Rosetta 3.4
Public Member Functions
core::scoring::constraints::BackboneStubConstraint Class Reference

This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location. More...

#include <BackboneStubConstraint.hh>

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List of all members.

Public Member Functions

virtual std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
 BackboneStubConstraint (pose::Pose const &pose, Size const seqpos, AtomID const &fixed_atom_id, conformation::Residue const &target_rsd, core::Real const &superposition_bonus, core::Real const &CB_force_constant)
virtual ~BackboneStubConstraint ()
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.
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
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 seqpos () const
 returns the private member seqpos_
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 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.

Detailed Description

This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location.


Constructor & Destructor Documentation

core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint ( pose::Pose const &  pose,
Size const  seqpos,
AtomID const &  fixed_atom_id,
conformation::Residue const &  target_rsd,
core::Real const &  superposition_bonus,
core::Real const &  CB_force_constant 
)
virtual core::scoring::constraints::BackboneStubConstraint::~BackboneStubConstraint ( ) [inline, virtual]

Member Function Documentation

virtual AtomID const& core::scoring::constraints::BackboneStubConstraint::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::BackboneStubConstraint::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 BackboneStubConstraint().

void core::scoring::constraints::BackboneStubConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const [virtual]
virtual Size core::scoring::constraints::BackboneStubConstraint::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::BackboneStubConstraint::operator== ( Constraint const &  other) const [virtual]

possibility to compare constraint according to data and not just pointers

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

ConstraintOP core::scoring::constraints::BackboneStubConstraint::remapped_clone ( pose::Pose const &  src,
pose::Pose const &  dest,
id::SequenceMappingCOP  map = NULL 
) const [virtual]

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.

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

References BackboneStubConstraint(), core::conformation::ResidueFactory::create_residue(), core::chemical::ChemicalManager::get_instance(), core::chemical::ChemicalManager::residue_type_set(), and core::id::AtomID::rsd().

void core::scoring::constraints::BackboneStubConstraint::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::conformation::Residue::aa(), core::chemical::aa_gly, protocols::comparative_modeling::features::E, core::conformation::Residue::is_protein(), core::scoring::constraints::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), core::scoring::constraints::TR(), and core::conformation::Residue::xyz().

core::Size core::scoring::constraints::BackboneStubConstraint::seqpos ( ) const

returns the private member seqpos_

void core::scoring::constraints::BackboneStubConstraint::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.

virtual std::string core::scoring::constraints::BackboneStubConstraint::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.


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