parse_pdbqt.cpp File Reference

#include <fstream>
#include <sstream>
#include <cctype>
#include <boost/utility.hpp>
#include <boost/optional.hpp>
#include <boost/filesystem/fstream.hpp>
#include <boost/lexical_cast.hpp>
#include "parse_pdbqt.h"
#include "atom_constants.h"
#include "file.h"
#include "convert_substring.h"
#include "parse_error.h"

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Classes
struct	stream_parse_error
struct	parsed_atom
struct	atom_syntax_error
struct	atom_reference
struct	movable_atom
struct	rigid
struct	non_rigid_parsed
struct	parsing_struct
struct	parsing_struct::node_t< T >
struct	pdbqt_initializer

Typedefs
typedef std::vector< movable_atom >	mav
typedef std::pair< sz, sz >	axis_numbers
typedef boost::optional < axis_numbers >	axis_numbers_option

Functions
void	add_context (context &c, std::string &str)
std::string	omit_whitespace (const std::string &str, sz i, sz j)
template<typename T >
T	checked_convert_substring (const std::string &str, sz i, sz j, const std::string &dest_nature)
parsed_atom	parse_pdbqt_atom_string (const std::string &str)
unsigned	parse_one_unsigned (const std::string &str, const std::string &start, unsigned count)
void	parse_two_unsigneds (const std::string &str, const std::string &start, unsigned count, unsigned &first, unsigned &second)
void	parse_pdbqt_rigid (const path &name, rigid &r)
void	parse_pdbqt_root_aux (std::istream &in, unsigned &count, parsing_struct &p, context &c)
void	parse_pdbqt_root (std::istream &in, unsigned &count, parsing_struct &p, context &c)
void	parse_pdbqt_branch (std::istream &in, unsigned &count, parsing_struct &p, context &c, unsigned from, unsigned to)
void	parse_pdbqt_branch_aux (std::istream &in, unsigned &count, const std::string &str, parsing_struct &p, context &c)
void	parse_pdbqt_aux (std::istream &in, unsigned &count, parsing_struct &p, context &c, boost::optional< unsigned > &torsdof, bool residue)
void	parse_pdbqt_aux (std::stringstream &in, unsigned &count, parsing_struct &p, context &c, boost::optional< unsigned > &torsdof, bool residue)
void	add_bonds (non_rigid_parsed &nr, boost::optional< atom_reference > atm, const atom_range &r)
void	set_rotor (non_rigid_parsed &nr, boost::optional< atom_reference > axis_begin, boost::optional< atom_reference > axis_end)
void	nr_update_matrixes (non_rigid_parsed &nr)
template<typename B >
void	postprocess_branch (non_rigid_parsed &nr, parsing_struct &p, context &c, B &b)
void	postprocess_ligand (non_rigid_parsed &nr, parsing_struct &p, context &c, unsigned torsdof)
void	postprocess_residue (non_rigid_parsed &nr, parsing_struct &p, context &c)
void	parse_pdbqt_ligand (const path &name, non_rigid_parsed &nr, context &c)
void	parse_pdbqt_ligand (std::stringstream &ligSS, non_rigid_parsed &nr, context &c)
void	parse_pdbqt_residue (std::istream &in, unsigned &count, parsing_struct &p, context &c)
void	parse_pdbqt_flex (const path &name, non_rigid_parsed &nr, context &c)
model	parse_ligand_pdbqt (const path &name)
model	parse_ligand_pdbqt (std::stringstream &ligSS)
model	parse_receptor_pdbqt (const path &rigid_name, const path &flex_name)
model	parse_receptor_pdbqt (const path &rigid_name)

Typedef Documentation

typedef std::vector<movable_atom> mav

typedef std::pair<sz, sz> axis_numbers

typedef boost::optional<axis_numbers> axis_numbers_option

Function Documentation

void add_context	(	context &	c,
		std::string &	str
	)

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

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std::string omit_whitespace	(	const std::string &	str,
		sz	i,
		sz	j
	)

References VINA_CHECK.

Referenced by parse_pdbqt_atom_string().

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template<typename T >

T checked_convert_substring	(	const std::string &	str,
		sz	i,
		sz	j,
		const std::string &	dest_nature
	)

References VINA_CHECK.

parsed_atom parse_pdbqt_atom_string

(

const std::string &

str

)

References atom_type::acceptable_type(), is_non_ad_metal_name(), omit_whitespace(), string_to_ad_type(), substring_is_blank(), atom_type::xs, and XS_TYPE_Met_D.

Referenced by parse_pdbqt_branch(), parse_pdbqt_rigid(), and parse_pdbqt_root_aux().

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unsigned parse_one_unsigned	(	const std::string &	str,
		const std::string &	start,
		unsigned	count
	)

Referenced by parse_pdbqt_aux().

