Rosetta 3.4
Public Member Functions | Static Public Member Functions
core::scoring::constraints::AngleConstraint Class Reference

An Angular Constraint. More...

#include <AngleConstraint.hh>

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List of all members.

Public Member Functions

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.
void read_def (std::istream &data, pose::Pose const &pose, FuncFactory const &func_factory)
 read in constraint defiinition
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.
bool operator== (Constraint const &other) const
 possibility to compare constraint according to data and not just pointers
Real score (Vector const &xyz1, Vector const &xyz2, Vector const &xyz3) const
 compute score
void score (XYZ_Func const &xyz, EnergyMap const &, EnergyMap &emap) const
 compute score
void fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
 compute atom deriv
 AngleConstraint (AtomID const &a1, AtomID const &a2, AtomID const &a3, FuncOP func_in, ScoreType scotype=angle_constraint)
 Constructor.
 AngleConstraint (FuncOP func_in, ScoreType scoretype=angle_constraint)
 Constructor without atom IDs -- if you create an AngleConstraint with this constructor, you must never call its score( XYZFunc ) method! Dangerous and stupid!
Size natoms () const
 number of atoms --- always 3 for angles
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
 return AtomID for atom 1,2,3
Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, core::Real threshold=1) const
 output violation of constraint to out - returns 1 if violated ( i.e., func.show_violations() > 0 )
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.
Real func (Real const theta) const
 evaluate func at theta
Real dfunc (Real const theta) const
 evaluate dfunc at theta
void p1_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &F1, Vector &F2) const
void p2_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &F1, Vector &F2) const

Static Public Member Functions

static void p1_theta_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &f1, Vector &f2)
static void helper (Vector const &M, Vector const &w, Vector &F1, Vector &F2)

Detailed Description

An Angular Constraint.


Constructor & Destructor Documentation

core::scoring::constraints::AngleConstraint::AngleConstraint ( AtomID const &  a1,
AtomID const &  a2,
AtomID const &  a3,
FuncOP  func_in,
ScoreType  scotype = angle_constraint 
) [inline]

Constructor.

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

core::scoring::constraints::AngleConstraint::AngleConstraint ( FuncOP  func_in,
ScoreType  scoretype = angle_constraint 
) [inline]

Constructor without atom IDs -- if you create an AngleConstraint with this constructor, you must never call its score( XYZFunc ) method! Dangerous and stupid!


Member Function Documentation

id::AtomID const & core::scoring::constraints::AngleConstraint::atom ( Size const  n) const [virtual]

return AtomID for atom 1,2,3

Implements core::scoring::constraints::Constraint.

Referenced by remapped_clone(), show(), and show_def().

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

Real core::scoring::constraints::AngleConstraint::dfunc ( Real const  theta) const [inline]

evaluate dfunc at theta

Referenced by fill_f1_f2(), p1_deriv(), and p2_deriv().

void core::scoring::constraints::AngleConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const
Real core::scoring::constraints::AngleConstraint::func ( Real const  theta) const [inline]

evaluate func at theta

Previously private member functions made public so that in the absence of atom_ids, these functions could still be called externally.

Referenced by score().

void core::scoring::constraints::AngleConstraint::helper ( Vector const &  M,
Vector const &  w,
Vector F1,
Vector F2 
) [static]

Referenced by p1_theta_deriv().

Size core::scoring::constraints::AngleConstraint::natoms ( ) const [inline, virtual]

number of atoms --- always 3 for angles

Implements core::scoring::constraints::Constraint.

Referenced by show(), and show_def().

bool core::scoring::constraints::AngleConstraint::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::AngleConstraint::p1_deriv ( Vector const &  p1,
Vector const &  p2,
Vector const &  p3,
Vector F1,
Vector F2 
) const
void core::scoring::constraints::AngleConstraint::p1_theta_deriv ( Vector const &  p1,
Vector const &  p2,
Vector const &  p3,
Vector f1,
Vector f2 
) [static]

References make_table_of_pilot_apps::f, and helper().

Referenced by p1_deriv(), and p2_deriv().

void core::scoring::constraints::AngleConstraint::p2_deriv ( Vector const &  p1,
Vector const &  p2,
Vector const &  p3,
Vector F1,
Vector F2 
) const
void core::scoring::constraints::AngleConstraint::read_def ( std::istream &  data,
pose::Pose const &  pose,
FuncFactory const &  func_factory 
) [virtual]

read in constraint defiinition

one line definition "Angle atom1 res1 atom2 res2 atom3 res3 function_type function_definition" SML: It appears to be reading the angle in radians, because score ultimately uses std:acos, which returns radians.

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

References core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::scoring::constraints::FuncFactory::new_func(), core::scoring::constraints::ConstraintIO::parse_residue(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::constraints::TRACER(), and type().

ConstraintOP core::scoring::constraints::AngleConstraint::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 AngleConstraint(), core::id::AtomID::atomno(), and core::id::AtomID::rsd().

ConstraintOP core::scoring::constraints::AngleConstraint::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 AngleConstraint(), atom(), core::conformation::atom_id_to_named_atom_id(), 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::AngleConstraint::score ( XYZ_Func const &  xyz,
EnergyMap const &  ,
EnergyMap emap 
) const [virtual]
Real core::scoring::constraints::AngleConstraint::score ( Vector const &  xyz1,
Vector const &  xyz2,
Vector const &  xyz3 
) const

compute score

References func().

Referenced by score().

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

output violation of constraint to out - returns 1 if violated ( i.e., func.show_violations() > 0 )

show violations of angular constraint. Control verbosity level between 1 .. 100 >80 : write MET 4 CA otherwise: compute angle and call func_->show_violations

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::AngleConstraint::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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