Rosetta Core  2014.35
Public Types | Public Member Functions | Private Attributes | List of all members
core::scoring::constraints::SequenceProfileConstraint Class Reference

#include <SequenceProfileConstraint.hh>

Public Types

typedef
core::sequence::SequenceProfile 
SequenceProfile
 
typedef
core::sequence::SequenceProfileCOP 
SequenceProfileCOP
 
typedef core::id::SequenceMapping SequenceMapping
 
typedef core::pose::Pose Pose
 
typedef
core::conformation::Conformation 
Conformation
 
typedef core::scoring::EnergyMap EnergyMap
 
typedef
core::scoring::func::FuncFactory 
FuncFactory
 
typedef
core::scoring::func::XYZ_Func 
XYZ_Func
 
typedef
core::scoring::constraints::ConstraintOP 
ConstraintOP
 
- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 

Public Member Functions

 SequenceProfileConstraint ()
 
 SequenceProfileConstraint (Pose const &, core::Size, SequenceProfileCOP profile=NULL, core::id::SequenceMappingCOP mapping=NULL)
 
 SequenceProfileConstraint (core::Size, SequenceProfileCOP profile=NULL, core::id::SequenceMappingCOP mapping=NULL)
 
virtual ~SequenceProfileConstraint ()
 
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. More...
 
virtual std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
virtual void read_def (std::istream &, Pose const &, func::FuncFactory const &)
 used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file) More...
 
virtual void show_def (std::ostream &, Pose const &) const
 Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given func::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. More...
 
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. More...
 
core::Size seqpos () const
 
void seqpos (core::Size seqpos)
 
void set_sequence_profile (SequenceProfileCOP profile, core::id::SequenceMappingCOP mapping=NULL)
 
SequenceProfileCOP sequence_profile () const
 
core::id::SequenceMappingCOP profile_mapping () const
 
virtual core::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. More...
 
virtual AtomID const & atom (core::Size const ) const
 Returns the AtomID referred to by index. More...
 
virtual utility::vector1
< core::Size
residues () const
 Returns the pose numbers of the residues involved in this constraint, in no particular order. More...
 
virtual ConstraintOP remap_resid (SequenceMapping const &) 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. More...
 
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. More...
 
virtual void score (XYZ_Func const &, EnergyMap const &, EnergyMap &) 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. More...
 
virtual void fill_f1_f2 (AtomID const &, XYZ_Func const &, core::Vector &, core::Vector &, EnergyMap const &) const
 Fill the f1 and f2 vectors, necessary for considering the derivative this constraint during minimization. (someone please reference Bill Wedermeyer's paper here, as I'm in an airport and can't fill it in myself!) More...
 
void weight (core::Real const w)
 
core::Real weight () const
 
- Public Member Functions inherited from core::scoring::constraints::Constraint
 Constraint (ScoreType const &t)
 Constructor for Constraint class. More...
 
virtual ~Constraint ()
 Virtual destructor. More...
 
virtual ConstraintOP clone (core::scoring::func::FuncOP) const
 
virtual void read_constraint (std::istream &, core::pose::Pose const &)
 This method is totally redundant with read_def YAY. More...
 
ScoreType const & score_type () const
 Returns the ScoreType that this Constraint object will use. More...
 
virtual void read_data (std::istream &)
 initialize this Constraint from the given std::istream. It's amazing that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint, More...
 
virtual Real score (pose::Pose const &) const
 
virtual core::Real dist (core::pose::Pose const &) const
 return the "raw" distance before handed to the FUNC object More...
 
virtual core::Real dist (core::scoring::func::XYZ_Func const &) const
 
virtual void setup_for_scoring (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const
 
virtual void setup_for_derivatives (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const
 
virtual Real score (conformation::Conformation const &) 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. More...
 
virtual void steal_def (pose::Pose const &)
 
std::string to_string () const
 Convenience function, returns the results of show() as a string. Not to be overriden by derived classes. More...
 
virtual Size show_violations (std::ostream &out, pose::Pose const &, Size, 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 ... More...
 
virtual
core::scoring::func::Func
const & 
get_func () const
 Returns the func::Func object associated with this Constraint object. More...
 
virtual bool operator== (Constraint const &) const
 possibility to do object comparison instead of pointer comparison More...
 
bool operator!= (Constraint const &other) const
 possibility to do object comparison instead of pointer comparison More...
 
