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Rosetta 3.5
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Rosetta 3.5
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#include <SequenceCoupling1BDConstraint.hh>
Public Member Functions | |
| SequenceCoupling1BDConstraint () | |
| SequenceCoupling1BDConstraint (Pose const &, core::Size, SequenceProfileCOP profile) | |
| SequenceCoupling1BDConstraint (core::Size, SequenceProfileCOP profile) | |
| virtual | ~SequenceCoupling1BDConstraint () |
| 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 (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... | |
| 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::SequenceProfileConstraint | |
| SequenceProfileConstraint () | |
| SequenceProfileConstraint (Pose const &, core::Size, SequenceProfileCOP profile=NULL, core::id::SequenceMappingCOP mapping=NULL) | |
| SequenceProfileConstraint (core::Size, SequenceProfileCOP profile=NULL, core::id::SequenceMappingCOP mapping=NULL) | |
| virtual | ~SequenceProfileConstraint () |
| 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... | |
| core::Size | seqpos () const |
| void | seqpos (core::Size seqpos) |
| void | set_sequence_profile (SequenceProfileCOP profile, core::id::SequenceMappingCOP mapping=NULL) |
| SequenceProfileCOP | sequence_profile () const |
| core::id::SequenceMappingCOP | profile_mapping () 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 (core::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 ConstraintOP | remap_resid (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 ConstraintOP | remapped_clone (pose::Pose const &src, pose::Pose const &dest, 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 | weight (core::Real const w) |
| core::Real | weight () 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_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 |
Definition at line 34 of file SequenceCoupling1BDConstraint.hh.
| typedef core::conformation::Conformation protocols::constraints_additional::SequenceCoupling1BDConstraint::Conformation |
Definition at line 40 of file SequenceCoupling1BDConstraint.hh.
| typedef core::scoring::constraints::ConstraintOP protocols::constraints_additional::SequenceCoupling1BDConstraint::ConstraintOP |
Definition at line 44 of file SequenceCoupling1BDConstraint.hh.
| typedef core::scoring::EnergyMap protocols::constraints_additional::SequenceCoupling1BDConstraint::EnergyMap |
Definition at line 41 of file SequenceCoupling1BDConstraint.hh.
| typedef core::scoring::constraints::FuncFactory protocols::constraints_additional::SequenceCoupling1BDConstraint::FuncFactory |
Definition at line 42 of file SequenceCoupling1BDConstraint.hh.
Definition at line 39 of file SequenceCoupling1BDConstraint.hh.
| typedef core::sequence::SequenceCoupling protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling |
Definition at line 36 of file SequenceCoupling1BDConstraint.hh.
| typedef core::sequence::SequenceCouplingCOP protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCouplingCOP |
Definition at line 37 of file SequenceCoupling1BDConstraint.hh.
| typedef core::id::SequenceMapping protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceMapping |
Definition at line 38 of file SequenceCoupling1BDConstraint.hh.
| typedef core::scoring::constraints::XYZ_Func protocols::constraints_additional::SequenceCoupling1BDConstraint::XYZ_Func |
Definition at line 43 of file SequenceCoupling1BDConstraint.hh.
| protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint | ( | ) |
Definition at line 55 of file SequenceCoupling1BDConstraint.cc.
Referenced by clone().
| protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint | ( | Pose const & | pose, |
| core::Size | numpos, | ||
| SequenceProfileCOP | profile | ||
| ) |
Definition at line 59 of file SequenceCoupling1BDConstraint.cc.
| protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint | ( | core::Size | numpos, |
| SequenceProfileCOP | profile | ||
| ) |
Definition at line 66 of file SequenceCoupling1BDConstraint.cc.
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virtual |
Definition at line 71 of file SequenceCoupling1BDConstraint.cc.
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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.
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
Definition at line 74 of file SequenceCoupling1BDConstraint.cc.
References SequenceCoupling1BDConstraint().
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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!)
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
Definition at line 155 of file SequenceCoupling1BDConstraint.cc.
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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::SequenceProfileConstraint.
Definition at line 80 of file SequenceCoupling1BDConstraint.cc.
References core::pack::dunbrack::c, protocols::swa::rna::file_exists(), core::scoring::constraints::SequenceProfileConstraint::seqpos(), core::scoring::constraints::SequenceProfileConstraint::set_sequence_profile(), core::pose::Pose::total_residue(), and protocols::constraints_additional::TR().
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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.
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
Definition at line 134 of file SequenceCoupling1BDConstraint.cc.
References core::chemical::ResidueType::aa(), core::scoring::constraints::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), core::scoring::constraints::SequenceProfileConstraint::seqpos(), core::scoring::constraints::SequenceProfileConstraint::sequence_profile(), protocols::constraints_additional::TR(), and core::conformation::Residue::type().
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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::SequenceProfileConstraint.
Definition at line 124 of file SequenceCoupling1BDConstraint.cc.
References core::scoring::constraints::SequenceProfileConstraint::seqpos(), and core::scoring::constraints::SequenceProfileConstraint::sequence_profile().
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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::SequenceProfileConstraint.
Definition at line 65 of file SequenceCoupling1BDConstraint.hh.
1.8.4