Namespaces
namespace	CGAL
namespace	PDB
Classes
class	Radius_of_atom
class	Name_and_radius_of_atom
class	Name_of_pair
struct	Generic_classifier
struct	Weight_of_atoms
struct	Select_by_resname
struct	Select_by_atmname
struct	Select_by_element
class	Select_by_chainids
class	All_atom_system_builder
class	Radius_of_coarse_atom
struct	Color_of_atom
class	Color_of_residues
class	Coarse_creator_two_barycenters
class	Coarse_creator_closest_to_barycenter
class	Coarse_atom
class	Coarse_residue
struct	Coarse_atoms_iterators
struct	System_items_with_coarse_grain
struct	Not_functor
class	And_functors
class	Or_functors
struct	Traits_for_grid
struct	Grid_of_cubes
class	Line_reader
class	PDB_line_selector
class	PDB_line_selector_two_systems
class	PDB_line_selector_chain
class	Generic_line_selector
class	Molecular_system
class	Molecular_model
class	Molecular_chain
class	Molecular_residue
class	Molecular_atom
struct	Default_system_items
struct	No_occupancy_policy
struct	Accept_all_occupancy_policy
struct	Accept_none_occupancy_policy
class	Max_occupancy_policy
class	Min_occupancy_policy
class	Atom_list_occupancy_policy
class	Selected_atom_iterator
class	System_updater_from_xdrfile
class	Weighted_atom_iterator
class	Point_3
Typedefs
typedef Molecular_system < Default_system_items, Point_3 >	Default_system
typedef Molecular_system < System_items_with_coarse_grain, Point_3 >	Default_system_with_coarse_grain
Enumerations
enum	Reading_mode { ASCII, BZIP2, GZIP }
Functions
template<class NT , class Atom >
NT	get_radius (const Radius_of_atom< NT, Atom > &property)
template<class NT , class Coarse_atom >
NT	get_radius (const Radius_of_coarse_atom< NT, Coarse_atom > &property)
template<class Input_iterator , class System >
void	insert_coarse_atoms (Input_iterator first, Input_iterator last, System &system, int modelid=1, char chainid='Z', std::string resname="SOL", int starting_res_index=1)
template<class Model >
Coarse_atoms_iterators< Model > ::const_iterator	coarse_atoms_begin (const Model &model)
template<class Model >
Coarse_atoms_iterators< Model > ::const_iterator	coarse_atoms_end (const Model &model)
template<class Model >
Coarse_atoms_iterators< Model > ::iterator	coarse_atoms_begin (Model &model)
template<class Model >
Coarse_atoms_iterators< Model > ::iterator	coarse_atoms_end (Model &model)
template<class Point_3 , class Output_iterator >
void	fcc_lattice (const Point_3 &center, double radius, double min_edge_length, Output_iterator out)
template<class Point_3 , class Output_iterator >
void	fcc_lattice (const std::pair< Point_3, double > &cube, double radius, double expand_value, Output_iterator out)
template<class Atom >
bool	is_backbone (const Atom &atom)
template<class Atom >
bool	is_side_chain_or_CA (const Atom &atom)
template<class Atom >
bool	is_hydrogen (const Atom &atom)
template<class Atom >
bool	is_water (const Atom &atom)
template<class Atom_iterator , class Classifier_with_radius , class Color_of >
void	write_to_cgo (const std::string &filename, Atom_iterator first, Atom_iterator last, const Classifier_with_radius &classifier, const Color_of &color_of)
template<Reading_mode mode, class Line_selector , class Builder , class Occupancy_handler >
bool	read_a_pdb_file (const std::string &filename, Line_selector &sel, Builder &builder, const Occupancy_handler &occupancy, char altloc=' ')
template<class Line_selector , class Builder , class Occupancy_handler >
bool	read_a_pdb_file (const std::string &filename, Line_selector &sel, Builder &builder, const Occupancy_handler &occupancy, char altloc=' ')
template<class System >
char	get_chain_identifier (const Molecular_chain< System > &c)
template<class System >
const std::string &	get_residue_name (const Molecular_residue< System > &r)
template<class System >
int	get_residue_sequence_number (const Molecular_residue< System > &r)
