common.h File Reference

#include <cassert>
#include <string>
#include <limits>
#include <utility>
#include <algorithm>
#include <vector>
#include <cmath>
#include <iostream>
#include <fstream>
#include <iomanip>
#include <sstream>
#include <boost/serialization/vector.hpp>
#include <boost/serialization/base_object.hpp>
#include <boost/filesystem/path.hpp>
#include "macros.h"

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Classes
struct	vec
struct	mat
struct	internal_error

Macros
#define	VINA_CHECK(P)   assert(P)

Typedefs
typedef double	fl
typedef std::size_t	sz
typedef std::pair< fl, fl >	pr
typedef std::vector< vec >	vecv
typedef std::pair< vec, vec >	vecp
typedef std::vector< fl >	flv
typedef std::vector< pr >	prv
typedef std::vector< sz >	szv
typedef boost::filesystem::path	path

Functions
template<typename T >
T	sqr (T x)
vec	operator* (fl s, const vec &v)
vec	cross_product (const vec &a, const vec &b)
vec	elementwise_product (const vec &a, const vec &b)
sz	fl_to_sz (fl x, sz max_sz)
bool	eq (fl a, fl b)
bool	eq_r2 (fl a, fl b)
bool	eq (const vec &a, const vec &b)
template<typename T >
bool	eq (const std::vector< T > &a, const std::vector< T > &b)
const vec	zero_vec (0, 0, 0)
const vec	max_vec (max_fl, max_fl, max_fl)
bool	not_max (fl x)
fl	vec_distance_sqr (const vec &a, const vec &b)
fl	sqr (const vec &v)
template<typename T >
sz	vector_append (std::vector< T > &x, const std::vector< T > &y)
template<typename T >
sz	find_min (const std::vector< T > &v)
void	normalize_angle (fl &x)
fl	normalized_angle (fl x)
template<typename T >
std::string	to_string (const T &x, std::streamsize width=0, char fill= ' ')
template<typename T >
T	sum (const std::vector< T > &v)
fl	pK_to_energy (fl pK)
void	print (fl x, std::ostream &out=std::cout)
void	print (sz x, std::ostream &out=std::cout)
void	print (const vec &v, std::ostream &out=std::cout)
template<typename T >
void	print (const std::vector< T > &v, std::ostream &out=std::cout)
template<typename T >
void	printnl (const T &x, std::ostream &out=std::cout)
bool	starts_with (const std::string &str, const std::string &start)
template<typename T >
bool	has (const std::vector< T > &v, const T &element)

Variables
const fl	not_a_num = std::sqrt(fl(-1))
const fl	pi = fl(3.1415926535897931)
const fl	fl_tolerance = fl(0.001)
const fl	fl_tolerance_r2 = fl(0.000001)
const fl	max_fl = (std::numeric_limits<fl>::max)()
const sz	max_sz = (std::numeric_limits<sz>::max)()
const unsigned	max_unsigned = (std::numeric_limits<unsigned>::max)()
const fl	epsilon_fl = std::numeric_limits<fl>::epsilon()
const fl	pK_to_energy_factor = -8.31 * 0.001 * 300 / 4.184 * std::log(10.0)

Macro Definition Documentation

#define VINA_CHECK

(

P

)

assert(P)

Referenced by ad_type_to_el_type(), parsing_struct::add(), model::append(), strictly_triangular_matrix< distance_type >::append(), model::assign_types(), average_difference(), axis_frame::axis_frame(), model::check_internal_pairs(), checked_convert_substring(), atom_type::covalent_radius(), current_weights(), do_search(), ad4_solvation::eval(), terms::eval_additive_aux(), naive_non_cache::eval_deriv(), terms::evale(), terms::evale_robust(), terms::evali(), term_set< additive >::filter(), terms::filter_external(), terms::filter_internal(), generate_external(), model::get_ligand_coords(), model::get_ligand_internal_coords(), conf_independent_inputs::get_names(), term_set< additive >::get_names(), get_type_pair_index(), model::gyration_radius(), parsing_struct::immobile_atom_coords(), precalculate_element::init_from_smooth_fst(), pdbqt_initializer::initialize_from_nrp(), pdbqt_initializer::initialize_from_rigid(), parsing_struct::insert_immobile(), parsing_struct::insert_immobile_inflex(), main_procedure(), manifold_phase(), monte_carlo::many_runs(), mutate_conf(), omit_whitespace(), monte_carlo::operator()(), manifold::operator()(), parallel_iter< F, Container, Input, Sync >::aux::operator()(), change::operator()(), parse_bundle(), parse_pdbqt_flex(), parse_pdbqt_ligand(), pearson(), postprocess_branch(), postprocess_ligand(), postprocess_residue(), precalculate::precalculate(), matrix< distance_type >::resize(), strictly_triangular_matrix< distance_type >::resize(), rmsd(), model::rmsd_ligands_upper_bound(), model::rmsd_lower_bound_asymmetric(), rmsd_upper_bound(), model::rmsd_upper_bound(), segment::segment(), set_rotor(), solvation_parameter(), string_write_coord(), model::verify_bond_lengths(), volume(), weighted_terms::weighted_terms(), precalculate_element::widen_smooth_fst(), write_all_output(), and model::write_ligand().