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void parse_two_unsigneds	(	const std::string &	str,
		const std::string &	start,
		unsigned	count,
		unsigned &	first,
		unsigned &	second
	)

Referenced by parse_pdbqt_branch(), and parse_pdbqt_branch_aux().

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void parse_pdbqt_rigid	(	const path &	name,
		rigid &	r
	)

References rigid::atoms, atom_syntax_error::nature, parse_pdbqt_atom_string(), and starts_with().

Referenced by parse_receptor_pdbqt().

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void parse_pdbqt_root_aux	(	std::istream &	in,
		unsigned &	count,
		parsing_struct &	p,
		context &	c
	)

References parsing_struct::add(), add_context(), atom_syntax_error::nature, parse_pdbqt_atom_string(), and starts_with().

Referenced by parse_pdbqt_root().

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void parse_pdbqt_root	(	std::istream &	in,
		unsigned &	count,
		parsing_struct &	p,
		context &	c
	)

References add_context(), parse_pdbqt_root_aux(), and starts_with().

Referenced by parse_pdbqt_aux().

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void parse_pdbqt_branch	(	std::istream &	in,
		unsigned &	count,
		parsing_struct &	p,
		context &	c,
		unsigned	from,
		unsigned	to
	)

References parsing_struct::add(), add_context(), parsing_struct::atoms, parsing_struct::immobile_atom, atom_syntax_error::nature, parsed_atom::number, parse_pdbqt_atom_string(), parse_pdbqt_branch_aux(), parse_two_unsigneds(), and starts_with().

Referenced by parse_pdbqt_branch_aux().

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void parse_pdbqt_branch_aux	(	std::istream &	in,
		unsigned &	count,
		const std::string &	str,
		parsing_struct &	p,
		context &	c
	)

References parsing_struct::atoms, parse_pdbqt_branch(), and parse_two_unsigneds().

Referenced by parse_pdbqt_aux(), and parse_pdbqt_branch().

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void parse_pdbqt_aux	(	std::istream &	in,
		unsigned &	count,
		parsing_struct &	p,
		context &	c,
		boost::optional< unsigned > &	torsdof,
		bool	residue
	)

References add_context(), parse_one_unsigned(), parse_pdbqt_branch_aux(), parse_pdbqt_root(), and starts_with().

Referenced by parse_pdbqt_ligand(), and parse_pdbqt_residue().

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void parse_pdbqt_aux	(	std::stringstream &	in,
		unsigned &	count,
		parsing_struct &	p,
		context &	c,
		boost::optional< unsigned > &	torsdof,
		bool	residue
	)

References add_context(), parse_one_unsigned(), parse_pdbqt_branch_aux(), parse_pdbqt_root(), and starts_with().

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void add_bonds	(	non_rigid_parsed &	nr,
		boost::optional< atom_reference >	atm,
		const atom_range &	r
	)

References non_rigid_parsed::atoms_atoms_bonds, non_rigid_parsed::atoms_inflex_bonds, atom_range::begin, DISTANCE_FIXED, atom_range::end, atom_reference::index, atom_reference::inflex, and VINA_RANGE.

Referenced by postprocess_branch().

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void set_rotor	(	non_rigid_parsed &	nr,
		boost::optional< atom_reference >	axis_begin,
		boost::optional< atom_reference >	axis_end
	)

References non_rigid_parsed::atoms_atoms_bonds, non_rigid_parsed::atoms_inflex_bonds, DISTANCE_ROTOR, atom_reference::index, atom_reference::inflex, non_rigid_parsed::inflex_inflex_bonds, and VINA_CHECK.

Referenced by postprocess_branch().

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void nr_update_matrixes

(

non_rigid_parsed &

nr

)

References non_rigid_parsed::atoms, non_rigid_parsed::atoms_atoms_bonds, non_rigid_parsed::atoms_inflex_bonds, DISTANCE_FIXED, DISTANCE_VARIABLE, non_rigid_parsed::inflex, non_rigid_parsed::inflex_inflex_bonds, matrix< T >::resize(), and strictly_triangular_matrix< T >::resize().

Referenced by postprocess_branch(), postprocess_ligand(), and postprocess_residue().

