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Rosetta 3.4
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Rosetta 3.4
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#include <SequenceCoupling1BDConstraint.hh>
Public Types | |
| typedef core::sequence::SequenceCoupling | SequenceCoupling |
| 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 | |
| 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. | |
| 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 (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. | |
| 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::SequenceCoupling1BDConstraint::Conformation |
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
| typedef core::scoring::constraints::ConstraintOP protocols::constraints_additional::SequenceCoupling1BDConstraint::ConstraintOP |
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
| typedef core::scoring::EnergyMap protocols::constraints_additional::SequenceCoupling1BDConstraint::EnergyMap |
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
| typedef core::scoring::constraints::FuncFactory protocols::constraints_additional::SequenceCoupling1BDConstraint::FuncFactory |
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
| typedef core::sequence::SequenceCoupling protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling |
| typedef core::sequence::SequenceCouplingCOP protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCouplingCOP |
| typedef core::id::SequenceMapping protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceMapping |
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
| typedef core::scoring::constraints::XYZ_Func protocols::constraints_additional::SequenceCoupling1BDConstraint::XYZ_Func |
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
| protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint | ( | ) |
Referenced by clone().
| protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint | ( | Pose const & | pose, |
| core::Size | numpos, | ||
| SequenceProfileCOP | profile | ||
| ) |
| protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint | ( | core::Size | numpos, |
| SequenceProfileCOP | profile | ||
| ) |
| protocols::constraints_additional::SequenceCoupling1BDConstraint::~SequenceCoupling1BDConstraint | ( | ) | [virtual] |
| ConstraintOP protocols::constraints_additional::SequenceCoupling1BDConstraint::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.
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
References SequenceCoupling1BDConstraint().
| void protocols::constraints_additional::SequenceCoupling1BDConstraint::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!)
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
| void protocols::constraints_additional::SequenceCoupling1BDConstraint::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::SequenceProfileConstraint.
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().
| void protocols::constraints_additional::SequenceCoupling1BDConstraint::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.
Reimplemented from core::scoring::constraints::SequenceProfileConstraint.
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().
| void protocols::constraints_additional::SequenceCoupling1BDConstraint::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::SequenceProfileConstraint.
References core::scoring::constraints::SequenceProfileConstraint::seqpos(), and core::scoring::constraints::SequenceProfileConstraint::sequence_profile().
| virtual std::string protocols::constraints_additional::SequenceCoupling1BDConstraint::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::SequenceProfileConstraint.
1.7.4