template<class System >
char	get_insertion_code (const Molecular_residue< System > &r)
template<class System , class Point >
bool	get_is_hetatm (const Molecular_atom< System, Point > &a)
template<class System , class Point >
int	get_atom_serial_number (const Molecular_atom< System, Point > &a)
template<class System , class Point >
const std::string &	get_atom_name (const Molecular_atom< System, Point > &a)
template<class System , class Point >
char	get_alternate_location (const Molecular_atom< System, Point > &a)
template<class System , class Point >
double	get_occupancy (const Molecular_atom< System, Point > &a)
template<class System , class Point >
double	get_temperature_factor (const Molecular_atom< System, Point > &a)
template<class System , class Point >
const std::string &	get_element (const Molecular_atom< System, Point > &a)
template<class System , class Point >
int	get_charge (const Molecular_atom< System, Point > &a)
template<class System , class Point >
char	get_chain_identifier (const Molecular_atom< System, Point > &a)
template<class System , class Point >
const std::string &	get_residue_name (const Molecular_atom< System, Point > &a)
template<class System , class Point >
int	get_residue_sequence_number (const Molecular_atom< System, Point > &a)
template<class System , class Point >
char	get_insertion_code (const Molecular_atom< System, Point > &a)
template<class System , class Point >
char	get_x (const Molecular_atom< System, Point > &a)
template<class System , class Point >
char	get_y (const Molecular_atom< System, Point > &a)
template<class System , class Point >
char	get_z (const Molecular_atom< System, Point > &a)
template<class Mandatory_fields >
bool	get_is_hetatm (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
int	get_atom_serial_number (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
std::string	get_atom_name (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
char	get_alternate_location (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
double	get_occupancy (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
double	get_temperature_factor (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
std::string	get_element (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
int	get_charge (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
char	get_chain_identifier (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
std::string	get_residue_name (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
int	get_residue_sequence_number (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
char	get_insertion_code (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
char	get_x (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
char	get_y (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Mandatory_fields >
char	get_z (const std::pair< PDB::Line_format< Mandatory_fields >, std::string > &p)
template<class Model , class Subset_functor , bool is_const>
Selected_atom_iterator< Model, Subset_functor, is_const >	make_selected_atom_iterator (internal::Atoms_iterator_from_model< Model, is_const > iterator, const Subset_functor &functor)
template<class Subset_functor , class Model , bool is_const>
Selected_atom_iterator< Model, Subset_functor, is_const >	make_selected_atom_iterator (internal::Atoms_iterator_from_model< Model, is_const > iterator)
template<class NT >
NT	square (const NT &n)
template<class Point1 , class Point2 >
double	squared_distance (const Point1 &p1, const Point2 &p2)
template<class Iterator >
double	rms_no_align (Iterator begin1, Iterator end1, Iterator begin2, Iterator end2)
template<class Point_3 , class Iterator >
std::pair< Point_3, Point_3 >	bounding_box (Iterator begin, Iterator end)
template<class Point_3 , class Iterator >
std::pair< Point_3, double >	bounding_cube (Iterator begin, Iterator end)