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
 

Private Attributes

core::Size seqpos_
 
SequenceProfileCOP sequence_profile_
 
core::id::SequenceMappingCOP mapping_
 A mapping of current pose numbers onto profile numbers. More...
 
core::Real weight_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::constraints::SequenceProfileConstraint::SequenceProfileConstraint ( )
core::scoring::constraints::SequenceProfileConstraint::SequenceProfileConstraint ( Pose const &  ,
core::Size  seqpos,
SequenceProfileCOP  profile = NULL,
core::id::SequenceMappingCOP  mapping = NULL 
)
core::scoring::constraints::SequenceProfileConstraint::SequenceProfileConstraint ( core::Size  seqpos,
SequenceProfileCOP  profile = NULL,
core::id::SequenceMappingCOP  mapping = NULL 
)
core::scoring::constraints::SequenceProfileConstraint::~SequenceProfileConstraint ( )
virtual

Member Function Documentation

virtual AtomID const& core::scoring::constraints::SequenceProfileConstraint::atom ( core::Size  index) const
inlinevirtual

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.

References core::id::BOGUS_ATOM_ID, and utility_exit_with_message.

ConstraintOP core::scoring::constraints::SequenceProfileConstraint::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.

void core::scoring::constraints::SequenceProfileConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz_func,
core::Vector F1,
core::Vector F2,
EnergyMap const &  weights 
) const
virtual

Fill the f1 and f2 vectors, necessary for considering the derivative this constraint during minimization. (someone please reference Bill Wedermeyer's paper here, as I'm in an airport and can't fill it in myself!)

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

virtual core::Size core::scoring::constraints::SequenceProfileConstraint::natoms ( ) const
inlinevirtual

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.

core::id::SequenceMappingCOP core::scoring::constraints::SequenceProfileConstraint::profile_mapping ( ) const

References mapping_.

void core::scoring::constraints::SequenceProfileConstraint::read_def ( std::istream &  is,
Pose const &  pose,
func::FuncFactory const &   
)
virtual

used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file)

one line definition "SequenceProfile resindex profilefilename" (profilefilename can also be set to "none" in the constraints file, and specified by -in::file::pssm)

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

References file_exists(), utility::pointer::owning_ptr< T >::get(), mapping_, option, seqpos_, sequence_profile_, t_debug, core::pose::Pose::total_residue(), core::scoring::constraints::TR, user, utility_exit, utility_exit_with_message, and version.

ConstraintOP core::scoring::constraints::SequenceProfileConstraint::remap_resid ( 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 mapping_, seqpos_, sequence_profile_, t_debug, and core::scoring::constraints::TR.

ConstraintOP core::scoring::constraints::SequenceProfileConstraint::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 mapping_, seqpos_, sequence_profile_, t_debug, and core::scoring::constraints::TR.

utility::vector1< core::Size > core::scoring::constraints::SequenceProfileConstraint::residues ( ) const
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.

References seqpos_.

void core::scoring::constraints::SequenceProfileConstraint::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 core::chemical::ResidueType::aa(), mapping_, profile, core::scoring::func::XYZ_Func::residue(), runtime_assert, core::scoring::constraints::Constraint::score_type(), seqpos_, sequence_profile_, t_trace, core::scoring::constraints::TR, core::conformation::Residue::type(), and weight().

core::Size core::scoring::constraints::SequenceProfileConstraint::seqpos ( ) const
inline

References seqpos_.

Referenced by seqpos().

void core::scoring::constraints::SequenceProfileConstraint::seqpos ( core::Size  seqpos)
inline

References seqpos(), and seqpos_.

SequenceProfileCOP core::scoring::constraints::SequenceProfileConstraint::sequence_profile ( ) const

References sequence_profile_.

void core::scoring::constraints::SequenceProfileConstraint::set_sequence_profile ( SequenceProfileCOP  profile,
core::id::SequenceMappingCOP  mapping = NULL 
)

References mapping_, and sequence_profile_.

void core::scoring::constraints::SequenceProfileConstraint::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 mapping_, seqpos_, sequence_profile_, and core::io::serialization::size().

Referenced by show_def().

void core::scoring::constraints::SequenceProfileConstraint::show_def ( std::ostream &  ,
Pose const &   
) const
virtual

Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given func::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 show().

virtual std::string core::scoring::constraints::SequenceProfileConstraint::type ( ) const
inlinevirtual

Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.

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

void core::scoring::constraints::SequenceProfileConstraint::weight ( core::Real const  w)

References weight_.

core::Real core::scoring::constraints::SequenceProfileConstraint::weight ( ) const

References weight_.

Referenced by score().

Member Data Documentation

core::id::SequenceMappingCOP core::scoring::constraints::SequenceProfileConstraint::mapping_
private

A mapping of current pose numbers onto profile numbers.

Referenced by profile_mapping(), read_def(), remap_resid(), remapped_clone(), score(), set_sequence_profile(), and show().

core::Size core::scoring::constraints::SequenceProfileConstraint::seqpos_
private
SequenceProfileCOP core::scoring::constraints::SequenceProfileConstraint::sequence_profile_
private
core::Real core::scoring::constraints::SequenceProfileConstraint::weight_
private

Referenced by weight().


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