Typedef Documentation

typedef double fl

typedef std::size_t sz

typedef std::pair<fl, fl> pr

typedef std::vector<vec> vecv

typedef std::pair<vec, vec> vecp

typedef std::vector<fl> flv

typedef std::vector<pr> prv

typedef std::vector<sz> szv

typedef boost::filesystem::path path

Function Documentation

template<typename T >

T sqr

(

T

x

)

Referenced by recent_history::add(), model::assign_bonds(), pdb::check(), curl(), deviation(), naive_non_cache::eval(), non_cache::eval(), ad4_solvation::eval(), num_tors_sqr::eval(), non_cache::eval_deriv(), eval_interacting_pairs_deriv(), terms::evale(), terms::evale_robust(), terms::evali(), gaussian(), vec::norm_sqr(), pearson(), recent_history::possibly_smaller_than(), quaternion_norm_sqr(), quaternion_normalize(), quaternion_normalize_approx(), random_inside_sphere(), rmsd(), sqr(), rigid_conf::too_close(), vec_distance_sqr(), and precalculate_element::widen_smooth_fst().

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vec operator* ( fl  s, const vec &  v  )

inline

vec cross_product ( const vec &  a, const vec &  b  )

inline

Referenced by branches_derivative(), and atom_frame::sum_force_and_torque().

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vec elementwise_product ( const vec &  a, const vec &  b  )

inline

Referenced by grid::evaluate_aux().

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sz fl_to_sz ( fl  x, sz  max_sz  )

inline

References max_sz.

Referenced by manifold_phase(), and szv_grid::possibilities().

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bool eq ( fl  a, fl  b  )

inline

References fl_tolerance.

Referenced by angle_to_quaternion(), eq(), cache::load(), quaternion_is_normalized(), quaternion_normalize(), quaternion_normalize_approx(), quaternion_to_r3(), and segment::segment().

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bool eq_r2 ( fl  a, fl  b  )

inline

References fl_tolerance_r2.

Referenced by model::verify_bond_lengths().

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bool eq ( const vec &  a, const vec &  b  )

inline

References eq().

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template<typename T >

bool eq	(	const std::vector< T > &	a,
		const std::vector< T > &	b
	)

References eq(), and VINA_FOR_IN.

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const vec zero_vec	(	0	,
		0	,
		0
	)

Referenced by pdbqt_initializer::initialize_from_nrp(), quaternion_to_angle(), and rigid_conf::set_to_null().

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const vec max_vec	(	max_fl	,
		max_fl	,
		max_fl
	)

bool not_max ( fl  x )

inline

Referenced by curl(), do_search(), ad4_solvation::eval(), and model::rmsd_lower_bound_asymmetric().

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fl vec_distance_sqr ( const vec &  a, const vec &  b  )

inline

References sqr().

Referenced by beads::add(), model::assign_bonds(), brick_distance_sqr(), pdb::check(), model::clash_penalty_aux(), model::distance_sqr_between(), eval_interacting_pairs(), model::eval_intramolecular(), terms::evale(), terms::evale_robust(), terms::evali(), model::gyration_radius(), cache::populate(), model::rmsd_ligands_upper_bound(), model::rmsd_lower_bound_asymmetric(), rmsd_upper_bound(), model::rmsd_upper_bound(), and rigid_conf::too_close().

