phoenix::Atom Class Reference
[Graph/Tree Types and Classes]

Atom Class Class Atom represents the nodes in the molecular graph and the last layer in the hirachical tree. An Atom has an parent Residue, an Element (class ELE), a Geometry (class GEO), 3d coordinates (Vec3_t) and a list of bonds. It can also have a name, a forcefield type, a charge and a formal charge. More...

#include <atom.hpp>

List of all members.

Public Member Functions

ResidueKey Parent () const
 returns the parent ResidueKey
ELE Element () const
 returns the element of the atom
void Element (ELE e)
 sets the element of the atom
GEO Geometry () const
 returns the geometry of the atom
void Geometry (GEO g)
 sets the geometry of the atom
Vec3_t Coord () const
 returns the coordinates of the atom
void Coord (Vec3_t c)
 sets the coordinates of the atom
string Name () const
 returns the name of the atom
void Name (string n)
 sets the name of the atom
unsigned int FFType () const
 returns the forcefield type of the atom
void FFType (unsigned int t)
 sets the forcefield type of the atom
Float_t Charge () const
 returns the charge of the atom
void Charge (Float_t c)
 sets the charge of the atom
Float_t FormalCharge () const
 returns the formal charge of the atom
void FormalCharge (Float_t c)
 sets the formal charge of the atom
bool Valid () const
 returns a validation flag, only with -DDEBUG

Friends

AtomKey aCreate (ResidueKey p, ELE e, Vec3_t c, GEO g)
 Create a new atom.
void aDelete (AtomKey k)
 Delete an atom.
BondKey bCreate (AtomKey a1, AtomKey a2, BT bt)
 Create a new bond.
void bDelete (BondKey k)
 Delete a bond.


Detailed Description

Atom Class Class Atom represents the nodes in the molecular graph and the last layer in the hirachical tree. An Atom has an parent Residue, an Element (class ELE), a Geometry (class GEO), 3d coordinates (Vec3_t) and a list of bonds. It can also have a name, a forcefield type, a charge and a formal charge.

Friends And Related Function Documentation

AtomKey aCreate ( ResidueKey  p,
ELE  e,
Vec3_t  c,
GEO  g 
) [friend]

Create a new atom.

Create a new atom with element e, coordinates c and geometrie g at the end of residue p and return the new AtomKey.

void aDelete ( AtomKey  k  )  [friend]

Delete an atom.

Delete atom a and all of its bonds.

BondKey bCreate ( AtomKey  a1,
AtomKey  a2,
BT  bt 
) [friend]

Create a new bond.

Create a new bond with bond type bt from atom a1 to atom a2 and return the new BondKey. If a bond between this atoms already exists it will be overwriten.

void bDelete ( BondKey  k  )  [friend]

Delete a bond.

Delete bond b.


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

Generated on Mon Nov 23 08:31:45 2009 for ParaDockS by  doxygen 1.5.8