ell::RNAFreeEnergy Class Reference
#include <RNAFreeEnergy.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 18 of file RNAFreeEnergy.hh.
Public Types | |
| typedef std::pair< size_t, size_t > | SingleMove |
Public Member Functions | |
| void | applySingleMoveInPlace (const SingleMove &move) |
| virtual double | getEnergy () const |
| bool | isValidSingleMove (const SingleMove &move) const |
| size_t | nextCompatibleSingleMovePos (const size_t pos) const |
| RNAFreeEnergy & | operator= (const RNAFreeEnergy &rnaStruct2) |
| RNAFreeEnergy (const RNAFreeEnergy &rnaFreeEnerg) | |
| RNAFreeEnergy (biu::Sequence *rnaSeq, const biu::Structure *const rnaStructBracketDot, const bool seqIsShared=false) | |
| RNAFreeEnergy (const std::string &rnaSeqStr, const std::string &rnaStructBracketDotStr) | |
| virtual void | setStructure (const biu::Structure &str) |
| virtual | ~RNAFreeEnergy () |
Static Public Member Functions | |
| static const biu::Alphabet * | getSequenceAlphabet () |
Protected Member Functions | |
| virtual void | moleculeChanged () |
Protected Attributes | |
| double | energy |
Static Protected Attributes | |
| static const biu::Alphabet | COMMON_ALPHABET |
| static const biu::AllowedBasePairs | COMMON_BPAIRS |
| static const double | ENERGY_INF |
Member Typedef Documentation
| typedef std::pair<size_t, size_t> ell::RNAFreeEnergy::SingleMove |
A single move (open or close one bond) on a RNA structure at positions SingleMove.first and SingleMove.second.
Definition at line 41 of file RNAFreeEnergy.hh.
Constructor & Destructor Documentation
| ell::RNAFreeEnergy::RNAFreeEnergy | ( | const std::string & | rnaSeqStr, | |
| const std::string & | rnaStructBracketDotStr | |||
| ) |
Definition at line 26 of file RNAFreeEnergy.cc.
| ell::RNAFreeEnergy::RNAFreeEnergy | ( | biu::Sequence * | rnaSeq, | |
| const biu::Structure *const | rnaStructBracketDot, | |||
| const bool | seqIsShared = false | |||
| ) |
Definition at line 38 of file RNAFreeEnergy.cc.
| ell::RNAFreeEnergy::RNAFreeEnergy | ( | const RNAFreeEnergy & | rnaFreeEnerg | ) |
Definition at line 51 of file RNAFreeEnergy.cc.
| ell::RNAFreeEnergy::~RNAFreeEnergy | ( | ) | [virtual] |
Definition at line 56 of file RNAFreeEnergy.cc.
Member Function Documentation
| void ell::RNAFreeEnergy::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 73 of file RNAFreeEnergy.cc.
| double ell::RNAFreeEnergy::getEnergy | ( | ) | 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 ) !!!
Definition at line 145 of file RNAFreeEnergy.cc.
| static const biu::Alphabet* ell::RNAFreeEnergy::getSequenceAlphabet | ( | ) | [inline, static] |
Definition at line 76 of file RNAFreeEnergy.hh.
| bool ell::RNAFreeEnergy::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!
Definition at line 106 of file RNAFreeEnergy.cc.
| void ell::RNAFreeEnergy::moleculeChanged | ( | ) | [protected, virtual] |
Informs the molecule that the sequence or structure has been changed to force recalculation of lazy properties (e.g. energy)
Definition at line 179 of file RNAFreeEnergy.cc.
| size_t ell::RNAFreeEnergy::nextCompatibleSingleMovePos | ( | const size_t | pos | ) | const |
Returns the next position for a closing bond after pos which guarantes that the nested property will be preserved.
Returns biu::RNAStructure::INVALID_INDEX if there is no next valid position available.
Definition at line 60 of file RNAFreeEnergy.cc.
| RNAFreeEnergy & ell::RNAFreeEnergy::operator= | ( | const RNAFreeEnergy & | rnaStruct2 | ) |
Definition at line 166 of file RNAFreeEnergy.cc.
| void ell::RNAFreeEnergy::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
Definition at line 93 of file RNAFreeEnergy.cc.
Field Documentation
const biu::Alphabet ell::RNAFreeEnergy::COMMON_ALPHABET [static, protected] |
The common Alphabet object of all RNAFreeEnergy objects. It contains the elements A, C, G and U.
Definition at line 29 of file RNAFreeEnergy.hh.
const biu::AllowedBasePairs ell::RNAFreeEnergy::COMMON_BPAIRS [static, protected] |
The common BasePair object of all RNAFreeEnergy objects. The valid RNA base pairs are AU, CG und GU and their reverse.
Definition at line 24 of file RNAFreeEnergy.hh.
double ell::RNAFreeEnergy::energy [mutable, protected] |
free energy of the molecule calculated using the Vienna RNA package
Definition at line 35 of file RNAFreeEnergy.hh.
const double ell::RNAFreeEnergy::ENERGY_INF [static, protected] |
dummy value for energy to inform that recalculation is necessary
Definition at line 32 of file RNAFreeEnergy.hh.
The documentation for this class was generated from the following files:
- src/ell/rna/RNAFreeEnergy.hh
- src/ell/rna/RNAFreeEnergy.cc