--- /dev/null
+/** @file cmdline.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22.5
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CMDLINE_H
+#define CMDLINE_H
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_PACKAGE
+/** @brief the program name (used for printing errors) */
+#define CMDLINE_PARSER_PACKAGE "Kinfold"
+#endif
+
+#ifndef CMDLINE_PARSER_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define CMDLINE_PARSER_PACKAGE_NAME "Kinfold"
+#endif
+
+#ifndef CMDLINE_PARSER_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_VERSION VERSION
+#endif
+
+/** @brief Where the command line options are stored */
+struct gengetopt_args_info
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *full_help_help; /**< @brief Print help, including hidden options, and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ int dangle_arg; /**< @brief <0|1|2> set dangling end model to (none|normal|double) (default='2'). */
+ char * dangle_orig; /**< @brief <0|1|2> set dangling end model to (none|normal|double) original value given at command line. */
+ const char *dangle_help; /**< @brief <0|1|2> set dangling end model to (none|normal|double) help description. */
+ float Temp_arg; /**< @brief simulation temperature (default='37'). */
+ char * Temp_orig; /**< @brief simulation temperature original value given at command line. */
+ const char *Temp_help; /**< @brief simulation temperature help description. */
+ char * Par_arg; /**< @brief read energy-parameter-file. */
+ char * Par_orig; /**< @brief read energy-parameter-file original value given at command line. */
+ const char *Par_help; /**< @brief read energy-parameter-file help description. */
+ int logML_flag; /**< @brief use logarithmic multiloop energies instead of linear (default=on). */
+ const char *logML_help; /**< @brief use logarithmic multiloop energies instead of linear help description. */
+ int noShift_flag; /**< @brief turn off shift-moves (default=off). */
+ const char *noShift_help; /**< @brief turn off shift-moves help description. */
+ int noLP_flag; /**< @brief forbid structures with isolated base-pairs (default=off). */
+ const char *noLP_help; /**< @brief forbid structures with isolated base-pairs help description. */
+ char * seed_arg; /**< @brief set random number seed specify 3 integers as int=int=int (default='clock'). */
+ char * seed_orig; /**< @brief set random number seed specify 3 integers as int=int=int original value given at command line. */
+ const char *seed_help; /**< @brief set random number seed specify 3 integers as int=int=int help description. */
+ float time_arg; /**< @brief set maxtime of simulation (default='500'). */
+ char * time_orig; /**< @brief set maxtime of simulation original value given at command line. */
+ const char *time_help; /**< @brief set maxtime of simulation help description. */
+ int num_arg; /**< @brief set number of trajectories (default='1'). */
+ char * num_orig; /**< @brief set number of trajectories original value given at command line. */
+ const char *num_help; /**< @brief set number of trajectories help description. */
+ int start_flag; /**< @brief read start structure from stdin (otherwise use open chain) (default=off). */
+ const char *start_help; /**< @brief read start structure from stdin (otherwise use open chain) help description. */
+ int stop_flag; /**< @brief read stop structure(s) from stdin (optherwise use MFE) (default=off). */
+ const char *stop_help; /**< @brief read stop structure(s) from stdin (optherwise use MFE) help description. */
+ int met_flag; /**< @brief use Metropolis rule for rates (not Kawasaki rule) (default=off). */
+ const char *met_help; /**< @brief use Metropolis rule for rates (not Kawasaki rule) help description. */
+ int fpt_flag; /**< @brief compute first passage time (stop when a stop-structure is reached) (default=on). */
+ const char *fpt_help; /**< @brief compute first passage time (stop when a stop-structure is reached) help description. */
+ float grow_arg; /**< @brief grow chain every <float> time units (default='0'). */
+ char * grow_orig; /**< @brief grow chain every <float> time units original value given at command line. */
+ const char *grow_help; /**< @brief grow chain every <float> time units help description. */
+ int glen_arg; /**< @brief initial size of growing chain (default='15'). */
+ char * glen_orig; /**< @brief initial size of growing chain original value given at command line. */
+ const char *glen_help; /**< @brief initial size of growing chain help description. */
+ double phi_arg; /**< @brief set phi value. */
+ char * phi_orig; /**< @brief set phi value original value given at command line. */
+ const char *phi_help; /**< @brief set phi value help description. */
+ char * pbounds_arg; /**< @brief specify 3 floats for phi_min, phi_inc, phi_max in the form <d1=d2=d3>. */
+ char * pbounds_orig; /**< @brief specify 3 floats for phi_min, phi_inc, phi_max in the form <d1=d2=d3> original value given at command line. */
+ const char *pbounds_help; /**< @brief specify 3 floats for phi_min, phi_inc, phi_max in the form <d1=d2=d3> help description. */