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fl sqr ( const vec &  v )

inline

References sqr().

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template<typename T >

sz vector_append	(	std::vector< T > &	x,
		const std::vector< T > &	y
	)

Referenced by appender::append().

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template<typename T >

sz find_min

(

const std::vector< T > &

v

)

References VINA_FOR_IN.

void normalize_angle ( fl &  x )

inline

References pi.

Referenced by angle_to_quaternion(), normalized_angle(), and torsions_increment().

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fl normalized_angle ( fl  x )

inline

References normalize_angle().

Referenced by torsions_increment(), and torsions_too_close().

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template<typename T >

std::string to_string	(	const T &	x,
		std::streamsize	width = 0,
		char	fill = ' '
	)

Referenced by ad4_solvation::ad4_solvation(), electrostatic< i >::electrostatic(), gauss::gauss(), hydrophobic::hydrophobic(), non_dir_h_bond::non_dir_h_bond(), non_hydrophobic::non_hydrophobic(), repulsion::repulsion(), and vdw< i, j >::vdw().

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template<typename T >

T sum

(

const std::vector< T > &

v

)

References VINA_FOR_IN.

Referenced by minus_mat_vec_product(), conf_size::num_degrees_of_freedom(), model::rmsd_ligands_upper_bound(), model::rmsd_lower_bound_asymmetric(), and model::rmsd_upper_bound().

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fl pK_to_energy ( fl  pK )

inline

void print ( fl  x, std::ostream &  out = std::cout  )

inline

Referenced by print(), and printnl().

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void print ( sz  x, std::ostream &  out = std::cout  )

inline

void print ( const vec &  v, std::ostream &  out = std::cout  )

inline

References print(), and VINA_FOR_IN.

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template<typename T >

void print	(	const std::vector< T > &	v,
		std::ostream &	out = std::cout
	)

References print(), and VINA_FOR_IN.

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template<typename T >

void printnl	(	const T &	x,
		std::ostream &	out = std::cout
	)

References print().

Referenced by ligand_change::print(), ligand_conf::print(), residue_change::print(), residue_conf::print(), and model::print_stuff().

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bool starts_with ( const std::string &  str, const std::string &  start  )

inline

Referenced by parse_pdb(), parse_pdbqt_aux(), parse_pdbqt_branch(), parse_pdbqt_flex(), parse_pdbqt_rigid(), parse_pdbqt_root(), and parse_pdbqt_root_aux().

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template<typename T >

bool has	(	const std::vector< T > &	v,
		const T &	element
	)

Referenced by model::bonded_to(), model::get_movable_atom_types(), and model::initialize_pairs().

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Variable Documentation

const fl not_a_num = std::sqrt(fl(-1))

Referenced by mat::mat(), and vec::vec().

const fl pi = fl(3.1415926535897931)

Referenced by manifold_phase(), mutate_conf(), normalize_angle(), quaternion_to_angle(), torsions_randomize(), and volume().

const fl fl_tolerance = fl(0.001)

Referenced by eq().

const fl fl_tolerance_r2 = fl(0.000001)

Referenced by eq_r2().

const fl max_fl = (std::numeric_limits<fl>::max)()

Referenced by do_search(), find_closest(), manifold_phase(), monte_carlo::operator()(), refine_structure(), model::rmsd_lower_bound_asymmetric(), monte_carlo::single_run(), and smooth_div().

const sz max_sz = (std::numeric_limits<sz>::max)()

Referenced by fl_to_sz(), atom_type::get(), and num_atom_types().

const unsigned max_unsigned = (std::numeric_limits<unsigned>::max)()

const fl epsilon_fl = std::numeric_limits<fl>::epsilon()

Referenced by angle_to_quaternion(), axis_frame::axis_frame(), bfgs(), bfgs_update(), curl(), electrostatic< i >::eval(), vdw< i, j >::eval(), precalculate_element::eval_deriv(), grid::evaluate_aux(), extrapolate_cap(), mutate_conf(), pairwise_clash_penalty(), pearson(), precalculate::precalculate(), quaternion_normalize(), quaternion_normalize_approx(), quaternion_to_angle(), random_orientation(), and smooth_div().

const fl pK_to_energy_factor = -8.31 * 0.001 * 300 / 4.184 * std::log(10.0)