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), double fp=0, double fdp=0, 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), double fp=0, double fdp=0, 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, double fp, double fdp, bool hetero, str5 serial, str4 name, str4 segid, str2 element, str2 charge)
 atom (atom_group const &parent, atom const &other)
atom detached_copy () const
atomset_xyz (vec3 const &new_xyz)
atomset_sigxyz (vec3 const &new_sigxyz)
atomset_occ (double new_occ)
atomset_sigocc (double new_sigocc)
atomset_b (double new_b)
atomset_sigb (double new_sigb)
atomset_uij (sym_mat3 const &new_uij)
atomset_siguij (sym_mat3 const &)
atomset_fp (double new_fp)
atomset_fdp (double new_fdp)
atomset_hetero (double new_hetero)
atomset_serial (const char *new_serial)
atomset_name (const char *new_name)
atomset_segid (const char *new_segid)
atomset_element (const char *new_element)
atomset_charge (const char *new_charge)
std::size_t memory_id () const
shared_ptr< atom_group_dataparent_ptr () const
 Not available in Python.
boost::optional< atom_groupparent (bool optional=true) 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)
boost::optional< std::string > charge_tidy (bool strip=false) const
double distance (vec3 const &other_xyz)
double distance (atom const &other)
boost::optional< double > angle (vec3 const &atom_1_xyz, vec3 const &atom_3_xyz, bool deg=false)
boost::optional< double > angle (atom const &atom_1, atom const &atom_3, bool deg=false)

Static Public Member Functions

static std::size_t sizeof_data ()
static bool has_siguij ()

Public Attributes

shared_ptr< atom_datadata

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.

result must point to an array of size 81 (or greater). On return, result is null-terminated.

void format_pdb_element_charge_columns ( char *  result  )  const

Not available in Python.

result must point to an array of size 4 (or greater). On return, result is NOT null-terminated.

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

Not available in Python.

result must point to an array of size 81 (or greater). On return, result is null-terminated.

unsigned format_sigatm_record ( char *  result,
atom_label_columns_formatter label_formatter 
) const

Not available in Python.

result must point to an array of size 81 (or greater). On return, result is null-terminated.

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

Not available in Python.

result must point to an array of size 81 (or greater). On return, result is null-terminated.

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

Not available in Python.

result must point to an array of size 81 (or greater). On return, result is null-terminated.

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.

result must point to an array of size 324 (or greater). On return, result is null-terminated.


The documentation for this class was generated from the following file:

Generated on Thu Jun 19 15:35:08 2014 for cctbx by  doxygen 1.5.6