Typedef Documentation

typedef Molecular_system<Default_system_items,Point_3 > ESBTL::Default_system

A default declaration of an all-atom system.

typedef Molecular_system<System_items_with_coarse_grain,Point_3 > ESBTL::Default_system_with_coarse_grain

A default declaration of an all-atom and coarse grain system.

Enumeration Type Documentation

enum ESBTL::Reading_mode

Modes available to read a PDB file:

ASCII stands for a non-compressed standard text file.
BZIP2 stands for a compressed file using bzip2 algorithm (see http://www.bzip.org/).
GZIP stands for a compressed file using gzip algorithm (see http://www.gzip.org/).

Enumerator:

ASCII
BZIP2
GZIP

Function Documentation

template<class Point_3 , class Iterator >

std::pair<Point_3,Point_3> ESBTL::bounding_box	(	Iterator	begin,
		Iterator	end
	)

Computes the bounding box containing a set of points.

Template Parameters:

Iterator	is an iterator over a set of points.
Point_3	is a point type with access method x() ,y() and z().

Parameters:

begin	first iterator of the set.
end	past end iterator of the set.

Returns:: a pair containing the lower corner and the upper corner of the bounding box.

template<class Point_3 , class Iterator >

std::pair<Point_3,double> ESBTL::bounding_cube	(	Iterator	begin,
		Iterator	end
	)		`[inline]`

Computes a cube containing a set of points.

Template Parameters:

Iterator	is an iterator over a set of points.
Point_3	is a point type with access method x() ,y() and z().

Parameters:

begin	first iterator of the set.
end	past end iterator of the set.

Returns:: a pair containing the lower corner and the edge length of the bounding cube.

template<class Point_3 , class Output_iterator >

void ESBTL::fcc_lattice	(	const Point_3 &	center,
		double	radius,
		double	min_edge_length,
		Output_iterator	out
	)

Computes a cube filled with a face centered cubic lattice of balls.

Template Parameters:

Point_3	is a point type with access method x() ,y() and z().
Output_iterator	is an output iterator of Point_3.

Parameters:

center	is the center of the cube.
radius	is the radius used for the balls to compute the lattice.
min_edge_length	is a lower bound of the edge length of the cube.
out	is an output iterator of Point_3.

template<class Point_3 , class Output_iterator >

void ESBTL::fcc_lattice	(	const std::pair< Point_3, double > &	cube,
		double	radius,
		double	expand_value,
		Output_iterator	out
	)		`[inline]`

Computes a cube filled with a face centered cubic lattice of balls.

Template Parameters:

Point_3	is a point type with access method x() ,y() and z().
Output_iterator	is an output iterator of Point_3.

Parameters:

cube	is a pair containing the lower corner of the cube to be filled and its edge length.
radius	is the radius used for the balls to compute the lattice.
expand_value	is the value of which the edge length of the cube must be increased.
out	is an output iterator of Point_3.

template<class Mandatory_fields >

char ESBTL::get_alternate_location ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

char ESBTL::get_alternate_location ( const Molecular_atom< System, Point > & a )

template<class Mandatory_fields >

std::string ESBTL::get_atom_name ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

const std::string& ESBTL::get_atom_name ( const Molecular_atom< System, Point > & a )

template<class Mandatory_fields >

int ESBTL::get_atom_serial_number ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

int ESBTL::get_atom_serial_number ( const Molecular_atom< System, Point > & a )

template<class System >

char ESBTL::get_chain_identifier ( const Molecular_chain< System > & c )

template<class Mandatory_fields >

char ESBTL::get_chain_identifier ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

char ESBTL::get_chain_identifier ( const Molecular_atom< System, Point > & a )

template<class Mandatory_fields >

int ESBTL::get_charge ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

int ESBTL::get_charge ( const Molecular_atom< System, Point > & a )

template<class Mandatory_fields >

std::string ESBTL::get_element ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

const std::string& ESBTL::get_element ( const Molecular_atom< System, Point > & a )

template<class Mandatory_fields >

char ESBTL::get_insertion_code ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

char ESBTL::get_insertion_code ( const Molecular_atom< System, Point > & a )

template<class System >

char ESBTL::get_insertion_code ( const Molecular_residue< System > & r )

template<class Mandatory_fields >

bool ESBTL::get_is_hetatm ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

bool ESBTL::get_is_hetatm ( const Molecular_atom< System, Point > & a )

template<class Mandatory_fields >

double ESBTL::get_occupancy ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

double ESBTL::get_occupancy ( const Molecular_atom< System, Point > & a )

template<class NT , class Coarse_atom >

NT ESBTL::get_radius ( const Radius_of_coarse_atom< NT, Coarse_atom > & property )

