Loading / Saving Energy Parameter Sets — ViennaRNA Package

# Loading / Saving Energy Parameter Sets

Read and Write energy parameter sets from and to files or strings

  Defines

  VRNA_PARAMETER_FORMAT_DEFAULT

    Default Energy Parameter File format.

        #include <ViennaRNA/params/io.h>

    See also

    vrna_params_load(), vrna_params_load_from_string(), vrna_params_save()

  Enums

  enum parset

        #include <ViennaRNA/params/io.h>

    Values:

    enumerator UNKNOWN
    enumerator QUIT
    enumerator S
    enumerator S_H
    enumerator HP
    enumerator HP_H
    enumerator B
    enumerator B_H
    enumerator IL
    enumerator IL_H
    enumerator MMH
    enumerator MMH_H
    enumerator MMI
    enumerator MMI_H
    enumerator MMI1N
    enumerator MMI1N_H
    enumerator MMI23
    enumerator MMI23_H
    enumerator MMM
    enumerator MMM_H
    enumerator MME
    enumerator MME_H
    enumerator D5
    enumerator D5_H
    enumerator D3
    enumerator D3_H
    enumerator INT11
    enumerator INT11_H
    enumerator INT21
    enumerator INT21_H
    enumerator INT22
    enumerator INT22_H
    enumerator ML
    enumerator TL
    enumerator TRI
    enumerator HEX
    enumerator NIN
    enumerator MISC

  Functions

  int vrna_params_load(const char fname[], unsigned int options)

    Load energy parameters from a file.

        #include <ViennaRNA/params/io.h>

    SWIG Wrapper Notes:

      This function is available as overloaded function `params_load`(fname=””, options=VRNA_PARAMETER_FORMAT_DEFAULT). Here, the empty filename string indicates to load default RNA parameters, i.e. this is equivalent to calling vrna_params_load_defaults(). See, e.g. `RNA.fold_compound.params_load()` in the Python API.

    See also

    vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_defaults(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

    Parameters:

      - fname – The path to the file containing the energy parameters

      - options – File format bit-mask (usually VRNA_PARAMETER_FORMAT_DEFAULT)

    Returns:

      Non-zero on success, 0 on failure

  int vrna_params_save(const char fname[], unsigned int options)

    Save energy parameters to a file.

        #include <ViennaRNA/params/io.h>

    SWIG Wrapper Notes:

      This function is available as overloaded function `params_save`(fname, options=VRNA_PARAMETER_FORMAT_DEFAULT). See, e.g. `RNA.params_save()` in the Python API.

    See also

    vrna_params_load()

    Parameters:

      - fname – A filename (path) for the file where the current energy parameters will be written to

      - options – File format bit-mask (usually VRNA_PARAMETER_FORMAT_DEFAULT)

    Returns:

      Non-zero on success, 0 on failure

  int vrna_params_load_from_string(const char *string, const char *name, unsigned int options)

    Load energy paramters from string.

        #include <ViennaRNA/params/io.h>

    The string must follow the default energy parameter file convention! The optional `name` argument allows one to specify a name for the parameter set which is stored internally.

    SWIG Wrapper Notes:

      This function is available as overloaded function `params_load_from_string`(string, name=””, options=VRNA_PARAMETER_FORMAT_DEFAULT). See, e.g. `RNA.params_load_from_string()` in the Python API.

    See also

    vrna_params_load(), vrna_params_save(), vrna_params_load_defaults(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

    Parameters:

      - string – A 0-terminated string containing energy parameters

      - name – A name for the parameter set in `string` (Maybe `NULL`)

      - options – File format bit-mask (usually VRNA_PARAMETER_FORMAT_DEFAULT)

    Returns:

      Non-zero on success, 0 on failure

  int vrna_params_load_defaults(void)

    Load default RNA energy parameter set.

        #include <ViennaRNA/params/io.h>

    This is a convenience function to load the Turner 2004 RNA free energy parameters. It’s the same as calling vrna_params_load_RNA_Turner2004()

    SWIG Wrapper Notes:

      This function is available as overloaded function `params_load()`. See, e.g. `RNA.params_load()` in the Python API.

    See also

    vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

    Returns:

      Non-zero on success, 0 on failure

  int vrna_params_load_RNA_Turner2004(void)

    Load Turner 2004 RNA energy parameter set.

        #include <ViennaRNA/params/io.h>

    SWIG Wrapper Notes:

      This function is available as function `params_load_RNA_Turner2004()`. See, e.g. `RNA.params_load_RNA_Turner2004()` in the Python API.

    See also

    vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_defaults(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

    Warning

    This function also resets the default geometric parameters as stored in vrna_md_t to those of RNA. Only subsequently initialized vrna_md_t structures will be affected by this change.

