Class Molecule.Atom

java.lang.Object
  |
  +--Molecule.Atom

Enclosing class:

Molecule

public class Molecule.Atom

extends java.lang.Object

inner class Atom for use in Molecule

Field Summary

static int	HELIX Enumeration indicating helix structure
float	m_fOccupancy occupancy
float	m_fRadius radius of the atom
float	m_fTemperature temperature
java.lang.Integer	m_iResID residue id number
int	m_iSerial serial number (index)
int	m_iStructure structure
java.lang.String	m_strAltLoc alternate location
java.lang.String	m_strAtomName atom name
java.lang.String	m_strChain chain
java.lang.String	m_strCharge charge on the atom
java.lang.String	m_strInsertion insertion code
java.lang.String	m_strResName residue name
java.lang.String	m_strSegname segment name
java.lang.String	m_strSymbol atomic symbol
static int	NONE Enumeration indicating no structure
static int	SHEET Enumeration indicating sheet structure
static int	TURN Enumeration indicating turn structure

Constructor Summary

Molecule.Atom(int serial, java.lang.String name, java.lang.String loc, java.lang.String residue, java.lang.String chain, java.lang.String resid, java.lang.String insertion, float occ, float temp, java.lang.String segname, java.lang.String symbol, java.lang.String charge)
Constructor

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NONE

public static final int NONE

Enumeration indicating no structure

SHEET

public static final int SHEET

Enumeration indicating sheet structure

HELIX

public static final int HELIX

Enumeration indicating helix structure

TURN

public static final int TURN

Enumeration indicating turn structure

m_iSerial

public int m_iSerial

serial number (index)

m_strAtomName

public java.lang.String m_strAtomName

atom name

m_strAltLoc

public java.lang.String m_strAltLoc

alternate location

m_strResName

public java.lang.String m_strResName

residue name

m_strChain

public java.lang.String m_strChain

chain

m_iResID

public java.lang.Integer m_iResID

residue id number

m_strInsertion

public java.lang.String m_strInsertion

insertion code

m_fOccupancy

public float m_fOccupancy

occupancy

m_fTemperature

public float m_fTemperature

temperature

m_strSegname

public java.lang.String m_strSegname

segment name

m_strSymbol

public java.lang.String m_strSymbol

atomic symbol

m_strCharge

public java.lang.String m_strCharge

charge on the atom

m_fRadius

public float m_fRadius

radius of the atom

m_iStructure

public int m_iStructure

structure

Constructor Detail

Molecule.Atom

public Molecule.Atom(int serial,
                     java.lang.String name,
                     java.lang.String loc,
                     java.lang.String residue,
                     java.lang.String chain,
                     java.lang.String resid,
                     java.lang.String insertion,
                     float occ,
                     float temp,
                     java.lang.String segname,
                     java.lang.String symbol,
                     java.lang.String charge)

Constructor

Parameters:

serial - the serial number

name - the Atom name

loc - the location of the Atom

residue - the residue the Atom is in

chain - the chain the Atom is in

resid - the id for the residue the Atom is in

insertion - the insertion code

occ - the occupancy of the Atom

temp - the temperature of the Atom

segmentId - the id for the segment the Atom is in

symbol - the atomic symbol for the Atom

charge - the charge of the Atom