Rosetta 3.4
Public Types | Public Member Functions
core::scoring::constraints::SequenceProfileConstraint Class Reference

#include <SequenceProfileConstraint.hh>

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List of all members.

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::constraints::FuncFactory 
FuncFactory
typedef
core::scoring::constraints::XYZ_Func 
XYZ_Func
typedef
core::scoring::constraints::ConstraintOP 
ConstraintOP

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.
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 &, Pose const &, FuncFactory const &)
 used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file)
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 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 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.
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.
virtual AtomID const & atom (core::Size const ) 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 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.
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.
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.
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!)

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::constraints::SequenceProfileConstraint::SequenceProfileConstraint ( )
core::scoring::constraints::SequenceProfileConstraint::SequenceProfileConstraint ( Pose const &  pose,
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 [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.

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.

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

References SequenceProfileConstraint().

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.

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

virtual core::Size core::scoring::constraints::SequenceProfileConstraint::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.

core::id::SequenceMappingCOP core::scoring::constraints::SequenceProfileConstraint::profile_mapping ( ) const
void core::scoring::constraints::SequenceProfileConstraint::read_def ( std::istream &  is,
Pose const &  pose,
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.

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

References protocols::swa::rna::file_exists(), core::pose::Pose::total_residue(), and core::scoring::constraints::TR().

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 SequenceProfileConstraint(), 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 SequenceProfileConstraint(), 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.

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.

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

References core::chemical::ResidueType::aa(), core::scoring::constraints::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), core::scoring::constraints::TR(), and core::conformation::Residue::type().

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

References seqpos().

core::Size core::scoring::constraints::SequenceProfileConstraint::seqpos ( ) const [inline]
SequenceProfileCOP core::scoring::constraints::SequenceProfileConstraint::sequence_profile ( ) const
void core::scoring::constraints::SequenceProfileConstraint::set_sequence_profile ( SequenceProfileCOP  profile,
core::id::SequenceMappingCOP  mapping = NULL 
)
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.

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

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 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 [inline, virtual]

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

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.


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