/* functions from part_func.c */ /* calculate partition function and base pair probabilities */ #ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__ #define __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__ #include "data_structures.h" #ifdef __GNUC__ #define DEPRECATED(func) func __attribute__ ((deprecated)) #else #define DEPRECATED(func) func #endif /** * \file part_func_co.h * * \brief Partition function for two RNA sequences * * As for folding one RNA molecule, this computes the partition function * of all possible structures and the base pair probabilities. Uses the * same global #pf_scale variable to avoid overflows. * * To simplify the implementation the partition function computation is done * internally in a null model that does not include the duplex initiation * energy, i.e. the entropic penalty for producing a dimer from two * monomers). The resulting free energies and pair probabilities are initially * relative to that null model. In a second step the free energies can be * corrected to include the dimerization penalty, and the pair probabilities * can be divided into the conditional pair probabilities given that a re * dimer is formed or not formed. * * After computing the partition functions of all possible dimeres one * can compute the probabilities of base pairs, the concentrations out of * start concentrations and sofar and soaway. * * Dimer formation is inherently concentration dependent. Given the free * energies of the monomers A and B and dimers AB, AA, and BB one can compute * the equilibrium concentrations, given input concentrations of A and B, see * e.g. Dimitrov & Zuker (2004) */ /** * \brief Toggles no intrabp in 2nd mol */ extern int mirnatog; /** * \brief Free energies of the two monomers */ extern double F_monomer[2]; /** * \brief Calculate partition function and base pair probabilities * * This is the cofold partition function folding. The second molecule starts * at the #cut_point nucleotide. * * \note OpenMP: Since this function relies on the global parameters * #do_backtrack, #dangles, #temperature and #pf_scale it is not * threadsafe according to concurrent changes in these variables! * Use co_pf_fold_par() instead to circumvent this issue. * * \see co_pf_fold_par() * * \param sequence Concatenated RNA sequences * \param structure Will hold the structure or constraints * \return cofoldF structure containing a set of energies needed for * concentration computations. */ cofoldF co_pf_fold( char *sequence, char *structure); /** * \brief Calculate partition function and base pair probabilities * * This is the cofold partition function folding. The second molecule starts * at the #cut_point nucleotide. * * \see get_boltzmann_factors(), co_pf_fold() * * \param sequence Concatenated RNA sequences * \param structure Pointer to the structure constraint * \param parameters Data structure containing the precalculated Boltzmann factors * \param calculate_bppm Switch to turn Base pair probability calculations on/off (0==off) * \param is_constrained Switch to indicate that a structure contraint is passed via the * structure argument (0==off) * \return cofoldF structure containing a set of energies needed for * concentration computations. */ cofoldF co_pf_fold_par( char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained); /** * \brief Get a pointer to the base pair probability array * * Accessing the base pair probabilities for a pair (i,j) is achieved by * \verbatim FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; \endverbatim * * \see get_iindx() * \return A pointer to the base pair probability array */ FLT_OR_DBL *export_co_bppm(void); /** * \brief Free the memory occupied by co_pf_fold() */ void free_co_pf_arrays(void); /** * \brief Recalculate energy parameters * * This function recalculates all energy parameters given * the current model settings. * * \note This function relies on the global variables #pf_scale, #dangles and * #temperature. Thus it might not be threadsafe in certain situations. * Use update_co_pf_params_par() instead. * * \see get_boltzmann_factors(), update_co_pf_params_par() * * \param length Length of the current RNA sequence */ void update_co_pf_params(int length); /** * \brief Recalculate energy parameters * * This function recalculates all energy parameters given * the current model settings. * It's second argument can either be NULL or a data structure * containing the precomputed Boltzmann factors. In the first * scenario, the necessary data structure will be created automatically * according to the current global model settings, i.e. this * mode might not be threadsafe. * However, if the provided data structure is not NULL, threadsafety * for the model parameters #dangles, #pf_scale and #temperature is regained, since their * values are taken from this data structure during subsequent calculations. * * \see get_boltzmann_factors(), update_co_pf_params() * * \param length Length of the current RNA sequence * \param parameters data structure containing the precomputed Boltzmann factors */ void update_co_pf_params_par(int length, pf_paramT *parameters); /** * \brief Compute Boltzmann probabilities of dimerization without homodimers * * Given the pair probabilities and free energies (in the null model) for a * dimer AB and the two constituent monomers A and B, compute the conditional pair * probabilities given that a dimer AB actually forms. * Null model pair probabilities are given as a list as produced by * assign_plist_from_pr(), the dimer probabilities 'prAB' are modified in place. * * \param FAB free energy of dimer AB * \param FEA free energy of monomer A * \param FEB free energy of monomer B * \param prAB pair probabilities for dimer * \param prA pair probabilities monomer * \param prB pair probabilities monomer * \param Alength Length of molecule A */ void compute_probabilities(double FAB, double FEA, double FEB, struct plist *prAB, struct plist *prA, struct plist *prB, int Alength); /** * \brief Given two start monomer concentrations a and b, compute the * concentrations in thermodynamic equilibrium of all dimers and the monomers. * * This function takes an array 'startconc' of input concentrations with alternating * entries for the initial concentrations of molecules A and B (terminated by * two zeroes), then computes the resulting equilibrium concentrations * from the free energies for the dimers. Dimer free energies should be the * dimer-only free energies, i.e. the FcAB entries from the #cofoldF struct. * * \param FEAB Free energy of AB dimer (FcAB entry) * \param FEAA Free energy of AA dimer (FcAB entry) * \param FEBB Free energy of BB dimer (FcAB entry) * \param FEA Free energy of monomer A * \param FEB Free energy of monomer B * \param startconc List of start concentrations [a0],[b0],[a1],[b1],...,[an][bn],[0],[0] * \return ConcEnt array containing the equilibrium energies and start concentrations */ ConcEnt *get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc); /* ################################################# # DEPRECATED FUNCTIONS # ################################################# */ /** * DO NOT USE THIS FUNCTION ANYMORE * \deprecated{ This function is deprecated and will be removed soon!} * use \ref assign_plist_from_pr() instead! */ DEPRECATED(plist *get_plist( struct plist *pl, int length, double cut_off)); /** * DO NOT USE THIS FUNCTION ANYMORE * \deprecated{ This function is deprecated and will be removed soon!} */ DEPRECATED(void init_co_pf_fold(int length)); #endif