mainProcedure.cpp File Reference

#include "mainProcedure.h"
#include <iostream>
#include <fstream>
#include <exception>
#include <stack>
#include <vector>
#include <cmath>

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Functions
path	make_path (const std::string &str)
void	doing (int verbosity, const std::string &str, std::stringstream &log)
void	done (int verbosity, std::stringstream &log)
std::string	default_output (const std::string &input_name)
void	write_all_output (model &m, const output_container &out, sz how_many, std::stringstream &output_name, const std::vector< std::string > &remarks)
void	do_randomization (model &m, std::stringstream &out_name, const vec &corner1, const vec &corner2, int seed, int verbosity, std::stringstream &log)
void	refine_structure (model &m, const precalculate &prec, non_cache &nc, output_type &out, const vec &cap, sz max_steps=1000)
std::string	vina_remark (fl e, fl lb, fl ub)
output_container	remove_redundant (const output_container &in, fl min_rmsd)
void	do_search (model &m, const boost::optional< model > &ref, const scoring_function &sf, const precalculate &prec, const igrid &ig, const precalculate &prec_widened, const igrid &ig_widened, non_cache &nc, std::stringstream &out_name, const vec &corner1, const vec &corner2, const parallel_mc &par, fl energy_range, sz num_modes, int seed, int verbosity, bool score_only, bool local_only, std::stringstream &log, const terms &t, const flv &weights)
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)
model	parse_bundle (const std::string &rigid_name, const boost::optional< std::string > &flex_name_opt, std::stringstream &ligSS)
model	parse_bundle (const std::string &rigid_name, const boost::optional< std::string > &flex_name_opt, const std::vector< std::string > &ligand_names)
model	parse_bundle (const std::vector< std::string > &ligand_names)
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)
model	parse_bundle (const boost::optional< std::string > &rigid_name_opt, const boost::optional< std::string > &flex_name_opt, std::stringstream &ligSS)

Function Documentation

path make_path

(

const std::string &

str

)

Referenced by main(), and parse_bundle().

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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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std::string default_output

(

const std::string &

input_name

)

Referenced by main().

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void write_all_output	(	model &	m,
		const output_container &	out,
		sz	how_many,
		std::stringstream &	output_name,
		const std::vector< std::string > &	remarks
	)

References model::set(), VINA_CHECK, VINA_FOR, and model::write_model().

Referenced by do_search().

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void do_randomization	(	model &	m,
		std::stringstream &	out_name,
		const vec &	corner1,
		const vec &	corner2,
		int	seed,
		int	verbosity,
		std::stringstream &	log
	)

References model::clash_penalty(), model::get_initial_conf(), conf::randomize(), model::set(), VINA_FOR, and model::write_structure().

Referenced by main_procedure().

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void refine_structure	(	model &	m,
		const precalculate &	prec,
		non_cache &	nc,
		output_type &	out,
		const vec &	cap,
		sz	max_steps = 1000
	)

References output_type::c, output_type::coords, output_type::e, model::get_heavy_atom_movable_coords(), model::get_size(), max_fl, quasi_newton::max_steps, model::set(), non_cache::slope, VINA_FOR, and non_cache::within().

Referenced by do_search().

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std::string vina_remark	(	fl	e,
		fl	lb,
		fl	ub
	)

Referenced by do_search().

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output_container remove_redundant	(	const output_container &	in,
		fl	min_rmsd
	)

References add_to_output_container(), and VINA_FOR_IN.

Referenced by do_search().

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void do_search	(	model &	m,
		const boost::optional< model > &	ref,
		const scoring_function &	sf,
		const precalculate &	prec,
		const igrid &	ig,
		const precalculate &	prec_widened,
		const igrid &	ig_widened,
		non_cache &	nc,
		std::stringstream &	out_name,
		const vec &	corner1,
		const vec &	corner2,
		const parallel_mc &	par,
		fl	energy_range,
		sz	num_modes,
		int	seed,
		int	verbosity,
		bool	score_only,
		bool	local_only,
		std::stringstream &	log,
		const terms &	t,
		const flv &	weights
	)

References authentic_v, output_type::c, scoring_function::conf_independent(), doing(), done(), model::eval_adjusted(), model::eval_intramolecular(), terms::evale_robust(), ssd::evals, model::get_initial_conf(), model::get_size(), max_fl, parallel_mc::mc, not_max(), refine_structure(), remove_redundant(), model::rmsd_lower_bound(), model::rmsd_upper_bound(), model::set(), monte_carlo::ssd_par, VINA_CHECK, VINA_FOR_IN, vina_remark(), non_cache::within(), and write_all_output().

Referenced by main_procedure().

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

References model::append(), make_path(), parse_ligand_pdbqt(), and parse_receptor_pdbqt().

Referenced by dockjob(), main(), and parse_bundle().

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

References model::append(), make_path(), parse_ligand_pdbqt(), parse_receptor_pdbqt(), and VINA_FOR_IN.

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model parse_bundle

(

const std::vector< std::string > &

ligand_names

)

References make_path(), parse_ligand_pdbqt(), VINA_CHECK, and VINA_RANGE.

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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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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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