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

constraint on dihedral angle formed by 4 points More...

#include <DihedralConstraint.hh>

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List of all members.

Public Member Functions

Real score (Vector const &xyz1, Vector const &xyz2, Vector const &xyz3, Vector const &xyz4) const
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.
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 read_def (std::istream &in, pose::Pose const &pose, FuncFactory const &func_factory)
bool operator== (Constraint const &other) const
 possibility to compare constraint according to data and not just pointers
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.
Real score (conformation::Conformation const &conformation) 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.
void fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
 DihedralConstraint (AtomID const &a1, AtomID const &a2, AtomID const &a3, AtomID const &a4, FuncOP func, ScoreType scotype=dihedral_constraint)
 c-tor
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.
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.
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 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

constraint on dihedral angle formed by 4 points


Constructor & Destructor Documentation

core::scoring::constraints::DihedralConstraint::DihedralConstraint ( AtomID const &  a1,
AtomID const &  a2,
AtomID const &  a3,
AtomID const &  a4,
FuncOP  func,
ScoreType  scotype = dihedral_constraint 
) [inline]

c-tor

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


Member Function Documentation

id::AtomID const & core::scoring::constraints::DihedralConstraint::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(), show(), and show_def().

virtual ConstraintOP core::scoring::constraints::DihedralConstraint::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 DihedralConstraint(), and core::scoring::constraints::Constraint::score_type().

void core::scoring::constraints::DihedralConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const
Size core::scoring::constraints::DihedralConstraint::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.

Referenced by show(), and show_def().

bool core::scoring::constraints::DihedralConstraint::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().

void core::scoring::constraints::DihedralConstraint::read_def ( std::istream &  in,
pose::Pose const &  pose,
FuncFactory const &  func_factory 
) [virtual]
ConstraintOP core::scoring::constraints::DihedralConstraint::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(), DihedralConstraint(), and core::id::AtomID::rsd().

ConstraintOP core::scoring::constraints::DihedralConstraint::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(), DihedralConstraint(), 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::DihedralConstraint::score ( conformation::Conformation const &  ) const [virtual]

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.

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

References score(), and core::conformation::Conformation::xyz().

Real core::scoring::constraints::DihedralConstraint::score ( Vector const &  xyz1,
Vector const &  xyz2,
Vector const &  xyz3,
Vector const &  xyz4 
) const

Referenced by score().

void core::scoring::constraints::DihedralConstraint::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 score(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

void core::scoring::constraints::DihedralConstraint::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 atom(), and natoms().

void core::scoring::constraints::DihedralConstraint::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 atom(), core::conformation::atom_id_to_named_atom_id(), natoms(), and type().

Size core::scoring::constraints::DihedralConstraint::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(), core::pose::Pose::conformation(), core::pose::Pose::residue_type(), and core::id::AtomID::rsd().

virtual std::string core::scoring::constraints::DihedralConstraint::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().


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