mainProcedure.h File Reference

#include <string>
#include <sstream>
#include <boost/program_options.hpp>
#include <boost/filesystem/fstream.hpp>
#include <boost/filesystem/exception.hpp>
#include <boost/filesystem/convenience.hpp>
#include <boost/thread/thread.hpp>
#include "parse_pdbqt.h"
#include "parallel_mc.h"
#include "file.h"
#include "cache.h"
#include "non_cache.h"
#include "naive_non_cache.h"
#include "parse_error.h"
#include "everything.h"
#include "weighted_terms.h"
#include "current_weights.h"
#include "quasi_newton.h"
#include "coords.h"
#include "tokenize.h"

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Classes
struct	usage_error
struct	options_occurrence

Functions
void	doing (int verbosity, const std::string &str, std::stringstream &log)
void	done (int verbosity, std::stringstream &log)
path	make_path (const std::string &str)
model	parse_bundle (const boost::optional< std::string > &rigid_name_opt, const boost::optional< std::string > &flex_name_opt, std::stringstream &ligSS)
model	parse_bundle (const boost::optional< std::string > &rigid_name_opt, const boost::optional< std::string > &flex_name_opt, const std::vector< std::string > &ligand_names)
void	main_procedure (model &m, const boost::optional< model > &ref, std::stringstream &out_name, bool score_only, bool local_only, bool randomize_only, bool no_cache, const grid_dims &gd, int exhaustiveness, const flv &weights, int cpu, int seed, int verbosity, sz num_modes, fl energy_range, std::stringstream &log)
options_occurrence	get_occurrence (boost::program_options::variables_map &vm, boost::program_options::options_description &d)
void	check_occurrence (boost::program_options::variables_map &vm, boost::program_options::options_description &d)
std::string	default_output (const std::string &input_name)

Function Documentation

void doing	(	int	verbosity,
		const std::string &	str,
		std::stringstream &	log
	)

Referenced by do_search(), dockjob(), main(), and main_procedure().

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void done	(	int	verbosity,
		std::stringstream &	log
	)

Referenced by do_search(), dockjob(), main(), and main_procedure().

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path make_path

(

const std::string &

str

)

Referenced by main(), and parse_bundle().

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model parse_bundle	(	const boost::optional< std::string > &	rigid_name_opt,
		const boost::optional< std::string > &	flex_name_opt,
		std::stringstream &	ligSS
	)

References parse_bundle().

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model parse_bundle	(	const boost::optional< std::string > &	rigid_name_opt,
		const boost::optional< std::string > &	flex_name_opt,
		const std::vector< std::string > &	ligand_names
	)

References parse_bundle().

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void main_procedure	(	model &	m,
		const boost::optional< model > &	ref,
		std::stringstream &	out_name,
		bool	score_only,
		bool	local_only,
		bool	randomize_only,
		bool	no_cache,
		const grid_dims &	gd,
		int	exhaustiveness,
		const flv &	weights,
		int	cpu,
		int	seed,
		int	verbosity,
		sz	num_modes,
		fl	energy_range,
		std::stringstream &	log
	)

References precalculate::atom_typing_used(), parallel_mc::display_progress, do_randomization(), do_search(), doing(), done(), ssd::evals, model::get_movable_atom_types(), model::get_size(), monte_carlo::hunt_cap, parallel_mc::mc, monte_carlo::min_rmsd, conf_size::num_degrees_of_freedom(), model::num_movable_atoms(), monte_carlo::num_saved_mins, monte_carlo::num_steps, parallel_mc::num_tasks, parallel_mc::num_threads, cache::populate(), monte_carlo::ssd_par, VINA_CHECK, precalculate::widen(), and atom_type::XS.

Referenced by dockjob(), and main().

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options_occurrence get_occurrence	(	boost::program_options::variables_map &	vm,
		boost::program_options::options_description &	d
	)

References options_occurrence::all, options_occurrence::some, and VINA_FOR_IN.

Referenced by main().

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void check_occurrence	(	boost::program_options::variables_map &	vm,
		boost::program_options::options_description &	d
	)

References VINA_FOR_IN.

Referenced by main().

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std::string default_output

(

const std::string &

input_name

)

Referenced by main().

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