BALL
1.4.1
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Rotamer Library Class. More...
#include <BALL/STRUCTURE/rotamerLibrary.h>
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 | |
RotamerLibrary & | operator= (const RotamerLibrary &rhs) |
Assignment operator. | |
Accessors | |
ResidueRotamerSet * | getRotamerSet (const String &name) |
Return the residue set of the residue name. | |
ResidueRotamerSet * | getRotamerSet (const String &name, float phi, float psi) |
Return the residue set of the given name and torsions. | |
ResidueRotamerSet * | getRotamerSet (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 |
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.
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.
BALL::RotamerLibrary::RotamerLibrary | ( | const FragmentDB & | fragment_db | ) |
Detailed constructor.
BALL::RotamerLibrary::RotamerLibrary | ( | const RotamerLibrary & | library | ) |
Copy constructor.
virtual BALL::RotamerLibrary::~RotamerLibrary | ( | ) | [virtual] |
Destructor.
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
void BALL::RotamerLibrary::clear | ( | ) |
Clear rotamer library. Removes all rotamers and sets library to backbone independent.
Index BALL::RotamerLibrary::getNearestBackboneTorsion_ | ( | double | angle | ) | const [protected] |
Return total number of rotamers.
Size BALL::RotamerLibrary::getNumberOfRotamers | ( | const String & | name | ) | const |
Return the number of rotamers of the residue with the name.
returns the number of rotamer sets
ResidueRotamerSet* BALL::RotamerLibrary::getRotamerSet | ( | const String & | name | ) |
Return the residue set of the residue name.
ResidueRotamerSet* BALL::RotamerLibrary::getRotamerSet | ( | const String & | name, |
float | phi, | ||
float | psi | ||
) |
Return the residue set of the given name and torsions.
ResidueRotamerSet* BALL::RotamerLibrary::getRotamerSet | ( | const Residue & | residue | ) |
Return the residue set of the given residue.
bool BALL::RotamerLibrary::hasRotamers | ( | const String & | name | ) | const |
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.
void BALL::RotamerLibrary::setBackboneDependent | ( | bool | dependent | ) |
sets whether the rotamers are backbone dependent or not
void BALL::RotamerLibrary::sort | ( | ) |
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)
bool BALL::RotamerLibrary::backbone_dependent_ [protected] |
flag which is true when the library has backbone dependent rotamers
Definition at line 149 of file rotamerLibrary.h.
HashMap<Index, HashMap<Index, HashMap<String, ResidueRotamerSet> > > BALL::RotamerLibrary::bb_dep_sets_ [protected] |
Contains the available variants (phi, psi, name, rotamer set) in case of bb dep.
Definition at line 134 of file rotamerLibrary.h.
HashMap<String, ResidueRotamerSet> BALL::RotamerLibrary::bb_indep_sets_ [protected] |
Contains the available variants (name, rotamer set) in case of bb indep.
Definition at line 137 of file rotamerLibrary.h.
const String BALL::RotamerLibrary::DEFAULT_FRAGMENT_DB [static] |
Fragment DB used when calling the default constructor.
Definition at line 47 of file rotamerLibrary.h.
const String BALL::RotamerLibrary::DEFAULT_LIBRARY [static] |
Rotamer library used when calling the default constructor.
Definition at line 44 of file rotamerLibrary.h.
FragmentDB BALL::RotamerLibrary::fragment_db_ [protected] |
fragment db used in this class
Definition at line 146 of file rotamerLibrary.h.
Size BALL::RotamerLibrary::step_width_ [protected] |
discretization step width of the torsion angles
Definition at line 143 of file rotamerLibrary.h.