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dsrpdb::Atom

dsrpdb::Atom Class Reference

#include <Atom.h>

List of all members.

Detailed Description

A class repesenting an atom.

Definition at line 30 of file Atom.h.

Public Types

typedef PDB_index< Atom > Index
enum  Type

Public Member Functions

 Atom ()
Index index () const
void set_index (Index i)
const Point & cartesian_coords () const
void set_cartesian_coords (const Point &pt)
bool operator< (const Atom &o) const
bool operator== (const Atom &al) const
bool operator!= (const Atom &al) const
float occupancy () const
void set_occupancy (float o)
float temperature_factor () const
void set_temperature_factor (float f)
const char * segment_id () const
void set_segment_id (const char *c)
const char * element () const
void set_element (const char *c)
const char * charge () const
void set_charge (const char *c)
Type type () const
void set_type (Type t)

Protected Attributes

Index index_
Type type_
Point coordinates_
float occupancy_
float temp_factor_
std::string segID_
std::string element_
std::string charge_

Friends

class Residue

Member Typedef Documentation

typedef PDB_index<Atom> dsrpdb::Atom::Index
 

The type to represent the atoms index in the PDB file.

Definition at line 34 of file Atom.h.

Member Enumeration Documentation

enum dsrpdb::Atom::Type
 

The type (element) of an atom. The currently supported types are C,N,H,O,S, INVALID.

Definition at line 37 of file Atom.h.

Constructor & Destructor Documentation

dsrpdb::Atom::Atom (   )  [inline]
 

Construct and invalid atom.

Definition at line 165 of file Atom.h.

Member Function Documentation

const Point & dsrpdb::Atom::cartesian_coords (   )  const [inline]
 

Cartesian coordinates (x,y,z) for the atom.

Definition at line 102 of file Atom.h.

References coordinates_.

const char * dsrpdb::Atom::charge (   )  const [inline]
 

The PDB charge field.

Definition at line 157 of file Atom.h.

References charge_.

const char * dsrpdb::Atom::element (   )  const [inline]
 

The PDB element field.

Definition at line 149 of file Atom.h.

References element_.

Atom::Index dsrpdb::Atom::index (   )  const [inline]
 

The int index of the atom (atom number in a PDB -1).

Note:
these are 0 based, and the PDB is 1 based, so this is the PDB index -1

Definition at line 88 of file Atom.h.

References index_.

Referenced by dsrpdb::Protein::Bonds_iterator::cur_bond().

float dsrpdb::Atom::occupancy (   )  const [inline]
 

The PDB occupancy field.

Definition at line 125 of file Atom.h.

References occupancy_.

const char * dsrpdb::Atom::segment_id (   )  const [inline]
 

The PDB segment ID char.

Definition at line 141 of file Atom.h.

References segID_.

void dsrpdb::Atom::set_cartesian_coords (  const Point &  pt  )  [inline]
 

Set the cartesian coordinates.

Definition at line 106 of file Atom.h.

References coordinates_.

void dsrpdb::Atom::set_charge (  const char *  c  )  [inline]
 

Set the PDB charge field value.

Definition at line 161 of file Atom.h.

References charge_.

void dsrpdb::Atom::set_element (  const char *  c  )  [inline]
 

Set the element.

Definition at line 153 of file Atom.h.

References element_.

void dsrpdb::Atom::set_index (  Index  i  )  [inline]
 

Set the index.

Definition at line 93 of file Atom.h.

References index_.

void dsrpdb::Atom::set_occupancy (  float  o  )  [inline]
 

Set the PDB occupancy field.

Definition at line 129 of file Atom.h.

References occupancy_.

void dsrpdb::Atom::set_segment_id (  const char *  c  )  [inline]
 

Set the PDB segment ID char.

Definition at line 145 of file Atom.h.

References segID_.

void dsrpdb::Atom::set_temperature_factor (  float  f  )  [inline]
 

Set the PDB temperature factor field.

Definition at line 137 of file Atom.h.

References temp_factor_.

void dsrpdb::Atom::set_type (  Type  t  )  [inline]
 

Set the element.

Definition at line 100 of file Atom.h.

References type_.

float dsrpdb::Atom::temperature_factor (   )  const [inline]
 

The PDB temperature factor field.

Definition at line 133 of file Atom.h.

References temp_factor_.

Atom::Type dsrpdb::Atom::type (   )  const [inline]
 

The type of the atoms (basically what element).

Definition at line 98 of file Atom.h.

References type_.

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