meshi.PDB
Class PdbLine

java.lang.Object
  meshi.PDB.PdbLine

public class PdbLine
extends java.lang.Object

from http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------------------- 1 - 6 Record name "ATOM " 7 - 11 Integer serial Atom serial number. 13 - 16 Atom name Atom name. 17 Character altLoc Alternate location indicator. 18 - 20 Residue name resName Residue name. 22 Character chainID Chain identifier. 23 - 26 Integer resSeq Residue sequence number. 27 AChar iCode Code for insertion of residues. 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms. 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms. 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms. 55 - 60 Real(6.2) occupancy Occupancy. 61 - 66 Real(6.2) tempFactor Temperature factor. 73 - 76 LString(4) segID Segment identifier, left-justified. 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom.

Field Summary

private java.lang.String	alternateLocation
private java.lang.String	chain
private java.lang.String	line
private java.lang.String	name
private int	number
private double	occupancy
private java.lang.String	residueName
private int	residueNumber
private double	temperatureFactor
private double	x
private double	y
private double	z

Constructor Summary

PdbLine()

PdbLine(int number, java.lang.String name, java.lang.String alternativeLocation, java.lang.String residueName, java.lang.String chain, int residueNumber, double x, double y, double z, double occupancy, double temperatureFactor)

PdbLine(java.lang.String line)

Method Summary

java.lang.String	alternateLocation()
java.lang.String	chain()
int	getModel()
boolean	isAComment()
boolean	isAHeteroAtom()
boolean	isAModel()
boolean	isAnAtom()
boolean	isAnAtomOrHeteroAtom()
boolean	isSEQRES()
int	length()
java.lang.String	name()
void	needsToBeAnAtom()
int	number()
double	occupancy()
private java.lang.String	printLine(int number, java.lang.String name, java.lang.String alternativeLocation, java.lang.String residueName, java.lang.String chain, int residueNumber, double x, double y, double z, double occupancy, double temperatureFactor)
java.lang.String	residueName()
java.lang.Integer	residueNumber()
double	temperatureFactor()
java.lang.String	toString()
AtomType	type()
double	x()
double	y()
double	z()

Methods inherited from class java.lang.Object

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

Field Detail

line

private java.lang.String line

number

private int number

name

private java.lang.String name

alternateLocation

private java.lang.String alternateLocation

residueName

private java.lang.String residueName

chain

private java.lang.String chain

residueNumber

private int residueNumber

x

private double x

y

private double y

z

private double z

occupancy

private double occupancy

temperatureFactor

private double temperatureFactor

Constructor Detail

PdbLine

public PdbLine(java.lang.String line)

PdbLine

public PdbLine(int number,
               java.lang.String name,
               java.lang.String alternativeLocation,
               java.lang.String residueName,
               java.lang.String chain,
               int residueNumber,
               double x,
               double y,
               double z,
               double occupancy,
               double temperatureFactor)

PdbLine

public PdbLine()

Method Detail

printLine

private java.lang.String printLine(int number,
                                   java.lang.String name,
                                   java.lang.String alternativeLocation,
                                   java.lang.String residueName,
                                   java.lang.String chain,
                                   int residueNumber,
                                   double x,
                                   double y,
                                   double z,
                                   double occupancy,
                                   double temperatureFactor)

isAnAtom

public boolean isAnAtom()

isAHeteroAtom

public boolean isAHeteroAtom()

isAnAtomOrHeteroAtom

public boolean isAnAtomOrHeteroAtom()

needsToBeAnAtom

public void needsToBeAnAtom()

isAComment

public boolean isAComment()

isSEQRES

public boolean isSEQRES()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

x

public double x()

y

public double y()

z

public double z()

chain

public java.lang.String chain()

residueName

public java.lang.String residueName()

name

public java.lang.String name()

residueNumber

public java.lang.Integer residueNumber()

number

public int number()

isAModel

public boolean isAModel()

getModel

public int getModel()

temperatureFactor

public double temperatureFactor()

occupancy

public double occupancy()

alternateLocation

public java.lang.String alternateLocation()

type

public AtomType type()

length

public int length()