ell::RNAFreeEnergy_TB Class Reference
#include <RNAFreeEnergy_TB.hh>
Detailed Description
This subclass of RNAStructure implements the free energy as the underlying energy function with the constant alphabet ACGU and the constant valid RNA base pairs AU, CG and GU (and their reverse).
Definition at line 19 of file RNAFreeEnergy_TB.hh.
Public Types | |
| typedef std::pair< size_t, size_t > | SingleMove |
Public Member Functions | |
| void | applySingleMoveInPlace (const SingleMove &move) |
| virtual double | getEnergy (void) const |
| bool | isValidSingleMove (const SingleMove &move) const |
| RNAFreeEnergy_TB & | operator= (const RNAFreeEnergy_TB &rnaStruct2) |
| RNAFreeEnergy_TB (const RNAFreeEnergy_TB &rnaFreeEnerg) | |
| RNAFreeEnergy_TB (biu::Sequence *rnaSeq, const biu::Structure *const rnaStructBracketDot, const bool seqIsShared=false, const double energy=ENERGY_INF) | |
| RNAFreeEnergy_TB (const std::string &rnaSeqStr, const std::string &rnaStructBracketDotStr, const double energy=ENERGY_INF) | |
| virtual void | setEnergy (const double energy) |
| virtual void | setStructure (const biu::Structure &str) |
| virtual | ~RNAFreeEnergy_TB () |
Static Public Member Functions | |
| static const biu::Alphabet * | getSequenceAlphabet () |
Static Public Attributes | |
| static bool | calculateEnergyChanges |
Protected Member Functions | |
| virtual void | moleculeChanged () |
| virtual void | updateSeqVienna () |
Static Protected Member Functions | |
| static void | setViennaFoldParams (void) |
Protected Attributes | |
| double | energy |
| short * | pairTable |
| short * | seqVienna |
Static Protected Attributes | |
| static const biu::Alphabet | COMMON_ALPHABET |
| static const biu::AllowedBasePairs | COMMON_BPAIRS |
| static const double | ENERGY_INF |
| static bool | ViennaFoldParamsSet |
Member Typedef Documentation
| typedef std::pair<size_t, size_t> ell::RNAFreeEnergy_TB::SingleMove |
A single move (open or close one bond) on a RNA structure at positions SingleMove.first and SingleMove.second.
Definition at line 51 of file RNAFreeEnergy_TB.hh.
Constructor & Destructor Documentation
| ell::RNAFreeEnergy_TB::RNAFreeEnergy_TB | ( | const std::string & | rnaSeqStr, | |
| const std::string & | rnaStructBracketDotStr, | |||
| const double | energy = ENERGY_INF | |||
| ) |
Definition at line 42 of file RNAFreeEnergy_TB.cc.
| ell::RNAFreeEnergy_TB::RNAFreeEnergy_TB | ( | biu::Sequence * | rnaSeq, | |
| const biu::Structure *const | rnaStructBracketDot, | |||
| const bool | seqIsShared = false, |
|||
| const double | energy = ENERGY_INF | |||
| ) |
Definition at line 60 of file RNAFreeEnergy_TB.cc.
| ell::RNAFreeEnergy_TB::RNAFreeEnergy_TB | ( | const RNAFreeEnergy_TB & | rnaFreeEnerg | ) |
Definition at line 79 of file RNAFreeEnergy_TB.cc.
| ell::RNAFreeEnergy_TB::~RNAFreeEnergy_TB | ( | ) | [virtual] |
Definition at line 87 of file RNAFreeEnergy_TB.cc.
Member Function Documentation
| void ell::RNAFreeEnergy_TB::applySingleMoveInPlace | ( | const SingleMove & | move | ) |
Applies inplace a single move at the positions given by move. In case of invalid moves, the behaviour of the program is not specified.
