Basic Atom class for handling atom properties. More...

#include <Atom.hpp>

Classes
class	UnsetProperty
	DEPRECATED exception class...use loos::UnsetProperty instead. More...

Public Types
enum	bits { nullbit = 0 , coordsbit = 1 , bondsbit = coordsbit << 1 , massbit = bondsbit << 1 , chargebit = massbit << 1 , anumbit = chargebit << 1 , flagbit = anumbit << 1 , usr1bit = flagbit << 1 , usr2bit = usr1bit << 1 , usr3bit = usr2bit << 1 , indexbit = usr3bit << 1 , velbit = indexbit << 1 }
	Bits in the bitmask that flag what properties have actually been set.

Public Member Functions
	Atom (const int i, const std::string s, const GCoord &c)
	Constructs an atom with the atomid i, atomname s, and coordinates c.

int	id (void) const

void	id (const int)

uint	index (void) const

void	index (const uint i)

int	resid (void) const

void	resid (const int)

int	atomic_number (void) const

void	atomic_number (const int)

std::string	name (void) const

void	name (const std::string)

std::string	altLoc (void) const

void	altLoc (const std::string)

std::string	chainId (void) const

void	chainId (const std::string)

std::string	resname (void) const

void	resname (const std::string)

std::string	segid (void) const

void	segid (const std::string)

std::string	iCode (void) const

void	iCode (const std::string)

std::string	PDBelement (void) const

void	PDBelement (const std::string)

const GCoord &	coords (void) const

GCoord &	coords (void)
	Returns a writable ref to the internally stored coords.

const GCoord &	velocities (void) const
	Returns ref to the internally stored velocities (a GCoord)

GCoord &	velocities ()

void	coords (const GCoord &)
	Sets the coords to c.

void	velocities (const GCoord &)
	Sets the velocities.

double	bfactor (void) const

void	bfactor (const double)

double	occupancy (void) const

void	occupancy (const double)

double	charge (void) const

void	charge (const double)
	Sets the charge of the atom as a double. This is NOT the PDB spec...

double	mass (void) const

void	mass (const double)

int	atomType () const

void	atomType (const int)

std::string	recordName (void) const

void	recordName (const std::string)

void	clearBonds (void)
	Clear all stored bonds.

void	addBond (const pAtom &)
	Add a bond given a pAtom (extracting the atomid of the bond)

void	addBond (const int)
	Add a bond to an atom-id.

void	deleteBond (const int)
	Deletes the specified bond.

void	deleteBond (const pAtom &)
	Deletes a bond by extracting the atom-id from the passed pAtom.

std::vector< int >	getBonds (void) const
	Returns a copy of the bond list.

void	setBonds (const std::vector< int > &list)
	Sets the bonds list.

bool	hasBonds (void) const

bool	isBoundTo (const int)
	Checks to see if this atom is bound to another atom.

bool	isBoundTo (const pAtom &)

bool	checkProperty (const bits bitmask)
	Given a bit-mask, checks to see if those bits are set.

void	setProperty (const bits bitmask)
	Sets user-defined bits.

void	clearProperty (const bits bitmask)
	Clears user-defined bits...

std::string	asString () const

Friends
std::ostream &	operator<< (std::ostream &, const Atom &)
	Outputs an atom in pseudo-XML.

Detailed Description

Basic Atom class for handling atom properties.

This class handles atoms and atom properties. It stores a GCoord coordinate internally. Bonds are included, but are represented as a vector of atom-id's, which are assumed to be unique per atom...

Most properties are derived from the PDB file specification. Exceptions are noted below. Accessors for each property are provided and should be self-explanatory...

Constructor & Destructor Documentation

◆ Atom()

loos::Atom::Atom	(	const int	i,
		const std::string	s,
		const GCoord &	c )

inline

Constructs an atom with the atomid i, atomname s, and coordinates c.

Constructs a new atom.

Parameters

i	atom-id
s	atom-name
c	Coordinates

Member Function Documentation

◆ checkProperty()

bool loos::Atom::checkProperty ( const bits bitmask )

Given a bit-mask, checks to see if those bits are set.

For example, to check whether or not the coords have been set, do,

checkProperty(Atom::coordsbit)

You can combine checks by or'ing the bit flags, such as the following which checks whether both mass and charge have been set,

checkProperty(Atom::massbit | Atom::chargebit)

◆ coords() [1/2]

GCoord & loos::Atom::coords ( void )

Returns a writable ref to the internally stored coords.

This can cause problems since we track whether the coords are set or not via the bitmask. We assume that if you're accessing this as non-const, your intention is to set the coords, so the bit flagging coords is set automatically.

◆ coords() [2/2]

const GCoord & loos::Atom::coords ( void ) const

Returns a const ref to internally stored coordinates. This returns a const ref mainly for efficiency, rather than copying the coords...

◆ recordName()

std::string loos::Atom::recordName ( void ) const

Recordname imported from the PDB for this Atom This is mainly for atoms that come from a PDB, i.e. whether or not they were an ATOM or a HETATM

◆ setProperty()

void loos::Atom::setProperty ( const bits bitmask )

Sets user-defined bits.

The user-available property bits are flagbit, usr1bit, usr2bit, and usr3bit. Attempting to set any other bits will cause a logic_error exception to be thrown.

This facility is useful if you want to tag atoms for later processing without putting them in a separate group, for example...

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

src/Atom.hpp
src/Atom.cpp

Classes

Public Types

Public Member Functions

Friends