+ char * log_arg; /**< @brief set basename of log-file (default='kinout'). */
+ char * log_orig; /**< @brief set basename of log-file original value given at command line. */
+ const char *log_help; /**< @brief set basename of log-file help description. */
+ int silent_flag; /**< @brief no output to stdout (default=off). */
+ const char *silent_help; /**< @brief no output to stdout help description. */
+ int verbose_flag; /**< @brief more information to stdout (default=off). */
+ const char *verbose_help; /**< @brief more information to stdout help description. */
+ int lmin_flag; /**< @brief output only local minima to stdout (default=off). */
+ const char *lmin_help; /**< @brief output only local minima to stdout help description. */
+ float cut_arg; /**< @brief output structures with E <= <float> to stdout (default='20'). */
+ char * cut_orig; /**< @brief output structures with E <= <float> to stdout original value given at command line. */
+ const char *cut_help; /**< @brief output structures with E <= <float> to stdout help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int full_help_given ; /**< @brief Whether full-help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int dangle_given ; /**< @brief Whether dangle was given. */
+ unsigned int Temp_given ; /**< @brief Whether Temp was given. */
+ unsigned int Par_given ; /**< @brief Whether Par was given. */
+ unsigned int logML_given ; /**< @brief Whether logML was given. */
+ unsigned int noShift_given ; /**< @brief Whether noShift was given. */
+ unsigned int noLP_given ; /**< @brief Whether noLP was given. */
+ unsigned int seed_given ; /**< @brief Whether seed was given. */
+ unsigned int time_given ; /**< @brief Whether time was given. */
+ unsigned int num_given ; /**< @brief Whether num was given. */
+ unsigned int start_given ; /**< @brief Whether start was given. */
+ unsigned int stop_given ; /**< @brief Whether stop was given. */
+ unsigned int met_given ; /**< @brief Whether met was given. */
+ unsigned int fpt_given ; /**< @brief Whether fpt was given. */
+ unsigned int grow_given ; /**< @brief Whether grow was given. */
+ unsigned int glen_given ; /**< @brief Whether glen was given. */
+ unsigned int phi_given ; /**< @brief Whether phi was given. */
+ unsigned int pbounds_given ; /**< @brief Whether pbounds was given. */
+ unsigned int log_given ; /**< @brief Whether log was given. */
+ unsigned int silent_given ; /**< @brief Whether silent was given. */
+ unsigned int verbose_given ; /**< @brief Whether verbose was given. */
+ unsigned int lmin_given ; /**< @brief Whether lmin was given. */
+ unsigned int cut_given ; /**< @brief Whether cut was given. */
+
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure gengetopt_args_info (default 1) */
+ int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+ int check_ambiguity; /**< @brief whether to check for options already specified in the option structure gengetopt_args_info (default 0) */
+ int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *gengetopt_args_info_purpose;
+/** @brief the usage string of the program */
+extern const char *gengetopt_args_info_usage;
+/** @brief all the lines making the help output */
+extern const char *gengetopt_args_info_help[];
+/** @brief all the lines making the full help output (including hidden options) */
+extern const char *gengetopt_args_info_full_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser (int argc, char **argv,
+ struct gengetopt_args_info *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_ext() instead
+ */
+int cmdline_parser2 (int argc, char **argv,
+ struct gengetopt_args_info *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_ext (int argc, char **argv,
+ struct gengetopt_args_info *args_info,
+ struct cmdline_parser_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_dump(FILE *outfile,
+ struct gengetopt_args_info *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_file_save(const char *filename,
+ struct gengetopt_args_info *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_print_help(void);
+/**
+ * Print the full help (including hidden options)
+ */
+void cmdline_parser_print_full_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_params_init(struct cmdline_parser_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_params structure
+ */
+struct cmdline_parser_params *cmdline_parser_params_create(void);
+
+/**
+ * Initializes the passed gengetopt_args_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_init (struct gengetopt_args_info *args_info);
+/**
+ * Deallocates the string fields of the gengetopt_args_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_free (struct gengetopt_args_info *args_info);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ * possible errors
+ * @return
+ */
+int cmdline_parser_required (struct gengetopt_args_info *args_info,
+ const char *prog_name);
+
+extern const char *cmdline_parser_dangle_values[]; /**< @brief Possible values for dangle. */
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CMDLINE_H */
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