Definition at line 94 of file RNAFreeEnergy_TB.cc.
| virtual double ell::RNAFreeEnergy_TB::getEnergy | ( | void | ) | const [virtual] |
Returns the free energy of this RNA structure allowing AU, CG and GU base base pairs. The energy is calculated via the Vienna RNA package functions. NOTE : The value UNIT is given ( kcal / mol ) !!!
| static const biu::Alphabet* ell::RNAFreeEnergy_TB::getSequenceAlphabet | ( | ) | [inline, static] |
Definition at line 80 of file RNAFreeEnergy_TB.hh.
| bool ell::RNAFreeEnergy_TB::isValidSingleMove | ( | const SingleMove & | move | ) | const |
Returns whether a move produces a valid RNA structure. A move can only be valid if the first move position move.first is less than the second move position move.second!
| virtual void ell::RNAFreeEnergy_TB::moleculeChanged | ( | ) | [protected, virtual] |
Informs the molecule that the sequence or structure has been changed to force recalculation of lazy properties (e.g. energy)
| RNAFreeEnergy_TB & ell::RNAFreeEnergy_TB::operator= | ( | const RNAFreeEnergy_TB & | rnaStruct2 | ) |
Definition at line 202 of file RNAFreeEnergy_TB.cc.
| virtual void ell::RNAFreeEnergy_TB::setEnergy | ( | const double | energy | ) | [virtual] |
Sets the energy of this RNA structure such that it is not calculated via the Vienna RNA package.
NOTE: It has to be the same energy as calculated by the Vienna RNA 'energy_of_struct' function, otherwise assertions will be broken.
NOTE : The value UNIT is given ( kcal / mol ) !!!
- Parameters:
-
energy the energy of this structure
| virtual void ell::RNAFreeEnergy_TB::setStructure | ( | const biu::Structure & | str | ) | [virtual] |
Sets the RNA structure in bracket notation.
- Parameters:
-
str the structure to set in bracket notation of correct length
| void ell::RNAFreeEnergy_TB::setViennaFoldParams | ( | void | ) | [static, protected] |
sets the Vienna package fold parameters and sets the variable ViennaFoldParamsSet to TRUE.
Definition at line 272 of file RNAFreeEnergy_TB.cc.
| void ell::RNAFreeEnergy_TB::updateSeqVienna | ( | ) | [protected, virtual] |
Updates seqVienna to contain the structure encoding in Vienna RNA style.
Definition at line 220 of file RNAFreeEnergy_TB.cc.
Field Documentation
bool ell::RNAFreeEnergy_TB::calculateEnergyChanges [static] |
whether or not the structure should calculate the energy difference if the structure is changed via moves or not
Definition at line 46 of file RNAFreeEnergy_TB.hh.
const biu::Alphabet ell::RNAFreeEnergy_TB::COMMON_ALPHABET [static, protected] |
The common Alphabet object of all RNAFreeEnergy_TB objects. It contains the elements A, C, G and U.
Definition at line 30 of file RNAFreeEnergy_TB.hh.
const biu::AllowedBasePairs ell::RNAFreeEnergy_TB::COMMON_BPAIRS [static, protected] |
The common BasePair object of all RNAFreeEnergy_TB objects. The valid RNA base pairs are AU, CG und GU and their reverse.
Definition at line 25 of file RNAFreeEnergy_TB.hh.
double ell::RNAFreeEnergy_TB::energy [mutable, protected] |
free energy of the molecule calculated using the Vienna RNA package
Definition at line 36 of file RNAFreeEnergy_TB.hh.
const double ell::RNAFreeEnergy_TB::ENERGY_INF [static, protected] |
dummy value for energy to inform that recalculation is necessary
Definition at line 33 of file RNAFreeEnergy_TB.hh.
short* ell::RNAFreeEnergy_TB::pairTable [protected] |
Definition at line 39 of file RNAFreeEnergy_TB.hh.
short* ell::RNAFreeEnergy_TB::seqVienna [protected] |
Definition at line 38 of file RNAFreeEnergy_TB.hh.
bool ell::RNAFreeEnergy_TB::ViennaFoldParamsSet [static, protected] |
whether or not the fold parameters of the Vienna package are already set or not
Definition at line 130 of file RNAFreeEnergy_TB.hh.
The documentation for this class was generated from the following files:
- src/ell/rna/RNAFreeEnergy_TB.hh
- src/ell/rna/RNAFreeEnergy_TB.cc