starfish.chemistry
Class AtomParser

java.lang.Object
  starfish.chemistry.AtomParser

public class AtomParser
extends java.lang.Object

Field Summary

java.lang.String	atomName
double	bfactor
java.lang.String	chainID
double	charge
java.lang.String	elemName
java.lang.String	loc
double	occupancy
java.lang.String	resName
java.lang.String	resNum
java.lang.String	segment
double	x
double	y
double	z

Constructor Summary

AtomParser(java.lang.String string)

AtomParser(java.lang.String string, boolean swapToIUPAC)

Method Summary

static void	addTranslation(int i, java.lang.String type, java.lang.String aa, java.lang.String aname)
static java.lang.String	currentToIUPAC(java.lang.String resName, java.lang.String atomName)
static java.lang.String	getTranslation(java.lang.String type, int i)
static int	getTranslation(java.lang.String type, java.lang.String aa, java.lang.String aname)
static java.lang.String	iupacToCurrent(java.lang.String resName, java.lang.String atomName)
static java.lang.String	pdbResToPRFName(java.lang.String resName, char RD)

Methods inherited from class java.lang.Object

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

Field Detail

resNum

public java.lang.String resNum

resName

public java.lang.String resName

atomName

public java.lang.String atomName

elemName

public java.lang.String elemName

chainID

public java.lang.String chainID

segment

public java.lang.String segment

loc

public java.lang.String loc

x

public double x

y

public double y

z

public double z

occupancy

public double occupancy

bfactor

public double bfactor

charge

public double charge

Constructor Detail

AtomParser

public AtomParser(java.lang.String string)

AtomParser

public AtomParser(java.lang.String string,
                  boolean swapToIUPAC)

Method Detail

addTranslation

public static void addTranslation(int i,
                                  java.lang.String type,
                                  java.lang.String aa,
                                  java.lang.String aname)

getTranslation

public static int getTranslation(java.lang.String type,
                                 java.lang.String aa,
                                 java.lang.String aname)

getTranslation

public static java.lang.String getTranslation(java.lang.String type,
                                              int i)

iupacToCurrent

public static java.lang.String iupacToCurrent(java.lang.String resName,
                                              java.lang.String atomName)

currentToIUPAC

public static java.lang.String currentToIUPAC(java.lang.String resName,
                                              java.lang.String atomName)

pdbResToPRFName

public static java.lang.String pdbResToPRFName(java.lang.String resName,
                                               char RD)