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

#include <CoordinateConstraint.hh>

Inheritance diagram for core::scoring::constraints::CoordinateConstraint:
Inheritance graph
[legend]
Collaboration diagram for core::scoring::constraints::CoordinateConstraint:
Collaboration graph
[legend]

List of all members.

Public Member Functions

 CoordinateConstraint ()
 CoordinateConstraint (AtomID const &a1, AtomID const &fixed_atom_in, Vector const &xyz_target_in, FuncOP func, ScoreType scotype=coordinate_constraint)
 c-tor
 ~CoordinateConstraint ()
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.
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 &)
bool operator== (Constraint const &other_cst) const
 possibility to do object comparison instead of pointer comparison
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 non_virtual_score (Vector const &xyz) const
virtual 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.
virtual void fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
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 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.
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 ...

Detailed Description

CoordinateConstraint compares the coordinates of a given atom (AtomID atom_) to a fixed coordinate triplet (Vector xyz_target_). Its other argument, fixed_atom_, is somewhat nonobvious. CoordinateConstraints are meant to be used with a Pose that has a nonmoving virtual root residue. An AtomID in this virtual root residue should be passed as fixed_atom_. CoordinateConstraint does not use fixed_atom_, but the ScoreFunction code detects when fixed_atom_ and atom_ move relative to one another, and trigger re-scoring at that time. In other words, CoordinateConstraints are really context-independent one body energies, but we wish them to be evaluated as context-independent two-body energies. (Ideally, ScoreFunction would detect when atom_ moves relative to xyz_target_, but since ScoreFunction functions on atoms and not floating coordinate triplets, this is a good workaround.) -- SML


Constructor & Destructor Documentation

core::scoring::constraints::CoordinateConstraint::CoordinateConstraint ( )

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

core::scoring::constraints::CoordinateConstraint::CoordinateConstraint ( AtomID const &  a1,
AtomID const &  fixed_atom_in,
Vector const &  xyz_target_in,
FuncOP  func,
ScoreType  scotype = coordinate_constraint 
)

c-tor

core::scoring::constraints::CoordinateConstraint::~CoordinateConstraint ( )

Member Function Documentation

core::id::AtomID const & core::scoring::constraints::CoordinateConstraint::atom ( Size const  index) const [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.

Referenced by remapped_clone().

ConstraintOP core::scoring::constraints::CoordinateConstraint::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 CoordinateConstraint().

Real core::scoring::constraints::CoordinateConstraint::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::CoordinateConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const [virtual]
Size core::scoring::constraints::CoordinateConstraint::natoms ( ) const [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.

Real core::scoring::constraints::CoordinateConstraint::non_virtual_score ( Vector const &  xyz) const

Referenced by score().

bool core::scoring::constraints::CoordinateConstraint::operator== ( Constraint const &  other_cst) const [virtual]

possibility to do object comparison instead of pointer comparison

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

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

void core::scoring::constraints::CoordinateConstraint::read_def ( std::istream &  data,
pose::Pose const &  pose,
FuncFactory const &  func_factory 
) [virtual]
ConstraintOP core::scoring::constraints::CoordinateConstraint::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::AtomID::atomno(), CoordinateConstraint(), core::id::AtomID::rsd(), and core::scoring::constraints::Constraint::score_type().

ConstraintOP core::scoring::constraints::CoordinateConstraint::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::conformation::atom_id_to_named_atom_id(), CoordinateConstraint(), core::conformation::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().

void core::scoring::constraints::CoordinateConstraint::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 non_virtual_score(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

void core::scoring::constraints::CoordinateConstraint::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 core::id::AtomID::atomno(), and core::id::AtomID::rsd().

void core::scoring::constraints::CoordinateConstraint::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::conformation::atom_id_to_named_atom_id(), and type().

Size core::scoring::constraints::CoordinateConstraint::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::CoordinateConstraint::steal_def ( pose::Pose const &  pose) [virtual]
std::string core::scoring::constraints::CoordinateConstraint::type ( ) const [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().


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines