# Deprecated List

Global base_pair
  Do not use this variable anymore!

Global centroid (int length, double *dist)
  This function is deprecated and should not be used anymore as it is not threadsafe!

Global energy_of_circ_struct (const char *string, const char *structure)

  This function is deprecated and should not be used in future programs Use energy_of_circ_structure() instead!

Global energy_of_struct (const char *string, const char *structure)

  This function is deprecated and should not be used in future programs! Use energy_of_structure() instead!

Global energy_of_struct_pt (const char *string, short *ptable, short *s, short *s1)

  This function is deprecated and should not be used in future programs! Use energy_of_structure_pt() instead!

Global expHairpinEnergy (int u, int type, short si1, short sj1, const char *string)
  Use exp_E_Hairpin() from loop_energies.h instead

Global expLoopEnergy (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)
  Use exp_E_IntLoop() from loop_energies.h instead

Global get_plist (struct plist *pl, int length, double cut_off)
  { This function is deprecated and will be removed soon!} use assign_plist_from_pr() instead!

Global HairpinE (int size, int type, int si1, int sj1, const char *string)
  {This function is deprecated and will be removed soon. Use E_Hairpin() instead!}

Global iindx
  Do not use this variable anymore!

Global init_co_pf_fold (int length)
  { This function is deprecated and will be removed soon!}

Global init_pf_fold (int length)
  This function is obsolete and will be removed soon!

Global initialize_cofold (int length)
  {This function is obsolete and will be removed soon!}

Global initialize_fold (int length)

  {This function is deprecated and will be removed soon!}

Global LoopEnergy (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)
  {This function is deprecated and will be removed soon. Use E_IntLoop() instead!}

Global Make_bp_profile (int length)

  This function is deprecated and will be removed soon! See Make_bp_profile_bppm() for a replacement

Global mean_bp_dist (int length)
  This function is not threadsafe and should not be used anymore. Use mean_bp_distance() instead!

Global pr
  Do not use this variable anymore!

Global PS_dot_plot (char *string, char *file)
  This function is deprecated and will be removed soon! Use PS_dot_plot_list() instead!