BALL  1.4.1
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BALL::RotamerLibrary Class Reference

Rotamer Library Class. More...

#include <BALL/STRUCTURE/rotamerLibrary.h>

List of all members.

Public Member Functions

Constructors and Destructors
 RotamerLibrary ()
 RotamerLibrary (const String &filename, const FragmentDB &fragment_db)
 Detailed constructor, provided for convenience.
 RotamerLibrary (const FragmentDB &fragment_db)
 Detailed constructor.
 RotamerLibrary (const RotamerLibrary &library)
 Copy constructor.
virtual ~RotamerLibrary ()
 Destructor.
Assignment
RotamerLibraryoperator= (const RotamerLibrary &rhs)
 Assignment operator.
Accessors
ResidueRotamerSetgetRotamerSet (const String &name)
 Return the residue set of the residue name.
ResidueRotamerSetgetRotamerSet (const String &name, float phi, float psi)
 Return the residue set of the given name and torsions.
ResidueRotamerSetgetRotamerSet (const Residue &residue)
 Return the residue set of the given residue.
Size getNumberOfRotamers () const
 Return total number of rotamers.
Size getNumberOfRotamers (const String &name) const
 Return the number of rotamers of the residue with the name.
Size getNumberOfRotamerSets () const
 returns the number of rotamer sets
void addRotamer (const String &name, const Rotamer &rotamer, Size number_of_torsions, Index phi, Index psi)
 adds rotamer with specific phi/psi backbone torsion
void addRotamer (const String &name, const Rotamer &rotamer, Size number_of_torsions)
 adds a rotamer with name
bool isBackboneDependent () const
 returns true if the rotamers are backbone dependent
void setBackboneDependent (bool dependent)
 sets whether the rotamers are backbone dependent or not
bool hasRotamers (const String &name) const
 returns true if the library contains rotamers with this name
bool validate ()
 method to test the validity of this library, typically called after the building (see SCWRLLibraryFile)
void sort ()
 method to sort the Rotamers of each ResidueRotamerSet descendingly according to the probability
void clear ()

Static Public Attributes

String constants
static const String DEFAULT_LIBRARY
 Rotamer library used when calling the default constructor.
static const String DEFAULT_FRAGMENT_DB
 Fragment DB used when calling the default constructor.

Protected Attributes

HashMap< Index, HashMap< Index,
HashMap< String,
ResidueRotamerSet > > > 
bb_dep_sets_
 Contains the available variants (phi, psi, name, rotamer set) in case of bb dep.
HashMap< String,
ResidueRotamerSet
bb_indep_sets_
 Contains the available variants (name, rotamer set) in case of bb indep.
Size step_width_
 discretization step width of the torsion angles
FragmentDB fragment_db_
 fragment db used in this class
bool backbone_dependent_
 flag which is true when the library has backbone dependent rotamers
Index getNearestBackboneTorsion_ (double angle) const

Detailed Description

Rotamer Library Class.

A rotamer library contains a list of possible rotamers for each of the 18 amino acid side chains (GLY and ALA do not have rotamers).

Definition at line 33 of file rotamerLibrary.h.


Constructor & Destructor Documentation

Default constructor. Uses rotamer library RotamerLibrary::DEFAULT_LIBRARY and fragment db RotamerLibrary::DEFAULT_FRAGMENT_DB.

BALL::RotamerLibrary::RotamerLibrary ( const String filename,
const FragmentDB fragment_db 
)

Detailed constructor, provided for convenience.

Detailed constructor.

Copy constructor.

Destructor.


Member Function Documentation

void BALL::RotamerLibrary::addRotamer ( const String name,
const Rotamer rotamer,
Size  number_of_torsions,
Index  phi,
Index  psi 
)

adds rotamer with specific phi/psi backbone torsion

void BALL::RotamerLibrary::addRotamer ( const String name,
const Rotamer rotamer,
Size  number_of_torsions 
)

adds a rotamer with name

Clear rotamer library. Removes all rotamers and sets library to backbone independent.

Return total number of rotamers.

Return the number of rotamers of the residue with the name.

returns the number of rotamer sets

Return the residue set of the residue name.

Return the residue set of the given name and torsions.

Return the residue set of the given residue.

returns true if the library contains rotamers with this name

returns true if the rotamers are backbone dependent

RotamerLibrary& BALL::RotamerLibrary::operator= ( const RotamerLibrary rhs)

Assignment operator.

sets whether the rotamers are backbone dependent or not

method to sort the Rotamers of each ResidueRotamerSet descendingly according to the probability

method to test the validity of this library, typically called after the building (see SCWRLLibraryFile)


Member Data Documentation

flag which is true when the library has backbone dependent rotamers

Definition at line 149 of file rotamerLibrary.h.

Contains the available variants (phi, psi, name, rotamer set) in case of bb dep.

Definition at line 134 of file rotamerLibrary.h.

Contains the available variants (name, rotamer set) in case of bb indep.

Definition at line 137 of file rotamerLibrary.h.

Fragment DB used when calling the default constructor.

Definition at line 47 of file rotamerLibrary.h.

Rotamer library used when calling the default constructor.

Definition at line 44 of file rotamerLibrary.h.

fragment db used in this class

Definition at line 146 of file rotamerLibrary.h.

discretization step width of the torsion angles

Definition at line 143 of file rotamerLibrary.h.

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