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

#include <LocalCoordinateConstraint.hh>

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List of all members.

Public Member Functions

 LocalCoordinateConstraint ()
 LocalCoordinateConstraint (id::AtomID const &a1, id::StubID const &fixed_stub_in, Vector const &xyz_target_in, FuncOP func, ScoreType scotype=coordinate_constraint)
 c-tor
 ~LocalCoordinateConstraint ()
virtual std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
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.
virtual ConstraintOP remap_resid (core::id::SequenceMapping const &seqmap) 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.
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 read_def (std::istream &, pose::Pose const &, FuncFactory const &)
void show_def (std::ostream &out, pose::Pose const &pose) 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 steal_def (pose::Pose const &)
Real score (Vector const &xyz, Vector const &s1, Vector const &s2, Vector const &s3) const
void score (XYZ_Func const &xyz, EnergyMap const &, 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.
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!)
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.
AtomID const & atom (Size const n) const
 Returns the AtomID referred to by index.
Real dist (pose::Pose const &pose) const
 return the "raw" distance before handed to the FUNC object
virtual Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, 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 ...
void set_fixed_stub (id::StubID new_stub)
Vector xyz_target (core::pose::Pose const &local_frame_pose) const
void set_xyz_target (Vector const &xyz_in, core::pose::Pose const &local_frame_pose)

Constructor & Destructor Documentation

core::scoring::constraints::LocalCoordinateConstraint::LocalCoordinateConstraint ( ) [inline]

Referenced by clone(), remap_resid(), and remapped_clone().

core::scoring::constraints::LocalCoordinateConstraint::LocalCoordinateConstraint ( id::AtomID const &  a1,
id::StubID const &  fixed_stub_in,
Vector const &  xyz_target_in,
FuncOP  func,
ScoreType  scotype = coordinate_constraint 
) [inline]
core::scoring::constraints::LocalCoordinateConstraint::~LocalCoordinateConstraint ( ) [inline]

Member Function Documentation

AtomID const& core::scoring::constraints::LocalCoordinateConstraint::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.

References core::id::StubID::atom().

Referenced by remapped_clone(), and protocols::topology_broker::CoordConstraintClaimer::superimpose().

virtual ConstraintOP core::scoring::constraints::LocalCoordinateConstraint::clone ( ) const [inline, 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 LocalCoordinateConstraint().

Real core::scoring::constraints::LocalCoordinateConstraint::dist ( pose::Pose const &  ) const [virtual]

return the "raw" distance before handed to the FUNC object

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

References core::pose::Pose::conformation(), and protocols::kinmatch::xyz().

Referenced by fill_f1_f2(), and show_violations().

void core::scoring::constraints::LocalCoordinateConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz_func,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const [inline, 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.

References dist(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

Size core::scoring::constraints::LocalCoordinateConstraint::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 core::scoring::constraints::LocalCoordinateConstraint::read_def ( std::istream &  data,
pose::Pose const &  pose,
FuncFactory const &  func_factory 
) [virtual]
ConstraintOP core::scoring::constraints::LocalCoordinateConstraint::remap_resid ( core::id::SequenceMapping const &  ) const [virtual]

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.

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

References core::id::StubID::atom(), core::id::AtomID::atomno(), LocalCoordinateConstraint(), core::id::AtomID::rsd(), and core::scoring::constraints::Constraint::score_type().

ConstraintOP core::scoring::constraints::LocalCoordinateConstraint::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 atom(), core::pose::atom_id_to_named_atom_id(), LocalCoordinateConstraint(), core::pose::named_atom_id_to_atom_id(), core::id::AtomID::rsd(), core::id::NamedAtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().

Real core::scoring::constraints::LocalCoordinateConstraint::score ( Vector const &  xyz,
Vector const &  s1,
Vector const &  s2,
Vector const &  s3 
) const

References core::kinematics::Stub::global2local().

Referenced by score().

void core::scoring::constraints::LocalCoordinateConstraint::score ( XYZ_Func const &  xyz_func,
EnergyMap const &  weights,
EnergyMap emap 
) const [inline, 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::id::StubID::atom(), score(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

void core::scoring::constraints::LocalCoordinateConstraint::set_fixed_stub ( id::StubID  new_stub) [inline]
void core::scoring::constraints::LocalCoordinateConstraint::set_xyz_target ( Vector const &  xyz_in,
core::pose::Pose const &  local_frame_pose 
)
void core::scoring::constraints::LocalCoordinateConstraint::show ( std::ostream &  ) const [inline, 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 core::id::AtomID::atomno(), and core::id::AtomID::rsd().

void core::scoring::constraints::LocalCoordinateConstraint::show_def ( std::ostream &  ,
pose::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 core::id::NamedStubID::atom(), core::conformation::atom_id_to_named_atom_id(), core::pose::stub_id_to_named_stub_id(), and type().

Size core::scoring::constraints::LocalCoordinateConstraint::show_violations ( std::ostream &  out,
pose::Pose const &  ,
Size  ,
Real  threshold = 1 
) const [virtual]

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 ...

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

References core::id::AtomID::atomno(), dist(), core::pose::Pose::residue_type(), and core::id::AtomID::rsd().

void core::scoring::constraints::LocalCoordinateConstraint::steal_def ( pose::Pose const &  pose) [virtual]
virtual std::string core::scoring::constraints::LocalCoordinateConstraint::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.

Referenced by read_def(), and show_def().

Vector core::scoring::constraints::LocalCoordinateConstraint::xyz_target ( core::pose::Pose const &  local_frame_pose) const

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