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core::scoring::constraints::Constraints Class Reference

#include <Constraints.hh>

Inheritance diagram for core::scoring::constraints::Constraints:
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Public Types

typedef id::AtomID AtomID
 
typedef conformation::Residue Residue
 
typedef conformation::Conformation Conformation
 
typedef
ConstraintCOPs::const_iterator 
const_iterator
 

Public Member Functions

 ~Constraints () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
 Constraints ()
 Default constructor creates an empy Constraints object. More...
 
 Constraints (Constraints const &)
 Copy constructor copies all of the Constraint pointers so that two Poses may share the same constraints – this only works if constraints are immutable. More...
 
ConstraintsOP clone () const
 Create a copy of this Constraints object using the shallow-copy-constructor. More...
 
ConstraintsOP deep_clone () const
 Create a deep copy of this Constraints object, cloning all of the individual constraints. More...
 
Constraintsoperator= (Constraints const &rhs)
 Copy the contents of the rhs Constraints object into this Constraints object. More...
 
void setup_for_scoring (core::scoring::func::XYZ_Func const &xyz_func, ScoreFunction const &scfxn) const
 
void setup_for_derivatives (core::scoring::func::XYZ_Func const &xyz_func, ScoreFunction const &scfxn) const
 
void residue_pair_energy (Residue const &rsd1, Residue const &rsd2, EnergyMap const &weights, EnergyMap &emap) const
 will fail if Residues dont contain all the necessary atoms More...
 
void intra_residue_energy (Residue const &rsd, EnergyMap const &weights, EnergyMap &emap) const
 will fail if Residue doesnt contain all the necessary atoms More...
 
void conformation_energy (Conformation const &conformation, EnergyMap const &weights, EnergyMap &emap) const
 
void eval_intrares_atom_derivative (id::AtomID const &atom_id, conformation::Residue const &residue, EnergyMap const &weights, Vector &F1, Vector &F2) const
 Evaluate derivatives giving the Constraint objects held within this object a single residue. Warning: if this Constraints object contains Constraint objects that operate on other residues besides the one being given them, then this function will cause the program to exit. More...
 
void eval_respair_atom_derivative (id::AtomID const &atom_id, conformation::Residue const &residue1, conformation::Residue const &residue2, EnergyMap const &weights, Vector &F1, Vector &F2) const
 Evaluate derivatives giving the Constraint objects held within this object two residues. Warning: if this Constraints object contains Constraint objects that operate on other residues besides the two being given them, then this function will cause the program to exit. More...
 
void eval_ws_atom_derivative (AtomID const &atom_id, Conformation const &conformation, EnergyMap const &weights, Vector &F1, Vector &F2) const
 Evaluate derivatives giving the Constraint objects held within this object the entire Conformation (a whole structure, ws) with which to work. More...
 
void add_constraint (ConstraintCOP cst)
 
bool remove_constraint (ConstraintCOP cst, bool object_comparison)
 Returns true iff the constraint was successfully found and removed. More...
 
const_iterator begin () const
 
const_iterator end () const
 
void show (std::ostream &out)
 
void show_definition (std::ostream &out, pose::Pose const &pose) const
 
virtual Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, core::Real threshold=1)
 
Size size () const
 
void clear ()
 
ConstraintCOPs const & constraints () const
 

Private Member Functions

void energy (core::scoring::func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const
 
void copy_from (Constraints const &)
 
void deep_copy_from (Constraints const &)
 

Private Attributes

ConstraintCOPs constraints_
 

Member Typedef Documentation

typedef ConstraintCOPs::const_iterator core::scoring::constraints::Constraints::const_iterator

Constructor & Destructor Documentation

core::scoring::constraints::Constraints::~Constraints ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

core::scoring::constraints::Constraints::Constraints ( )

Default constructor creates an empy Constraints object.

Referenced by clone(), and deep_clone().

core::scoring::constraints::Constraints::Constraints ( Constraints const &  other)

Copy constructor copies all of the Constraint pointers so that two Poses may share the same constraints – this only works if constraints are immutable.

References copy_from().

Member Function Documentation

void core::scoring::constraints::Constraints::add_constraint ( ConstraintCOP  cst)
Constraints::const_iterator core::scoring::constraints::Constraints::begin ( ) const

References constraints_.

void core::scoring::constraints::Constraints::clear ( )
ConstraintsOP core::scoring::constraints::Constraints::clone ( ) const

Create a copy of this Constraints object using the shallow-copy-constructor.