    Returns:

      Non-zero on success, 0 on failure

  int vrna_params_load_RNA_Turner1999(void)

    Load Turner 1999 RNA energy parameter set.

        #include <ViennaRNA/params/io.h>

    SWIG Wrapper Notes:

      This function is available as function `params_load_RNA_Turner1999()`. See, e.g. `RNA.params_load_RNA_Turner1999()` in the Python API.

    See also

    vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_defaults(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

    Warning

    This function also resets the default geometric parameters as stored in vrna_md_t to those of RNA. Only subsequently initialized vrna_md_t structures will be affected by this change.

    Returns:

      Non-zero on success, 0 on failure

  int vrna_params_load_RNA_Andronescu2007(void)

    Load Andronsecu 2007 RNA energy parameter set.

        #include <ViennaRNA/params/io.h>

    SWIG Wrapper Notes:

      This function is available as function `params_load_RNA_Andronescu2007()`. See, e.g. `RNA.params_load_RNA_Andronescu2007()` in the Python API.

    See also

    vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_defaults(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

    Warning

    This function also resets the default geometric parameters as stored in vrna_md_t to those of RNA. Only subsequently initialized vrna_md_t structures will be affected by this change.

    Returns:

      Non-zero on success, 0 on failure

  int vrna_params_load_RNA_Langdon2018(void)

    Load Langdon 2018 RNA energy parameter set.

        #include <ViennaRNA/params/io.h>

    SWIG Wrapper Notes:

      This function is available as function `params_load_RNA_Langdon2018()`. See, e.g. `RNA.params_load_RNA_Langdon2018()` in the Python API.

    See also

    vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_defaults(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

    Warning

    This function also resets the default geometric parameters as stored in vrna_md_t to those of RNA. Only subsequently initialized vrna_md_t structures will be affected by this change.

    Returns:

      Non-zero on success, 0 on failure

  int vrna_params_load_RNA_misc_special_hairpins(void)

    Load Misc Special Hairpin RNA energy parameter set.

        #include <ViennaRNA/params/io.h>

    SWIG Wrapper Notes:

      This function is available as function `params_load_RNA_misc_special_hairpins()`. See, e.g. `RNA.params_load_RNA_misc_special_hairpins()` in the Python API.

    See also

    vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_defaults(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

    Warning

    This function also resets the default geometric parameters as stored in vrna_md_t to those of RNA. Only subsequently initialized vrna_md_t structures will be affected by this change.

    Returns:

      Non-zero on success, 0 on failure

  int vrna_params_load_DNA_Mathews2004(void)

    Load Mathews 2004 DNA energy parameter set.

        #include <ViennaRNA/params/io.h>

    SWIG Wrapper Notes:

      This function is available as function `params_load_DNA_Mathews2004()`. See, e.g. `RNA.params_load_DNA_Mathews2004()` in the Python API.

    See also

    vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_defaults(), vrna_params_load_DNA_Mathews1999()

    Warning

    This function also resets the default geometric parameters as stored in vrna_md_t to those of DNA. Only subsequently initialized vrna_md_t structures will be affected by this change.

    Returns:

      Non-zero on success, 0 on failure

  int vrna_params_load_DNA_Mathews1999(void)

    Load Mathews 1999 DNA energy parameter set.

        #include <ViennaRNA/params/io.h>

    SWIG Wrapper Notes:

      This function is available as function `params_load_DNA_Mathews1999()`. See, e.g. `RNA.params_load_DNA_Mathews1999()` in the Python API.

    See also

    vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_defaults()

    Warning

    This function also resets the default geometric parameters as stored in vrna_md_t to those of DNA. Only subsequently initialized vrna_md_t structures will be affected by this change.

    Returns:

      Non-zero on success, 0 on failure

  const char *last_parameter_file(void)

    Get the file name of the parameter file that was most recently loaded.

        #include <ViennaRNA/params/io.h>

    Returns:

      The file name of the last parameter file, or NULL if parameters are still at defaults

  void read_parameter_file(const char fname[])

    Read energy parameters from a file.

        #include <ViennaRNA/params/io.h>

    Deprecated:

      Use vrna_params_load() instead!

    Parameters:

      - fname – The path to the file containing the energy parameters

  void write_parameter_file(const char fname[])

    Write energy parameters to a file.

        #include <ViennaRNA/params/io.h>

    Deprecated:

      Use vrna_params_save() instead!

    Parameters:

      - fname – A filename (path) for the file where the current energy parameters will be written to

  enum parset gettype(const char *ident)

        #include <ViennaRNA/params/io.h>

  char *settype(enum parset s)

        #include <ViennaRNA/params/io.h>