Extract the radius from a property of type ESBTL::Radius_of_coarse_atom

template<class NT , class Atom >

NT ESBTL::get_radius ( const Radius_of_atom< NT, Atom > & property )

Extract the radius from a property of type ESBTL::Radius_of_atom

template<class System >

const std::string& ESBTL::get_residue_name ( const Molecular_residue< System > & r )

template<class Mandatory_fields >

std::string ESBTL::get_residue_name ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

const std::string& ESBTL::get_residue_name ( const Molecular_atom< System, Point > & a )

template<class System >

int ESBTL::get_residue_sequence_number ( const Molecular_residue< System > & r )

template<class Mandatory_fields >

int ESBTL::get_residue_sequence_number ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

int ESBTL::get_residue_sequence_number ( const Molecular_atom< System, Point > & a )

template<class Mandatory_fields >

double ESBTL::get_temperature_factor ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

double ESBTL::get_temperature_factor ( const Molecular_atom< System, Point > & a )

template<class System , class Point >

char ESBTL::get_x ( const Molecular_atom< System, Point > & a )

template<class Mandatory_fields >

char ESBTL::get_x ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

char ESBTL::get_y ( const Molecular_atom< System, Point > & a )

template<class Mandatory_fields >

char ESBTL::get_y ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class System , class Point >

char ESBTL::get_z ( const Molecular_atom< System, Point > & a )

template<class Mandatory_fields >

char ESBTL::get_z ( const std::pair< PDB::Line_format< Mandatory_fields >, std::string > & p )

template<class Input_iterator , class System >

void ESBTL::insert_coarse_atoms	(	Input_iterator	first,
		Input_iterator	last,
		System &	system,
		int	modelid = `1`,
		char	chainid = `'Z'`,
		std::string	resname = `"SOL"`,
		int	starting_res_index = `1`
	)

Inserts a set of coarse grain atoms in a molecule using one residue per such atom.

Template Parameters:

Input_iterator	is an iterator type over point type objects. This type must be the one used to defined the coarse grain atom type in System.
System	is a coarse-grain system.

Parameters:

first	is the first iterator over the range of points.
last	is the past-end iterator over the range of points.
system	is the system in which coarse grain atoms must be inserted.
modelid	is the number of the model of the system in which coarse grain atoms must be inserted.
chainid	is the id of the chain of the model in which coarse grain atoms must be inserted.
resname	is the name of the residues in which coarse grain atoms must be inserted.
starting_res_index	is the residue sequence number of the first residue inserted. Other coarse grain atoms will use an increasing number starting from this value.

template<class Atom >

bool ESBTL::is_backbone ( const Atom & atom )

Check if an atom belong to the backbone of a protein. The check is done on the atom name. An atom is considered to belong to the backbone if its atom name is either N, C, CA, OXT or O.

Template Parameters:

Atom	must represent an atom, global function ESBTL::get_atom_name and ESBTL::get_is_hetatm, both taking an object of this type must exits.

Parameters:

atom	represents an atom.

template<class Atom >

bool ESBTL::is_hydrogen ( const Atom & atom )

Check if an atom is an hydrogen.

Template Parameters:

Atom	must represent an atom, global function ESBTL::get_element taking an object of this type must exits.

Parameters:

atom	represents an atom.

template<class Atom >

bool ESBTL::is_side_chain_or_CA ( const Atom & atom )

Check if an atom belong to a protein side-chain or is carbon alpha atom. The check is done on the atom name. An atom is considered to belong to the backbone if its atom name is either N, C, CA, OXT or O. Carbon alpha atom name is CA.

Template Parameters:

Atom	must represent an atom, global function ESBTL::get_atom_name and ESBTL::get_is_hetatm, both taking an object of this type must exits.

