Rosetta 3.4
Public Member Functions
protocols::frag_picker::scores::AtomBasedConstraintsScore Class Reference

A base class for all scoring methods that need atom coordinates. More...

#include <AtomBasedConstraintsScore.hh>

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List of all members.

Public Member Functions

 AtomBasedConstraintsScore (Size, Real, bool, Size, utility::vector1< std::string >, std::string)
 Prepare an atom-based score that utilizes some user-defined atoms.
 AtomBasedConstraintsScore (Size, Real, bool, Size, std::string)
 Prepare an atom-based score that utilizes the following predefined atoms: N, CA, C, O and CB.
void do_caching (VallChunkOP)
 In this case caching means copying coordinates of relevant atoms from a chunk's pose.
void clean_up ()
 Erases the internal array of coordinates.
bool has_atom (Size residue_id, Size atom_id)
 Returns true if a given atom has been successfully cached and one can use its coordinates.
numeric::xyzVector< Realget_atom_coordinates (Size residue_id, Size atom_id)
 Returns coordinates for a given atom.
std::map< std::string, Sizeget_constrainable_atoms_map ()
 Returns a map that defines all constrained atoms used by this scoring method.
Size get_constrained_atom_id (std::string atom_name)
 returns an internal ID assigned to a given atom name
std::string get_constrained_atom_name (Size atom_id)
 returns a name of a constrained atom when its internal ID is known
Size get_query_size ()
 provides an access to the size of the length of a query sequence

Detailed Description

A base class for all scoring methods that need atom coordinates.

Detailed: The base class provides an access to atom coordinates from the current chunk
It takes care of caching proper atoms from the pose for fast access.

Constructor & Destructor Documentation

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

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

Detailed: User may provide names of atoms that will be cached when a new
chunk is considered (i.e. at every do_caching() call)
Parameters:
priority- the priority for this scoring method. The lower the priority, the later the score will be evaluated Because a fragment may be discarded when a score is too low, the most accurate and meaningful scores should have the highest priority
lowest_acceptable_value- a fragment for which this score is below a certain threshold will be discarded
query_size- the number of residues in the query sequence
constrainable_atoms- a vector of strings providing names of constrained atoms. On every do_cahing() event these and only these atoms will be cached from a chunk's pose
score_name- name assigned to this scoring term; this string must show up in scores config file if the score is to be evaluated during picking
protocols::frag_picker::scores::AtomBasedConstraintsScore::AtomBasedConstraintsScore ( Size  priority,
Real  lowest_acceptable_value,
bool  use_lowest,
Size  query_size,
std::string  score_name 
)

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

Detailed: These atoms that will be cached when a new
chunk is considered (i.e. at every do_caching() call)
Parameters:
priority- the priority for this scoring method. The lower the priority, the later the score will be evaluated Because a fragment may be discarded when a score is too low, the most accurate and meaningful scores should have the highest priority
lowest_acceptable_value- a fragment for which this score is below a certain threshold will be discarded
query_size- the number of residues in the query sequence
score_name- name assigned to this scoring term; this string must show up in scores config file if the score is to be evaluated during picking

Member Function Documentation

void protocols::frag_picker::scores::AtomBasedConstraintsScore::clean_up ( ) [virtual]
void protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching ( VallChunkOP  chunk) [virtual]
numeric::xyzVector<Real> protocols::frag_picker::scores::AtomBasedConstraintsScore::get_atom_coordinates ( Size  residue_id,
Size  atom_id 
) [inline]

Returns coordinates for a given atom.

Parameters:
residue_idthe residue order number. The first is 1, the last one depends on the size of a pose i.e. the size of the current chunk
atom_idthe residue order number, the first is 1

Referenced by protocols::frag_picker::scores::InterbondAngleScore::cached_score(), protocols::frag_picker::scores::DihedralConstraintsScore::cached_score(), and protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score().

std::map<std::string, Size> protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrainable_atoms_map ( ) [inline]

Returns a map that defines all constrained atoms used by this scoring method.

Detailed: Returned map defines the order of atoms as they are stored inside this object.
Indexes defined y this map can be used as arguments for has_atom() and get_atom_coordinates() methods.
Size protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_id ( std::string  atom_name) [inline]

returns an internal ID assigned to a given atom name

Detailed: this ID remains the same for all residues
std::string protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_name ( Size  atom_id)

returns a name of a constrained atom when its internal ID is known

Detailed: this is the oposite to get_constrained_atom_id(std::string)
Size protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size ( ) [inline]
bool protocols::frag_picker::scores::AtomBasedConstraintsScore::has_atom ( Size  residue_id,
Size  atom_id 
) [inline]

Returns true if a given atom has been successfully cached and one can use its coordinates.

Parameters:
residue_idthe residue order number. The first is 1, the last one depends on the size of a pose i.e. the size of the current chunk
atom_idthe residue order number, the first is 1

Referenced by protocols::frag_picker::scores::InterbondAngleScore::cached_score(), protocols::frag_picker::scores::DihedralConstraintsScore::cached_score(), and protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score().


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