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protocols::frag_picker::scores::InterbondAngleScore Class Reference

Scores a fragment with a set of Dihedral constraints. More...

#include <InterbondAngleScore.hh>

Inheritance diagram for protocols::frag_picker::scores::InterbondAngleScore:
Inheritance graph
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Public Member Functions

 InterbondAngleScore (core::Size, core::Real, bool, std::string, core::Size, utility::vector1< std::string >)
 Prepare an atom-based score that utilizes some user-defined atoms. More...
 
 InterbondAngleScore (core::Size, core::Real, bool, std::string, core::Size)
 Prepare an atom-based score that utilizes the following predefined atoms: N, CA, C, O and CB. More...
 
bool cached_score (FragmentCandidateOP, FragmentScoreMapOP) override
 Calculates the score. More...
 
- Public Member Functions inherited from protocols::frag_picker::scores::AtomBasedConstraintsScore
 AtomBasedConstraintsScore (core::Size, core::Real, bool, core::Size, utility::vector1< std::string >, std::string)
 Prepare an atom-based score that utilizes some user-defined atoms. More...
 
 AtomBasedConstraintsScore (core::Size, core::Real, bool, core::Size, std::string)
 Prepare an atom-based score that utilizes the following predefined atoms: N, CA, C, O and CB. More...
 
void do_caching (VallChunkOP) override
 In this case caching means copying coordinates of relevant atoms from a chunk's pose. More...
 
void clean_up () override
 Erases the internal array of coordinates. More...
 
bool has_atom (core::Size residue_id, core::Size atom_id)
 Returns true if a given atom has been successfully cached and one can use its coordinates. More...
 
numeric::xyzVector< core::Realget_atom_coordinates (core::Size residue_id, core::Size atom_id)
 Returns coordinates for a given atom. More...
 
std::map< std::string, core::Sizeget_constrainable_atoms_map ()
 Returns a map that defines all constrained atoms used by this scoring method. More...
 
core::Size get_constrained_atom_id (std::string atom_name)
 returns an internal ID assigned to a given atom name More...
 
std::string get_constrained_atom_name (core::Size atom_id)
 returns a name of a constrained atom when its internal ID is known More...
 
core::Size get_query_size ()
 provides an access to the size of the length of a query sequence More...
 
- Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
 CachingScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)
 
bool score (FragmentCandidateOP, FragmentScoreMapOP) override
 
- Public Member Functions inherited from protocols::frag_picker::scores::FragmentScoringMethod
 FragmentScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)
 
std::string & get_score_name ()
 Returns a name of this scoring method. More...
 
core::Size get_id ()
 Returns an integer index assigned to this scoring method by a scoring manager. More...
 
void set_id (core::Size id)
 Sets a new integer index for this scoring method. More...
 
core::Size get_priority ()
 Returns a priority of this scoring method. More...
 
core::Real get_min_allowed_score ()
 Returns the lowest acceptable score value for this scoring method. More...
 
bool get_use_lowest ()
 Returns the boolean choice on using the above lowest acceptable score value. More...
 
void set_min_allowed_score (core::Real lowest_acceptable_value)
 Sets a new value of the lowest acceptable score. More...
 

Private Member Functions

void read_constraints (std::string)
 
core::Size get_atom_type (std::string atom_name)
 

Private Attributes

utility::vector1
< utility::vector1
< FourAtomsConstraintDataOP > > 
data_
 
core::scoring::func::FuncFactory factory_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
core::Size id_
 
core::Size priority_
 
std::string name_
 
core::Real lowest_acceptable_value_
 
bool use_lowest_
 

Detailed Description

Scores a fragment with a set of Dihedral constraints.

Constructor & Destructor Documentation

protocols::frag_picker::scores::InterbondAngleScore::InterbondAngleScore ( core::Size  priority,
core::Real  lowest_acceptable_value,
bool  use_lowest,
std::string  constraints_file_name,
core::Size  query_size,
utility::vector1< std::string >  constrainable_atoms 
)

Prepare an atom-based score that utilizes some user-defined atoms.

User may provide names of atoms that will be cached when a new chunk is considered (i.e. at every do_caching() call)

References core::scoring::func::FuncFactory::add_type(), data_, factory_, protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size(), and read_constraints().

protocols::frag_picker::scores::InterbondAngleScore::InterbondAngleScore ( core::Size  priority,
core::Real  lowest_acceptable_value,
bool  use_lowest,
std::string  constraints_file_name,
core::Size  query_size 
)

Prepare an atom-based score that utilizes the following predefined atoms: N, CA, C, O and CB.

These atoms that will be cached when a new chunk is considered (i.e. at every do_caching() call)

References core::scoring::func::FuncFactory::add_type(), data_, factory_, protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size(), and read_constraints().

Member Function Documentation

bool protocols::frag_picker::scores::InterbondAngleScore::cached_score ( FragmentCandidateOP  fragment,
FragmentScoreMapOP  scores 
)
overridevirtual
core::Size protocols::frag_picker::scores::InterbondAngleScore::get_atom_type ( std::string  atom_name)
private
void protocols::frag_picker::scores::InterbondAngleScore::read_constraints ( std::string  constraints_file_name)
private

Member Data Documentation

utility::vector1<utility::vector1<FourAtomsConstraintDataOP> > protocols::frag_picker::scores::InterbondAngleScore::data_
private
core::scoring::func::FuncFactory protocols::frag_picker::scores::InterbondAngleScore::factory_
private

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