.
Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.
Reimplemented from core::scoring::constraints::Constraint.
Definition at line 178 of file SequenceCouplingConstraint.cc.
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virtual |
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.
Implements core::scoring::constraints::Constraint.
Definition at line 206 of file SequenceCouplingConstraint.cc.
References core::chemical::ResidueType::aa(), core::scoring::constraints::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), seqpos1_, seqpos2_, sequence_coupling_, protocols::constraints_additional::TR(), and core::conformation::Residue::type().
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inline |
Definition at line 82 of file SequenceCouplingConstraint.hh.
References seqpos1_.
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inline |
Definition at line 83 of file SequenceCouplingConstraint.hh.
References seqpos2_.
| SequenceCouplingOP protocols::constraints_additional::SequenceCouplingConstraint::sequence_coupling | ( | ) |
Definition at line 172 of file SequenceCouplingConstraint.cc.
References sequence_coupling_.
| SequenceCouplingCOP protocols::constraints_additional::SequenceCouplingConstraint::sequence_coupling | ( | ) | const |
Definition at line 175 of file SequenceCouplingConstraint.cc.
References sequence_coupling_.
| void protocols::constraints_additional::SequenceCouplingConstraint::set_sequence_coupling | ( | SequenceCouplingOP | profile) |
Definition at line 166 of file SequenceCouplingConstraint.cc.
References sequence_coupling_.
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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::Constraint.
Definition at line 151 of file SequenceCouplingConstraint.cc.
References seqpos1_, seqpos2_, and sequence_coupling_.
Referenced by show_def().
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virtual |
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.
Reimplemented from core::scoring::constraints::Constraint.
Definition at line 145 of file SequenceCouplingConstraint.cc.
References show().
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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::Constraint.
Definition at line 68 of file SequenceCouplingConstraint.hh.
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private |
Definition at line 116 of file SequenceCouplingConstraint.hh.
Referenced by read_def(), residues(), score(), seqpos1(), and show().
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private |
Definition at line 117 of file SequenceCouplingConstraint.hh.
Referenced by read_def(), residues(), score(), seqpos2(), and show().
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private |
Definition at line 118 of file SequenceCouplingConstraint.hh.
Referenced by read_def(), score(), sequence_coupling(), set_sequence_coupling(), and show().
1.8.4