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Rosetta 3.4
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Rosetta 3.4
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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 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. | |
| virtual std::string | type () const |
| Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. | |
| 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) | |
| 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. | |
| 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. | |
| 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. | |
| virtual AtomID const & | atom (Size const ) const |
| Returns the AtomID referred to by index. | |
| virtual utility::vector1 < core::Size > | residues () const |
| Returns the pose numbers of the residues involved in this constraint, in no particular order. | |
| 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. | |
| 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!) | |
| typedef core::conformation::Conformation protocols::constraints_additional::SequenceCouplingConstraint::Conformation |
| typedef core::scoring::constraints::ConstraintOP protocols::constraints_additional::SequenceCouplingConstraint::ConstraintOP |
| typedef core::scoring::EnergyMap protocols::constraints_additional::SequenceCouplingConstraint::EnergyMap |
| typedef core::scoring::constraints::FuncFactory protocols::constraints_additional::SequenceCouplingConstraint::FuncFactory |
| typedef core::sequence::SequenceCoupling protocols::constraints_additional::SequenceCouplingConstraint::SequenceCoupling |
| typedef core::sequence::SequenceCouplingCOP protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingCOP |
| typedef core::sequence::SequenceCouplingOP protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingOP |
| typedef core::id::SequenceMapping protocols::constraints_additional::SequenceCouplingConstraint::SequenceMapping |
| typedef core::scoring::constraints::XYZ_Func protocols::constraints_additional::SequenceCouplingConstraint::XYZ_Func |
| protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingConstraint | ( | ) |
Referenced by clone().
| protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingConstraint | ( | Pose const & | pose, |
| core::Size | seqpos1, | ||
| core::Size | seqpos2, | ||
| SequenceCouplingOP | profile = NULL |
||
| ) |
| protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingConstraint | ( | core::Size | seqpos1, |
| core::Size | seqpos2, | ||
| SequenceCouplingOP | profile = NULL |
||
| ) |
| protocols::constraints_additional::SequenceCouplingConstraint::~SequenceCouplingConstraint | ( | ) | [virtual] |
| virtual AtomID const& protocols::constraints_additional::SequenceCouplingConstraint::atom | ( | Size | index | ) | const [inline, virtual] |
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.
| ConstraintOP protocols::constraints_additional::SequenceCouplingConstraint::clone | ( | ) | const [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.
References SequenceCouplingConstraint().
| void protocols::constraints_additional::SequenceCouplingConstraint::fill_f1_f2 | ( | AtomID const & | atom, |
| XYZ_Func const & | xyz_func, | ||
| core::Vector & | F1, | ||
| core::Vector & | F2, | ||
| EnergyMap const & | weights | ||
| ) | const [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.
| virtual core::Size protocols::constraints_additional::SequenceCouplingConstraint::natoms | ( | ) | const [inline, virtual] |
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.
| void protocols::constraints_additional::SequenceCouplingConstraint::read_def | ( | std::istream & | is, |
| Pose const & | pose, | ||
| FuncFactory const & | |||
| ) | [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.
References protocols::swa::rna::file_exists(), core::sequence::SequenceCoupling::read_from_file(), core::pose::Pose::total_residue(), and protocols::constraints_additional::TR().
| utility::vector1< core::Size > protocols::constraints_additional::SequenceCouplingConstraint::residues | ( | ) | const [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.
| void protocols::constraints_additional::SequenceCouplingConstraint::score | ( | XYZ_Func const & | xyz_func, |
| EnergyMap const & | weights, | ||
| EnergyMap & | emap | ||
| ) | const [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.
References core::chemical::ResidueType::aa(), core::scoring::constraints::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), protocols::constraints_additional::TR(), and core::conformation::Residue::type().
| core::Size protocols::constraints_additional::SequenceCouplingConstraint::seqpos1 | ( | ) | const [inline] |
| core::Size protocols::constraints_additional::SequenceCouplingConstraint::seqpos2 | ( | ) | const [inline] |
| SequenceCouplingOP protocols::constraints_additional::SequenceCouplingConstraint::sequence_coupling | ( | ) |
| SequenceCouplingCOP protocols::constraints_additional::SequenceCouplingConstraint::sequence_coupling | ( | ) | const |
| void protocols::constraints_additional::SequenceCouplingConstraint::set_sequence_coupling | ( | SequenceCouplingOP | profile | ) |
| void protocols::constraints_additional::SequenceCouplingConstraint::show | ( | std::ostream & | ) | const [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.
Referenced by show_def().
| void protocols::constraints_additional::SequenceCouplingConstraint::show_def | ( | std::ostream & | , |
| Pose const & | |||
| ) | const [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.
References show().
| virtual std::string protocols::constraints_additional::SequenceCouplingConstraint::type | ( | ) | const [inline, virtual] |
Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
Reimplemented from core::scoring::constraints::Constraint.
1.7.4