References Constraints().

void core::scoring::constraints::Constraints::conformation_energy ( Conformation const &  conformation,
EnergyMap const &  weights,
EnergyMap emap 
) const
ConstraintCOPs const& core::scoring::constraints::Constraints::constraints ( ) const
inline

References constraints_.

void core::scoring::constraints::Constraints::copy_from ( Constraints const &  other)
private

References constraints_.

Referenced by Constraints(), and operator=().

ConstraintsOP core::scoring::constraints::Constraints::deep_clone ( ) const

Create a deep copy of this Constraints object, cloning all of the individual constraints.

References Constraints().

void core::scoring::constraints::Constraints::deep_copy_from ( Constraints const &  other)
private

References constraints_.

Constraints::const_iterator core::scoring::constraints::Constraints::end ( ) const

References constraints_.

void core::scoring::constraints::Constraints::energy ( core::scoring::func::XYZ_Func const &  xyz_func,
EnergyMap const &  weights,
EnergyMap emap 
) const
private

private does not zero the emap entries before accumulating

References constraints_.

Referenced by conformation_energy(), intra_residue_energy(), and residue_pair_energy().

void core::scoring::constraints::Constraints::eval_intrares_atom_derivative ( id::AtomID const &  atom_id,
conformation::Residue const &  residue,
EnergyMap const &  weights,
Vector F1,
Vector F2 
) const

Evaluate derivatives giving the Constraint objects held within this object a single residue. Warning: if this Constraints object contains Constraint objects that operate on other residues besides the one being given them, then this function will cause the program to exit.

References constraints_.

Referenced by core::scoring::constraints::ConstraintsEnergy::eval_intrares_derivatives().

void core::scoring::constraints::Constraints::eval_respair_atom_derivative ( id::AtomID const &  atom_id,
conformation::Residue const &  residue1,
conformation::Residue const &  residue2,
EnergyMap const &  weights,
Vector F1,
Vector F2 
) const

Evaluate derivatives giving the Constraint objects held within this object two residues. Warning: if this Constraints object contains Constraint objects that operate on other residues besides the two being given them, then this function will cause the program to exit.

References constraints_.

Referenced by core::scoring::constraints::ConstraintsEnergy::eval_residue_pair_derivatives().

void core::scoring::constraints::Constraints::eval_ws_atom_derivative ( id::AtomID const &  atom_id,
conformation::Conformation const &  conformation,
EnergyMap const &  weights,
Vector F1,
Vector F2 
) const

Evaluate derivatives giving the Constraint objects held within this object the entire Conformation (a whole structure, ws) with which to work.

References constraints_.

Referenced by core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative(), and core::scoring::constraints::ConstraintSet::eval_multibody_atom_derivative().

void core::scoring::constraints::Constraints::intra_residue_energy ( Residue const &  rsd,
EnergyMap const &  weights,
EnergyMap emap 
) const

will fail if Residue doesnt contain all the necessary atoms

will fail if Residues dont contain all the necessary atoms

References energy().

Referenced by core::scoring::constraints::ConstraintsEnergy::eval_intrares_energy_ext().

Constraints & core::scoring::constraints::Constraints::operator= ( Constraints const &  rhs)

Copy the contents of the rhs Constraints object into this Constraints object.

References copy_from().

bool core::scoring::constraints::Constraints::remove_constraint ( ConstraintCOP  cst,
bool  object_comparison 
)

Returns true iff the constraint was successfully found and removed.

If this list contains the same constraint multiple times, only one copy of it is removed. I can't imagine why that scenario would ever come up, but still... flo jan '11 added object_comparison bool that triggers removal of constraint if the actual constraints are identical, even though they're different objects

References constraints_.

Referenced by core::scoring::constraints::ConstraintSet::remove_constraint().

void core::scoring::constraints::Constraints::residue_pair_energy ( Residue const &  rsd1,
Residue const &  rsd2,
EnergyMap const &  weights,
EnergyMap emap 
) const
void core::scoring::constraints::Constraints::setup_for_derivatives ( core::scoring::func::XYZ_Func const &  xyz_func,
ScoreFunction const &  scfxn 
) const
void core::scoring::constraints::Constraints::setup_for_scoring ( core::scoring::func::XYZ_Func const &  xyz_func,
ScoreFunction const &  scfxn 
) const
void core::scoring::constraints::Constraints::show ( std::ostream &  out)
void core::scoring::constraints::Constraints::show_definition ( std::ostream &  out,
pose::Pose const &  pose 
) const
Size core::scoring::constraints::Constraints::show_violations ( std::ostream &  out,
pose::Pose const &  pose,
Size  verbose_level,
core::Real  threshold = 1 
)
virtual
Size core::scoring::constraints::Constraints::size ( ) const

Member Data Documentation

ConstraintCOPs core::scoring::constraints::Constraints::constraints_
private

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