atom Class Reference

Atom attributes. More...

#include <hierarchy.h>

Inherited by atom_with_labels.

List of all members.

Public Member Functions

atom (atom_group const &parent, vec3 const &xyz=vec3(0, 0, 0), vec3 const &sigxyz=vec3(0, 0, 0), double occ=0, double sigocc=0, double b=0, double sigb=0, sym_mat3 const &uij=sym_mat3(-1,-1,-1,-1,-1,-1), sym_mat3 const &siguij=sym_mat3(-1,-1,-1,-1,-1,-1), bool hetero=false, const char *serial="", const char *name="", const char *segid="", const char *element="", const char *charge="")

atom (vec3 const &xyz=vec3(0, 0, 0), vec3 const &sigxyz=vec3(0, 0, 0), double occ=0, double sigocc=0, double b=0, double sigb=0, sym_mat3 const &uij=sym_mat3(-1,-1,-1,-1,-1,-1), sym_mat3 const &siguij=sym_mat3(-1,-1,-1,-1,-1,-1), bool hetero=false, const char *serial="", const char *name="", const char *segid="", const char *element="", const char *charge="")

atom (vec3 const &xyz, vec3 const &sigxyz, double occ, double sigocc, double b, double sigb, sym_mat3 const &uij, sym_mat3 const &siguij, bool hetero, str5 serial, str4 name, str4 segid, str2 element, str2 charge)

atom (atom_group const &parent, atom const &other)

atom detached_copy () const

atom & set_xyz (vec3 const &new_xyz)

atom & set_sigxyz (vec3 const &new_sigxyz)

atom & set_occ (double new_occ)

atom & set_sigocc (double new_sigocc)

atom & set_b (double new_b)

atom & set_sigb (double new_sigb)

atom & set_uij (sym_mat3 const &new_uij)

atom & set_siguij (sym_mat3 const &)

atom & set_hetero (double new_hetero)

atom & set_serial (const char *new_serial)

atom & set_name (const char *new_name)

atom & set_segid (const char *new_segid)

atom & set_element (const char *new_element)

atom & set_charge (const char *new_charge)

std::size_t memory_id () const

shared_ptr< atom_group_data > parent_ptr () const

Not available in Python.

boost::optional< atom_group > parent () const

int serial_as_int () const

bool uij_is_defined () const

void uij_erase () const

bool siguij_is_defined () const

void siguij_erase () const

void format_atom_record_serial_label_columns (char *result, atom_label_columns_formatter *label_formatter=0) const

Not available in Python.

unsigned format_atom_record_segid_element_charge_columns (char *result, unsigned segid_start, unsigned blanks_start_at) const

Not available in Python.

void format_pdb_element_charge_columns (char *result) const

Not available in Python.

std::string pdb_label_columns () const

small_str< 19 > pdb_label_columns_segid_small_str () const

Not available in Python.

std::string pdb_element_charge_columns () const

std::string id_str (bool pdbres=false, bool suppress_segid=false) const

model=" 1" pdb=" N GLY A 1 " segid="S001"

unsigned format_atom_record (char *result, atom_label_columns_formatter *label_formatter=0, const char *replace_floats_with=0) const

Not available in Python.

unsigned format_sigatm_record (char *result, atom_label_columns_formatter *label_formatter) const

Not available in Python.

unsigned format_anisou_record (char *result, atom_label_columns_formatter *label_formatter=0) const

Not available in Python.

unsigned format_siguij_record (char *result, atom_label_columns_formatter *label_formatter=0) const

Not available in Python.

unsigned format_atom_record_group (char *result, atom_label_columns_formatter *label_formatter, bool atom_hetatm, bool sigatm, bool anisou, bool siguij) const

Not available in Python.

std::string quote (bool full=false) const

atom_with_labels fetch_labels () const

bool element_is_hydrogen () const

boost::optional< std::string > determine_chemical_element_simple () const

bool set_chemical_element_simple_if_necessary (bool tidy_existing=true)

Static Public Member Functions

static std::size_t sizeof_data ()

static bool has_siguij ()

Public Attributes

shared_ptr< atom_data > data

Friends

class atom_group

Detailed Description

Atom attributes.

Member Function Documentation

void format_atom_record_serial_label_columns	(	char *	result,
		atom_label_columns_formatter *	label_formatter = `0`
	)			const

Not available in Python.

result must point to an array of size 27 (or greater). The first 6 characters are not modified. On return, result is NOT null-terminated.

unsigned format_atom_record_segid_element_charge_columns	(	char *	result,
		unsigned	segid_start,
		unsigned	blanks_start_at
	)			const

Not available in Python.