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template<typename B >

void postprocess_branch	(	non_rigid_parsed &	nr,
		parsing_struct &	p,
		context &	c,
		B &	b
	)

References parsing_struct::node_t< T >::a, add_bonds(), non_rigid_parsed::atoms, parsing_struct::atoms, non_rigid_parsed::atoms_atoms_bonds, non_rigid_parsed::atoms_inflex_bonds, parsing_struct::axis_begin, parsing_struct::axis_end, atom::coords, strictly_triangular_matrix< T >::dim(), matrix< T >::dim_1(), matrix< T >::dim_2(), DISTANCE_FIXED, parsing_struct::essentially_empty(), parsing_struct::immobile_atom, parsing_struct::immobile_atom_coords(), non_rigid_parsed::inflex, parsing_struct::node_t< T >::insert(), parsing_struct::node_t< T >::insert_immobiles(), nr_update_matrixes(), parsing_struct::node_t< T >::ps, set_rotor(), VINA_CHECK, VINA_FOR_IN, and VINA_RANGE.

Referenced by postprocess_ligand(), and postprocess_residue().

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void postprocess_ligand	(	non_rigid_parsed &	nr,
		parsing_struct &	p,
		context &	c,
		unsigned	torsdof
	)

References parsing_struct::atoms, non_rigid_parsed::ligands, nr_update_matrixes(), postprocess_branch(), and VINA_CHECK.

Referenced by parse_pdbqt_ligand().

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void postprocess_residue	(	non_rigid_parsed &	nr,
		parsing_struct &	p,
		context &	c
	)

References parsing_struct::node_t< T >::a, non_rigid_parsed::atoms, parsing_struct::atoms, non_rigid_parsed::atoms_atoms_bonds, non_rigid_parsed::atoms_inflex_bonds, atom::coords, strictly_triangular_matrix< T >::dim(), matrix< T >::dim_1(), matrix< T >::dim_2(), parsing_struct::essentially_empty(), non_rigid_parsed::flex, parsing_struct::immobile_atom_coords(), non_rigid_parsed::inflex, parsing_struct::node_t< T >::insert_immobiles_inflex(), parsing_struct::node_t< T >::insert_inflex(), nr_update_matrixes(), postprocess_branch(), parsing_struct::node_t< T >::ps, VINA_CHECK, and VINA_FOR_IN.

Referenced by parse_pdbqt_flex().

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void parse_pdbqt_ligand	(	const path &	name,
		non_rigid_parsed &	nr,
		context &	c
	)

References non_rigid_parsed::atoms, parsing_struct::atoms, non_rigid_parsed::atoms_atoms_bonds, strictly_triangular_matrix< T >::dim(), parse_pdbqt_aux(), postprocess_ligand(), stream_parse_error::to_parse_error(), and VINA_CHECK.

Referenced by parse_ligand_pdbqt().

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void parse_pdbqt_ligand	(	std::stringstream &	ligSS,
		non_rigid_parsed &	nr,
		context &	c
	)

References non_rigid_parsed::atoms, parsing_struct::atoms, non_rigid_parsed::atoms_atoms_bonds, strictly_triangular_matrix< T >::dim(), parse_pdbqt_aux(), postprocess_ligand(), stream_parse_error::to_parse_error(), and VINA_CHECK.

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void parse_pdbqt_residue	(	std::istream &	in,
		unsigned &	count,
		parsing_struct &	p,
		context &	c
	)

References parse_pdbqt_aux().

Referenced by parse_pdbqt_flex().

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void parse_pdbqt_flex	(	const path &	name,
		non_rigid_parsed &	nr,
		context &	c
	)

References add_context(), non_rigid_parsed::atoms, non_rigid_parsed::atoms_atoms_bonds, strictly_triangular_matrix< T >::dim(), parse_pdbqt_residue(), postprocess_residue(), starts_with(), stream_parse_error::to_parse_error(), and VINA_CHECK.

Referenced by parse_receptor_pdbqt().

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model parse_ligand_pdbqt

(

const path &

name

)

References pdbqt_initializer::initialize(), pdbqt_initializer::initialize_from_nrp(), pdbqt_initializer::m, non_rigid_parsed::mobility_matrix(), and parse_pdbqt_ligand().

Referenced by parse_bundle().

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model parse_ligand_pdbqt

(

std::stringstream &

ligSS

)

References pdbqt_initializer::initialize(), pdbqt_initializer::initialize_from_nrp(), pdbqt_initializer::m, non_rigid_parsed::mobility_matrix(), and parse_pdbqt_ligand().

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model parse_receptor_pdbqt	(	const path &	rigid_name,
		const path &	flex_name
	)

References pdbqt_initializer::initialize(), pdbqt_initializer::initialize_from_nrp(), pdbqt_initializer::initialize_from_rigid(), pdbqt_initializer::m, non_rigid_parsed::mobility_matrix(), parse_pdbqt_flex(), and parse_pdbqt_rigid().

Referenced by parse_bundle().

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model parse_receptor_pdbqt

(

const path &

rigid_name

)

References pdbqt_initializer::initialize(), pdbqt_initializer::initialize_from_rigid(), pdbqt_initializer::m, and parse_pdbqt_rigid().

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