Parameters:

atom	represents an atom.

template<class Atom >

bool ESBTL::is_water ( const Atom & atom )

Check if an atom belongs to a water molecule. An atom is considered to belong to a water molecule if its residue name is either HOH, SOL or WAT.

Template Parameters:

Atom	must represent an atom, global function ESBTL::get_residue_name taking an object of this type must exits.

Parameters:

atom	represents an atom.

template<class Model , class Subset_functor , bool is_const>

Selected_atom_iterator<Model,Subset_functor,is_const> ESBTL::make_selected_atom_iterator	(	internal::Atoms_iterator_from_model< Model, is_const >	iterator,
		const Subset_functor &	functor
	)

Short cut function to construct a Selected_atom_iterator.

template<class Subset_functor , class Model , bool is_const>

Selected_atom_iterator<Model,Subset_functor,is_const> ESBTL::make_selected_atom_iterator ( internal::Atoms_iterator_from_model< Model, is_const > iterator )

Short cut function to construct a Selected_atom_iterator.

template<Reading_mode mode, class Line_selector , class Builder , class Occupancy_handler >

bool ESBTL::read_a_pdb_file	(	const std::string &	filename,
		Line_selector &	sel,
		Builder &	builder,
		const Occupancy_handler &	occupancy,
		char	altloc = `' '`
	)		`[inline]`

Short cuts to read a PDB file. See the documentation of ESBTL::Line_reader::read for more details.

template<class Line_selector , class Builder , class Occupancy_handler >

bool ESBTL::read_a_pdb_file	(	const std::string &	filename,
		Line_selector &	sel,
		Builder &	builder,
		const Occupancy_handler &	occupancy,
		char	altloc = `' '`
	)		`[inline]`

template<class Iterator >

double ESBTL::rms_no_align	(	Iterator	begin1,
		Iterator	end1,
		Iterator	begin2,
		Iterator	end2
	)

Computes the root mean square deviation (RMSD) between two sets of atoms.

Precondition:: The two sets must have the same size, and corresponding atoms must be enumerated in the same order.

Template Parameters:

Iterator is an iterator over a point type providing access functions x(),y() and z().

Parameters:

begin1	is the first element of the first range of points.
end1	is the past-end iterator over elements of the first range of points.
begin2	is the first element of the second range of points.
end2	is the past-end iterator over elements of the second range of points.

Returns:: The RMSD between two sets of points.

template<class NT >

NT ESBTL::square ( const NT & n ) [inline]

Computes the square of n.

Template Parameters:

NT	is the number type of the input.

Parameters:

n	is the number to be squared.

Returns:: the square of n.

template<class Point1 , class Point2 >

double ESBTL::squared_distance	(	const Point1 &	p1,
		const Point2 &	p2
	)		`[inline]`

Computes the squared distance between two points.

Template Parameters:

Point1	is a point type providing access functions x(),y() and z().
Point2	is a point type providing access functions x(),y() and z().

Parameters:

p1	is the first point.
p2	is the second point.

Returns:: the squared distance between p1 and p2.

template<class Atom_iterator , class Classifier_with_radius , class Color_of >

void ESBTL::write_to_cgo	(	const std::string &	filename,
		Atom_iterator	first,
		Atom_iterator	last,
		const Classifier_with_radius &	classifier,
		const Color_of &	color_of
	)

Create a python script that can be run using PyMol and that load a cgo objects representing a set of (pseudo-) atoms as a set of balls.

Template Parameters:

Atom_iterator	iterator over a set of atoms.
Classifier_with_radius	is a classifier that attributes a radius to an atom.
Color_of	is a classifier that attributes a color to an atom (such as ESBTL::Color_of_atom).

Parameters:

filename	is the name of the script to be created.
first	is the iterator of the first atom of the set.
last	is the past-end iterator of the last atom of the set.
classifier	attributes a radius to an atom.
color_of	attributes a color to an atom.

Namespaces

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

Enumeration Type Documentation

Function Documentation