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).
| 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.
| virtual BALL::RotamerLibrary::~RotamerLibrary | ( | ) | [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.
Return the number of rotamers of the residue with the name.
| Size BALL::RotamerLibrary::getNumberOfRotamers | ( | ) | const |
Return total number of rotamers.
| 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, | |
| float | phi, | |||
| float | psi | |||
| ) |
Return the residue set of the given name and torsions.
| ResidueRotamerSet* BALL::RotamerLibrary::getRotamerSet | ( | const String & | name | ) |
Return the residue set of the residue name.
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)
bool BALL::RotamerLibrary::backbone_dependent_ [protected] |
flag which is true when the library has backbone dependent rotamers
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.
HashMap<String, ResidueRotamerSet> BALL::RotamerLibrary::bb_indep_sets_ [protected] |
Contains the available variants (name, rotamer set) in case of bb indep.
const String BALL::RotamerLibrary::DEFAULT_FRAGMENT_DB [static] |
Fragment DB used when calling the default constructor.
const String BALL::RotamerLibrary::DEFAULT_LIBRARY [static] |
Rotamer library used when calling the default constructor.
FragmentDB BALL::RotamerLibrary::fragment_db_ [protected] |
fragment db used in this class
Size BALL::RotamerLibrary::step_width_ [protected] |
discretization step width of the torsion angles