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protocols::pockets::PocketConstraint Class Reference

This constraint favors creating a pocket suitable for a small-molecule. More...

#include <PocketConstraint.hh>

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Public Member Functions

virtual std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
 PocketConstraint ()
 
 PocketConstraint (core::pose::Pose const &pose)
 
 PocketConstraint (const PocketConstraint &old)
 
void init (core::pose::Pose const &pose)
 
core::Size target_res () const
 
virtual ~PocketConstraint ()
 
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 core::id::AtomID const & atom (core::Size const index) const
 Returns the AtomID referred to by index. More...
 
void show_def (std::ostream &out, core::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. More...
 
void read_def (std::istream &in, core::pose::Pose const &pose, core::scoring::constraints::FuncFactory const &func_factory)
 
virtual void score (core::scoring::constraints::XYZ_Func const &xyz_func, core::scoring::EnergyMap const &weights, core::scoring::EnergyMap &emap) 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 (core::id::AtomID const &, core::scoring::constraints::XYZ_Func const &, core::Vector &, core::Vector &, core::scoring::EnergyMap const &weights) 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...
 
virtual
core::scoring::constraints::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...
 
void set_target_res (core::pose::Pose const &pose, core::Size new_seqpos)
 
void set_target_res_pdb (core::pose::Pose const &pose, std::string resid)
 
- 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 (FuncOP) 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. 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 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 ConstraintOP remap_resid (core::id::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 core::Real dist (core::pose::Pose const &) const
 return the "raw" distance before handed to the FUNC object More...
 
virtual core::Real dist (XYZ_Func const &) const
 
virtual void setup_for_scoring (XYZ_Func const &, ScoreFunction const &) const
 
virtual void setup_for_derivatives (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 show (std::ostream &) 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...
 
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 Func const & get_func () const
 Returns the 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_
 
core::Size totalres_
 
core::Size angles_
 
core::Real weight_
 
protocols::pockets::PocketGridOP pocketgrid_
 
utility::vector1< AtomIDatom_ids_
 
bool dumppdb_
 
std::vector
< core::conformation::ResidueOP
residues_
 

Additional Inherited Members

- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 

Detailed Description

This constraint favors creating a pocket suitable for a small-molecule.

Constructor & Destructor Documentation

protocols::pockets::PocketConstraint::PocketConstraint ( )

Referenced by clone().

protocols::pockets::PocketConstraint::PocketConstraint ( core::pose::Pose const &  pose)
protocols::pockets::PocketConstraint::PocketConstraint ( const PocketConstraint old)

References dumppdb_, pocketgrid_, seqpos_, and totalres_.

protocols::pockets::PocketConstraint::~PocketConstraint ( )
virtual

Member Function Documentation

virtual core::id::AtomID const& protocols::pockets::PocketConstraint::atom ( core::Size const  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 atom_ids_.

core::scoring::constraints::ConstraintOP protocols::pockets::PocketConstraint::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.

References PocketConstraint().

void protocols::pockets::PocketConstraint::fill_f1_f2 ( core::id::AtomID const &  atom,
core::scoring::constraints::XYZ_Func const &  xyz_func,
core::Vector F1,
core::Vector F2,
core::scoring::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.

References core::scoring::constraints::Constraint::score_type(), and protocols::pockets::TR().

void protocols::pockets::PocketConstraint::init ( core::pose::Pose const &  pose)
virtual core::Size protocols::pockets::PocketConstraint::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.

References atom_ids_.

void protocols::pockets::PocketConstraint::read_def ( std::istream &  in,
core::pose::Pose const &  pose,
core::scoring::constraints::FuncFactory const &  func_factory 
)
virtual
void protocols::pockets::PocketConstraint::score ( core::scoring::constraints::XYZ_Func const &  xyz_func,
core::scoring::EnergyMap const &  weights,
core::scoring::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 angles_, dumppdb_, pocketgrid_, core::scoring::constraints::XYZ_Func::residue(), residues_, core::scoring::constraints::Constraint::score_type(), seqpos_, totalres_, and weight_.

void protocols::pockets::PocketConstraint::set_target_res ( core::pose::Pose const &  pose,
core::Size  new_seqpos 
)
void protocols::pockets::PocketConstraint::set_target_res_pdb ( core::pose::Pose const &  pose,
std::string  resid 
)
void protocols::pockets::PocketConstraint::show_def ( std::ostream &  ,
core::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.

core::Size protocols::pockets::PocketConstraint::target_res ( ) const
inline

References seqpos_.

virtual std::string protocols::pockets::PocketConstraint::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.

Member Data Documentation

core::Size protocols::pockets::PocketConstraint::angles_
private

Referenced by init(), and score().

utility::vector1< AtomID > protocols::pockets::PocketConstraint::atom_ids_
private

Referenced by atom(), and natoms().

bool protocols::pockets::PocketConstraint::dumppdb_
private

Referenced by init(), PocketConstraint(), and score().

protocols::pockets::PocketGridOP protocols::pockets::PocketConstraint::pocketgrid_
mutableprivate
std::vector< core::conformation::ResidueOP > protocols::pockets::PocketConstraint::residues_
private

Referenced by read_def(), and score().

core::Size protocols::pockets::PocketConstraint::seqpos_
private
core::Size protocols::pockets::PocketConstraint::totalres_
private

Referenced by init(), PocketConstraint(), and score().

core::Real protocols::pockets::PocketConstraint::weight_
private

Referenced by init(), read_def(), and score().


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