Rosetta 3.4
Public Member Functions | Protected Attributes
core::scoring::constraints::MultiConstraint Class Reference

#include <MultiConstraint.hh>

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List of all members.

Public Member Functions

 MultiConstraint (ScoreType const &t=dof_constraint)
 default Constructor
 MultiConstraint (const ConstraintCOPs &cst_in, ScoreType const &t=dof_constraint)
 Constructor.
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 MultiConstraintOP empty_clone () const
Size natoms () const
 number of atoms involved in this MultiConstraint container
Size size () const
 number of constraints data
virtual std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
virtual void read_def (std::istream &data, pose::Pose const &pose, FuncFactory const &func_factory)
 read in constraint defiinition
virtual bool operator== (Constraint const &other) const
 possibility to compare constraint according to data and not just pointers
virtual void score (XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const
 compute score
virtual AtomID const & atom (Size const n) const
 Returns the AtomID referred to by index.
virtual utility::vector1
< core::Size
residues () const
 Returns the pose numbers of the residues involved in this constraint, in no particular order.
virtual void setup_for_scoring (XYZ_Func const &, ScoreFunction const &) const
virtual void add_individual_constraint (ConstraintCOP cst_in)
 add individual constraint into MultiConstraint
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.
virtual void fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
 compute atom deriv
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.
virtual 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 Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1.0) 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 ...
ConstraintCOPs const & member_constraints () const
virtual ConstraintOP remapped_clone (pose::Pose const &, pose::Pose const &, 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 set_effective_sequence_separation (core::Size setting)
virtual core::Size choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, numeric::random::RandomGenerator &)
virtual core::Size effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &) const

Protected Attributes

ConstraintCOPs member_constraints_

Constructor & Destructor Documentation

core::scoring::constraints::MultiConstraint::MultiConstraint ( ScoreType const &  t = dof_constraint) [inline]

default Constructor

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

core::scoring::constraints::MultiConstraint::MultiConstraint ( const ConstraintCOPs cst_in,
ScoreType const &  t = dof_constraint 
)

Constructor.

References add_individual_constraint().


Member Function Documentation

void core::scoring::constraints::MultiConstraint::add_individual_constraint ( ConstraintCOP  cst_in) [virtual]
virtual AtomID const& core::scoring::constraints::MultiConstraint::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.

core::Size core::scoring::constraints::MultiConstraint::choose_effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const &  sp,
numeric::random::RandomGenerator &  RG 
) [virtual]
virtual ConstraintOP core::scoring::constraints::MultiConstraint::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.

Reimplemented in core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::SiteConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

References member_constraints_, and MultiConstraint().

virtual core::Size core::scoring::constraints::MultiConstraint::effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const &  ) const [inline, virtual]
virtual MultiConstraintOP core::scoring::constraints::MultiConstraint::empty_clone ( ) const [inline, virtual]
void core::scoring::constraints::MultiConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const [virtual]

compute atom deriv

function that figures out what constraints this atom is part of and calculates the derivative for those

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

Reimplemented in core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::KofNConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

ConstraintCOPs const& core::scoring::constraints::MultiConstraint::member_constraints ( ) const [inline]
Size core::scoring::constraints::MultiConstraint::natoms ( ) const [inline, virtual]

number of atoms involved in this MultiConstraint container

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

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

possibility to compare constraint according to data and not just pointers

this function only checks whether the member_constraints_ are identical. should mean by inference that the member_residues_, member_atoms_ and AtomID_to_Csts_ are also identical

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

Reimplemented in core::scoring::constraints::AmbiguousConstraint.

References member_constraints_, and core::scoring::constraints::Constraint::score_type().

void core::scoring::constraints::MultiConstraint::read_def ( std::istream &  data,
pose::Pose const &  pose,
FuncFactory const &  func_factory 
) [virtual]
ConstraintOP core::scoring::constraints::MultiConstraint::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.

Reimplemented in core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::KofNConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

References member_constraints_, and MultiConstraint().

ConstraintOP core::scoring::constraints::MultiConstraint::remapped_clone ( pose::Pose const &  ,
pose::Pose const &  ,
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 empty_clone(), and member_constraints_.

virtual utility::vector1< core::Size > core::scoring::constraints::MultiConstraint::residues ( ) const [inline, virtual]

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

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

void core::scoring::constraints::MultiConstraint::score ( XYZ_Func const &  xyz_func,
EnergyMap const &  weights,
EnergyMap emap 
) const [virtual]
void core::scoring::constraints::MultiConstraint::set_effective_sequence_separation ( core::Size  setting) [inline]
void core::scoring::constraints::MultiConstraint::setup_for_scoring ( XYZ_Func const &  xyz,
ScoreFunction const &  scfxn 
) const [virtual]
void core::scoring::constraints::MultiConstraint::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.

Reimplemented in core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::SiteConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

References member_constraints_.

void core::scoring::constraints::MultiConstraint::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.

Reimplemented in core::scoring::constraints::AmbiguousNMRConstraint.

References make_table_of_pilot_apps::begin, member_constraints(), and type().

Referenced by read_def().

Size core::scoring::constraints::MultiConstraint::show_violations ( std::ostream &  out,
pose::Pose const &  ,
Size  ,
Real  threshold = 1.0 
) 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.

Reimplemented in core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::KofNConstraint, and protocols::constraints_additional::AmbiguousMultiConstraint.

References member_constraints_.

Size core::scoring::constraints::MultiConstraint::size ( ) const [inline]
virtual std::string core::scoring::constraints::MultiConstraint::type ( ) const [inline, virtual]

Member Data Documentation


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