Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Attributes | List of all members
protocols::pockets::PocketConstraint Class Reference

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

#include <PocketConstraint.hh>

Inheritance diagram for protocols::pockets::PocketConstraint:
Inheritance graph
[legend]

Public Member Functions

std::string type () const override
 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
 
 ~PocketConstraint () override
 
core::Size natoms () const override
 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...
 
core::id::AtomID const & atom (core::Size const index) const override
 Returns the AtomID referred to by index. More...
 
void show_def (std::ostream &out, core::pose::Pose const &pose) const override
 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...
 
void read_def (std::istream &in, core::pose::Pose const &pose, core::scoring::func::FuncFactory const &func_factory) override
 Reads the definition of a Constraint from the given std::istream, 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. More...
 
void score (core::scoring::func::XYZ_Func const &xyz_func, core::scoring::EnergyMap const &weights, core::scoring::EnergyMap &emap) const override
 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...
 
core::Real dist (core::scoring::func::XYZ_Func const &) const override
 
void fill_f1_f2 (core::id::AtomID const &, core::scoring::func::XYZ_Func const &, core::Vector &, core::Vector &, core::scoring::EnergyMap const &weights) const override
 
core::scoring::constraints::ConstraintOP clone () const override
 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. This function must return a deep copy of itself – meaning that if this Constraint holds pointers to other Constraints that it must invoke clone on those Constraints as well. If the Constraint holds a FuncOP, then the Func should also be cloned. More...
 
bool operator== (core::scoring::constraints::Constraint const &other) const override
 Equality operator to test whether two constraints are functionally identical. More...
 
bool same_type_as_me (core::scoring::constraints::Constraint const &other) const override
 Determine if the calling class has the same type as the input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it. 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...
 
 ~Constraint () override
 Virtual destructor. More...
 
virtual ConstraintOP clone (func::FuncOP) const
 Clone the constraint, but where a new Func object is to be used instead. More...
 
virtual ConstraintOP remapped_clone (pose::Pose const &, pose::Pose const &, id::SequenceMappingCOP map) 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 DON'T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL. 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 Real score (pose::Pose const &pose) const
 Returns the unweighted score of this constraint computed over the given pose. More...
 
virtual Real score (pose::Pose const &pose, EnergyMap const &weights) const
 Returns the weighted score of this constraint computed over the given pose. More...
 
virtual Real dist (core::pose::Pose const &) const
 return the raw "distance" before that distance is handed to the FUNC object More...
 
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 void fill_f1_f2 (AtomID const &atom, core::scoring::func::XYZ_Func const &xyz_func, Vector &F1, Vector &F2, EnergyMap const &weights) const =0
 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 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 &)
 take coordinates, distances, angles, etc from given pose More...
 
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...
 
bool operator!= (Constraint const &other) const
 Inequality operator to test whether two constraints are not functionally identical. 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::ResidueCOP
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 ( )
overridedefault

Member Function Documentation

core::id::AtomID const& protocols::pockets::PocketConstraint::atom ( core::Size const  index) const
inlineoverridevirtual

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
overridevirtual

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. This function must return a deep copy of itself – meaning that if this Constraint holds pointers to other Constraints that it must invoke clone on those Constraints as well. If the Constraint holds a FuncOP, then the Func should also be cloned.

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

References PocketConstraint().

core::Real protocols::pockets::PocketConstraint::dist ( core::scoring::func::XYZ_Func const &  ) const
inlineoverridevirtual

PocketConstraints don't have a single distance

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

void protocols::pockets::PocketConstraint::fill_f1_f2 ( core::id::AtomID const &  ,
core::scoring::func::XYZ_Func const &  ,
core::Vector ,
core::Vector ,
core::scoring::EnergyMap const &  weights 
) const
override
void protocols::pockets::PocketConstraint::init ( core::pose::Pose const &  pose)
core::Size protocols::pockets::PocketConstraint::natoms ( ) const
inlineoverridevirtual

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_.

bool protocols::pockets::PocketConstraint::operator== ( core::scoring::constraints::Constraint const &  ) const
overridevirtual

Equality operator to test whether two constraints are functionally identical.

This operator should use floating point comparison and should not decide that two floats are identical if they are within some epsilon > 0. This method allows developes to remove specific constraints from Poses, even if the constraints have been cloned. Remapped constraints should not be considered identical – i.e., if cst1 is between residues i and j and cst2 is between residues i+1 and j+1. All subclasses of Constraint must implement this method.

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

References angles_, atom_ids_, dumppdb_, pocketgrid_, residues_, same_type_as_me(), core::scoring::constraints::Constraint::same_type_as_me(), seqpos_, totalres_, and weight_.

void protocols::pockets::PocketConstraint::read_def ( std::istream &  ,
core::pose::Pose const &  ,
core::scoring::func::FuncFactory const &   
)
overridevirtual

Reads the definition of a Constraint from the given std::istream, 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.

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

References protocols::pockets::PocketGrid::getRelaxResidues(), init(), pocketgrid_, residues_, and weight_.

bool protocols::pockets::PocketConstraint::same_type_as_me ( core::scoring::constraints::Constraint const &  other) const
overridevirtual

Determine if the calling class has the same type as the input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it.

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

Referenced by operator==().

void protocols::pockets::PocketConstraint::score ( core::scoring::func::XYZ_Func const &  xyz_func,
core::scoring::EnergyMap const &  weights,
core::scoring::EnergyMap emap 
) const
overridevirtual

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_, core::pack::interaction_graph::debug, dumppdb_, pocketgrid_, core::scoring::func::XYZ_Func::residue(), residues_, core::scoring::constraints::Constraint::score_type(), seqpos_, totalres_, protocols::pockets::TR(), 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
overridevirtual

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.

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

References seqpos_.

std::string protocols::pockets::PocketConstraint::type ( ) const
inlineoverridevirtual

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(), operator==(), and score().

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

Referenced by atom(), natoms(), and operator==().

bool protocols::pockets::PocketConstraint::dumppdb_
private
protocols::pockets::PocketGridOP protocols::pockets::PocketConstraint::pocketgrid_
mutableprivate
std::vector< core::conformation::ResidueCOP > protocols::pockets::PocketConstraint::residues_
private

Referenced by operator==(), read_def(), and score().

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

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


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