Command Files

Functions to parse and interpret the content of constraint-formats-file.

Defines

VRNA_CMD_PARSE_HC
#include <ViennaRNA/commands.h>

Command parse/apply flag indicating hard constraints.

See also

vrna_cmd_t, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()

VRNA_CMD_PARSE_SC
#include <ViennaRNA/commands.h>

Command parse/apply flag indicating soft constraints.

See also

vrna_cmd_t, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()

VRNA_CMD_PARSE_UD
#include <ViennaRNA/commands.h>

Command parse/apply flag indicating unstructured domains.

See also

vrna_cmd_t, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()

VRNA_CMD_PARSE_SD
#include <ViennaRNA/commands.h>

Command parse/apply flag indicating structured domains.

See also

vrna_cmd_t, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()

VRNA_CMD_PARSE_DEFAULTS
#include <ViennaRNA/commands.h>

Command parse/apply flag indicating default set of commands.

See also

vrna_cmd_t, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()

VRNA_CMD_PARSE_SILENT
#include <ViennaRNA/commands.h>

Typedefs

typedef struct vrna_command_s *vrna_cmd_t
#include <ViennaRNA/commands.h>

A data structure that contains commands.

Functions

vrna_cmd_t vrna_file_commands_read(const char *filename, unsigned int options)
#include <ViennaRNA/commands.h>

Extract a list of commands from a command file.

Read a list of commands specified in the input file and return them as list of abstract commands

SWIG Wrapper Notes:

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

See also

vrna_commands_apply(), vrna_file_commands_apply(), vrna_commands_free()

Parameters:

  • filename – The filename

  • options – Options to limit the type of commands read from the file

Returns:

A list of abstract commands

int vrna_file_commands_apply(vrna_fold_compound_t *fc, const char *filename, unsigned int options)
#include <ViennaRNA/commands.h>

Apply a list of commands from a command file.

This function is a shortcut to directly parse a commands file and apply all successfully parsed commands to a vrna_fold_compound_t data structure. It is the same as: 

  int                   r;
  struct vrna_command_s *cmds;

  cmds  = vrna_file_commands_read(filename, options);
  r     = vrna_commands_apply(vc, cmds, options);

  vrna_commands_free(cmds);

  return r;

SWIG Wrapper Notes:

This function is attached as method file_commands_apply() to objects of type fold_compound. See, e.g. RNA.fold_compound.file_commands_apply() in the Python API .

Parameters:

  • fc – The vrna_fold_compound_t the command list will be applied to

  • filename – The filename

  • options – Options to limit the type of commands read from the file

Returns:

The number of commands successfully applied

int vrna_commands_apply(vrna_fold_compound_t *fc, vrna_cmd_t commands, unsigned int options)
#include <ViennaRNA/commands.h>

Apply a list of commands to a vrna_fold_compound_t.

SWIG Wrapper Notes:

This function is attached as method commands_apply() to objects of type fold_compound. See, e.g. RNA.fold_compound.commands_apply() in the Python API .

Parameters:

  • fc – The vrna_fold_compound_t the command list will be applied to

  • commands – The commands to apply

  • options – Options to limit the type of commands read from the file

Returns:

The number of commands successfully applied

void vrna_commands_free(vrna_cmd_t commands)
#include <ViennaRNA/commands.h>

Free memory occupied by a list of commands.

Release memory occupied by a list of commands

Parameters:

  • commands – A pointer to a list of commands