model.cpp File Reference

#include "model.h"
#include "file.h"
#include "curl.h"

Include dependency graph for model.cpp:

Classes
struct	branch_metrics
struct	appender_info
class	appender
struct	bond_less
struct	beads

Functions
template<typename T >
atom_range	get_atom_range (const T &t)
template<typename T >
branch_metrics	get_branch_metrics (const T &t)
void	string_write_coord (sz i, fl x, std::string &str)
std::string	coords_to_pdbqt_string (const vec &coords, const std::string &str)
fl	eval_interacting_pairs (const precalculate &p, fl v, const interacting_pairs &pairs, const vecv &coords)
fl	eval_interacting_pairs_deriv (const precalculate &p, fl v, const interacting_pairs &pairs, const vecv &coords, vecv &forces)
fl	pairwise_clash_penalty (fl r, fl covalent_r)

Function Documentation

template<typename T >

atom_range get_atom_range

(

const T &

t

)

References atom_range::begin, atom_range::end, and VINA_FOR_IN.

Referenced by ligand::set_range().

Here is the caller graph for this function:

template<typename T >

branch_metrics get_branch_metrics

(

const T &

t

)

References branch_metrics::corner2corner, branch_metrics::length, and VINA_FOR_IN.

Referenced by model::ligand_length(), and model::ligand_longest_branch().

Here is the caller graph for this function:

void string_write_coord	(	sz	i,
		fl	x,
		std::string &	str
	)

References VINA_CHECK, and VINA_FOR.

Referenced by coords_to_pdbqt_string().

Here is the caller graph for this function:

std::string coords_to_pdbqt_string	(	const vec &	coords,
		const std::string &	str
	)

References string_write_coord().

Referenced by model::write_context().

Here is the call graph for this function:

Here is the caller graph for this function:

fl eval_interacting_pairs	(	const precalculate &	p,
		fl	v,
		const interacting_pairs &	pairs,
		const vecv &	coords
	)

References interacting_pair::a, interacting_pair::b, curl(), precalculate::cutoff_sqr(), precalculate::eval_fast(), interacting_pair::type_pair_index, vec_distance_sqr(), and VINA_FOR_IN.

Referenced by model::eval(), model::eval_intramolecular(), model::evale(), and model::evali().

Here is the call graph for this function:

Here is the caller graph for this function:

fl eval_interacting_pairs_deriv	(	const precalculate &	p,
		fl	v,
		const interacting_pairs &	pairs,
		const vecv &	coords,
		vecv &	forces
	)

References interacting_pair::a, interacting_pair::b, curl(), precalculate::cutoff_sqr(), precalculate::eval_deriv(), sqr(), interacting_pair::type_pair_index, and VINA_FOR_IN.

Referenced by model::eval_deriv().

Here is the call graph for this function:

Here is the caller graph for this function:

fl pairwise_clash_penalty	(	fl	r,
		fl	covalent_r
	)

References epsilon_fl.

Referenced by model::clash_penalty_aux().

Here is the caller graph for this function: