BALL 1.5.0
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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.
BALL::RotamerLibrary::RotamerLibrary | ( | ) |
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.
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virtual |
Destructor.
void BALL::RotamerLibrary::addRotamer | ( | const String & | name, |
const Rotamer & | rotamer, | ||
Size | number_of_torsions ) |
adds a rotamer with name
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::clear | ( | ) |
Clear rotamer library. Removes all rotamers and sets library to backbone independent.
Size BALL::RotamerLibrary::getNumberOfRotamers | ( | ) | const |
Return total number of rotamers.
Return the number of rotamers of the residue with the name.
Size BALL::RotamerLibrary::getNumberOfRotamerSets | ( | ) | const |
returns the number of rotamer sets
ResidueRotamerSet * BALL::RotamerLibrary::getRotamerSet | ( | const Residue & | residue | ) |
Return the residue set of the given residue.
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.
returns true if the library contains rotamers with this name
bool BALL::RotamerLibrary::isBackboneDependent | ( | ) | const |
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
bool BALL::RotamerLibrary::validate | ( | ) |
method to test the validity of this library, typically called after the building (see SCWRLLibraryFile)
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protected |
flag which is true when the library has backbone dependent rotamers
Definition at line 149 of file rotamerLibrary.h.
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protected |
Contains the available variants (phi, psi, name, rotamer set) in case of bb dep.
Definition at line 134 of file rotamerLibrary.h.
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protected |
Contains the available variants (name, rotamer set) in case of bb indep.
Definition at line 137 of file rotamerLibrary.h.
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static |
Fragment DB used when calling the default constructor.
Definition at line 47 of file rotamerLibrary.h.
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static |
Rotamer library used when calling the default constructor.
Definition at line 44 of file rotamerLibrary.h.
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protected |
fragment db used in this class
Definition at line 146 of file rotamerLibrary.h.
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protected |
discretization step width of the torsion angles
Definition at line 143 of file rotamerLibrary.h.