Rosetta 3.4
Public Types | Public Member Functions
core::scoring::constraints::ResidueTypeLinkingConstraint Class Reference

This class favors a particular residue identity at a particular position by reducing its res_type energy. More...

#include <ResidueTypeLinkingConstraint.hh>

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List of all members.

Public Types

typedef core::Real Real

Public Member Functions

 ResidueTypeLinkingConstraint ()
 ResidueTypeLinkingConstraint (pose::Pose const &pose, Size seqpos1, Size seqpos2, Real bonus)
 ResidueTypeLinkingConstraint (pose::Pose const &pose, Size seqpos1, Size seqpos2, std::string AA1name, std::string AA2name, Real bonus)
virtual ~ResidueTypeLinkingConstraint ()
virtual 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 index) 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.
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.
bool operator== (Constraint const &other) const
 possibility to compare constraint according to data and not just pointers
virtual void score (XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) 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 &atom, XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) 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!)
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.

Detailed Description

This class favors a particular residue identity at a particular position by reducing its res_type energy.


Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::constraints::ResidueTypeLinkingConstraint::ResidueTypeLinkingConstraint ( )

Referenced by clone().

core::scoring::constraints::ResidueTypeLinkingConstraint::ResidueTypeLinkingConstraint ( pose::Pose const &  pose,
Size  seqpos1,
Size  seqpos2,
core::Real  bonus 
)
core::scoring::constraints::ResidueTypeLinkingConstraint::ResidueTypeLinkingConstraint ( pose::Pose const &  pose,
Size  seqpos1,
Size  seqpos2,
std::string  AA1name,
std::string  AA2name,
core::Real  bonus 
)
core::scoring::constraints::ResidueTypeLinkingConstraint::~ResidueTypeLinkingConstraint ( ) [virtual]

Member Function Documentation

virtual AtomID const& core::scoring::constraints::ResidueTypeLinkingConstraint::atom ( Size const  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 core::scoring::constraints::ResidueTypeLinkingConstraint::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 ResidueTypeLinkingConstraint().

void core::scoring::constraints::ResidueTypeLinkingConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz_func,
Vector F1,
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 Size core::scoring::constraints::ResidueTypeLinkingConstraint::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.

bool core::scoring::constraints::ResidueTypeLinkingConstraint::operator== ( Constraint const &  other) const [virtual]

possibility to compare constraint according to data and not just pointers

Reimplemented from core::scoring::constraints::Constraint.

References core::scoring::constraints::Constraint::score_type().

utility::vector1< core::Size > core::scoring::constraints::ResidueTypeLinkingConstraint::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 core::scoring::constraints::ResidueTypeLinkingConstraint::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::scoring::constraints::XYZ_Func::residue(), and core::scoring::constraints::Constraint::score_type().

void core::scoring::constraints::ResidueTypeLinkingConstraint::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.


The documentation for this class was generated from the following files:
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