Rosetta Core  2014.35
Public Member Functions | Private Attributes | Static Private Attributes | List of all members
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>

Public Member Functions

virtual std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
 BackboneStubConstraint (pose::Pose const &pose, Size const seqpos, AtomID const &fixed_atom_id, pose::Pose const &target_pose, Size const target_seqpos, core::Real const &superposition_bonus, core::Real const &force_constant)
 
 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 &force_constant, std::string const &sidechain_atom_name, std::string const &primary_backbone_atom_name, std::string const &backbone_atom1_name, std::string const &backbone_atom2_name)
 
 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 &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. More...
 
virtual AtomID const & atom (Size const index) const
 Returns the AtomID referred to by index. More...
 
bool operator== (Constraint const &other) const
 possibility to compare constraint according to data and not just pointers More...
 
virtual void score (func::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. More...
 
virtual void fill_f1_f2 (AtomID const &atom, func::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. More...
 
core::Size seqpos () const
 returns the private member seqpos_ More...
 
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 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...
 
- 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 (core::scoring::func::FuncOP) const
 
virtual utility::vector1
< core::Size
residues () const
 Returns the pose numbers of the residues involved in this constraint, in no particular order. More...
 
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 ConstraintOP remap_resid (core::id::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 Real score (pose::Pose const &) const
 
virtual core::Real dist (core::pose::Pose const &) const
 return the "raw" distance before handed to the FUNC object More...
 
virtual core::Real dist (core::scoring::func::XYZ_Func const &) const
 
virtual void setup_for_scoring (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const
 
virtual void setup_for_derivatives (core::scoring::func::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 fill_f1_f2 (AtomID const &atom, core::scoring::func::XYZ_Func const &xyz_func, Vector &F1, Vector &F2, EnergyMap const &weights) const =0
 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...
 
virtual void show_def (std::ostream &, pose::Pose const &) const
 Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given func::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...
 
virtual void read_def (std::istream &, pose::Pose const &, core::scoring::func::FuncFactory const &)
 
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
core::scoring::func::Func
const & 
get_func () const
 Returns the func::Func object associated with this Constraint object. 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
 

Private Attributes

core::Real superposition_bonus_
 
core::Real force_constant_
 
Size seqpos_
 
AtomID sidechain_atom_id_
 
AtomID primary_atom_id_
 
AtomID backbone_atom2_id_
 
AtomID backbone_atom1_id_
 
utility::vector1< AtomIDatom_ids_
 
core::Vector sidechain_target_
 
core::Vector primary_backbone_target_
 
core::Vector backbone2_target_
 
core::Vector backbone1_target_
 
core::Vector primary_sidechain_target_
 
core::Vector backbone1_2_target_
 
AtomID fixed_atom_id_
 
core::Vector fixed_reference_point_
 

Static Private Attributes

static
utility::pointer::owning_ptr
< AngleConstraint
ang_cst_
 why is this static? More...
 

Additional Inherited Members

- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 

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,
pose::Pose const &  target_pose,
Size const  target_seqpos,
core::Real const &  superposition_bonus,
core::Real const &  force_constant 
)
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 &  force_constant,
std::string const &  sidechain_atom_name,
std::string const &  primary_backbone_atom_name,
std::string const &  backbone_atom1_name,
std::string const &  backbone_atom2_name 
)
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 &  force_constant 
)
virtual core::scoring::constraints::BackboneStubConstraint::~BackboneStubConstraint ( )
inlinevirtual

Member Function Documentation

virtual AtomID const& core::scoring::constraints::BackboneStubConstraint::atom ( Size const  index) const
inlinevirtual

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.

References atom_ids_.

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,
func::XYZ_Func const &  xyz,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const
virtual
virtual Size core::scoring::constraints::BackboneStubConstraint::natoms ( ) const
inlinevirtual

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.

References atom_ids_.

bool core::scoring::constraints::BackboneStubConstraint::operator== ( Constraint const &  other) const
virtual
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 backbone1_target_, backbone2_target_, BackboneStubConstraint(), core::conformation::ResidueFactory::create_residue(), fixed_atom_id_, force_constant_, core::chemical::ChemicalManager::get_instance(), primary_backbone_target_, core::chemical::ChemicalManager::residue_type_set(), core::id::AtomID::rsd(), seqpos_, sidechain_target_, and superposition_bonus_.

void core::scoring::constraints::BackboneStubConstraint::score ( func::XYZ_Func const &  xyz_func,
EnergyMap const &  weights,
EnergyMap emap 
) const
virtual
core::Size core::scoring::constraints::BackboneStubConstraint::seqpos ( ) const

returns the private member seqpos_

References 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.

References force_constant_, seqpos_, and superposition_bonus_.

virtual std::string core::scoring::constraints::BackboneStubConstraint::type ( ) const
inlinevirtual

Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.

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

Member Data Documentation

utility::pointer::owning_ptr< AngleConstraint > core::scoring::constraints::BackboneStubConstraint::ang_cst_
staticprivate

why is this static?

Referenced by BackboneStubConstraint(), fill_f1_f2(), and score().

utility::vector1< AtomID > core::scoring::constraints::BackboneStubConstraint::atom_ids_
private
core::Vector core::scoring::constraints::BackboneStubConstraint::backbone1_2_target_
private
core::Vector core::scoring::constraints::BackboneStubConstraint::backbone1_target_
private
core::Vector core::scoring::constraints::BackboneStubConstraint::backbone2_target_
private
AtomID core::scoring::constraints::BackboneStubConstraint::backbone_atom1_id_
private
AtomID core::scoring::constraints::BackboneStubConstraint::backbone_atom2_id_
private
AtomID core::scoring::constraints::BackboneStubConstraint::fixed_atom_id_
private
core::Vector core::scoring::constraints::BackboneStubConstraint::fixed_reference_point_
private
core::Real core::scoring::constraints::BackboneStubConstraint::force_constant_
private
AtomID core::scoring::constraints::BackboneStubConstraint::primary_atom_id_
private
core::Vector core::scoring::constraints::BackboneStubConstraint::primary_backbone_target_
private
core::Vector core::scoring::constraints::BackboneStubConstraint::primary_sidechain_target_
private
Size core::scoring::constraints::BackboneStubConstraint::seqpos_
private
AtomID core::scoring::constraints::BackboneStubConstraint::sidechain_atom_id_
private
core::Vector core::scoring::constraints::BackboneStubConstraint::sidechain_target_
private
core::Real core::scoring::constraints::BackboneStubConstraint::superposition_bonus_
private

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